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193 results for “Heme”

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zenodo48/100

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice: dataset bone marrow HbAA mice injected or not with heme

The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease. Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease. All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. This dataset contains the results of the HbAA mice with and without heme. The corresponding HbSS mice with and without heme are deposited under number 10.5281/zenodo.10962782 Bone marrow RNA was extracted by Macherey Nagel kit, according to the manufacturer’s instructions. The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.

opencc-by-4.0Apr 2024View details →

zenodo48/100

EPR Characterization of the Heme Domain of a Self-Sufficient Cytochrome P450 (CYP116B5)

Description of the dataset: <ul> <li>Data type: Experimental spectroscopic measurements, computer simulation.</li> <li>Files are with filename extensions: .DSC, .DAT, .m</li> <li>Information on origin of the data:</li> </ul> <ul> <li>EPR spectroscopic measurements with filename extensions .DSC, .DTA.</li> <li>EPR spectroscopic simulation with filename extension .m.</li> </ul> <ul> <li>CW and Pulse X-band experiments were performed on a Bruker Elexys E580 X-band spectrometer (microwave frequency 9.68 GHz) equipped with a cylindrical dielectric cavity and a helium gas-flow cryostat from Oxford Inc.</li> <li>If the dataset includes multiple files that relate to each other: <ul> <li>Files in PARACAT_WP5_20220225_CW folder includes X-band CW-EPR spectroscopic measurements, original data are in DTA/DSC/txt.</li> <li>Files in PARACAT_WP5_20220225_HYSCORE folder includes HYSCORE spectroscopic measurements, data are in .DTA, .DSC, .txt formats.</li> <li>Files in PARACAT_WP5_20220225_MATLAB folder includes computer simulations/analyses of the EPR measurements, data are in .m formats.</li> </ul> </li> </ul>

opencc-by-4.0Apr 2022View details →

zenodo48/100

Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain - Datasets and Python notebooks

This dataset and the associated Python notebooks and R-code are related to the publication "Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain".

opencc-by-4.0Aug 2021View details →

zenodo44/100

Spatial transcriptome data from coronal mouse brain sections after striatal injection of heme and heme-hemopexin

This dataset and the associated Python notebooks are related to the publication "Spatial transcriptome data from coronal mouse brain sections after striatal injection of heme and heme-hemopexin".

opencc-by-4.0Nov 2021View details →

zenodo40/100

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for bone marrow, HbSS Townes mice injected or not with heme

The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease. Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease. All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. Here the dataset for HbSS mice injected or not with heme is uploaded. The corresponding dataset for the HbAA mice injected or not with heme can be found at 10.5281/zenodo.10961162 Bone marrow RNA was extracted by Macherey Nagel kit, according to the manufacturer’s instructions. The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.

opencc-by-4.0Apr 2024View details →

zenodo40/100

Interplay between Porphyromonas gingivalis hemophore-like protein HmuY and Kgp/RgpA gingipains plays a superior role in heme supply - yet unpublished supplementary data regarding Fig. 4C and Fig. 6D.

The upload contains raw data files for the article "Interplay between Porphyromonas gingivalis hemophore-like protein HmuY and Kgp/RgpA gingipains plays a superior role in heme supply" which shows the production of the HmuY protein in various P. gingivalis mutant strains. These data are not present in the supplementary data of publication. Article abstract To acquire heme as a source of iron and protoporphyrin IX, Porphyromonas gingivalis uses gingipains, Hmu, and Hus systems. The aim of this study was to assess the correlation between the production and function of the most important virulence factors of P. gingivalis involved in heme supply, namely, hemophore-like proteins (HmuY and HusA) and gingipains. Respective mutant strains were used, and the expression of genes at the transcript and protein levels, as well as the importance of these genes’ products for virulence potential, was examined. We found that HmuY and Kgp/RgpA gingipains are among the main P. gingivalis virulence factors synergistically engaged in heme supply. Their expression is related mainly when P. gingivalis grows in conditions rich in iron and heme sources, resembling those found in severe periodontitis. We confirmed that HmuY production is strictly dependent on the availability of heme and iron in the external environment, whereas we did not observe such dependence in the production of HusA. Moreover, we found that the HmuY protein can easily sequester heme from the HusA protein. The only correlation in the production of HmuY and HusA hemophore-like proteins could occur in P. gingivalis grown in conditions rich in iron and heme sources, mimicking an environment typical for severe periodontitis. Based on our observations, we suggest that HmuY is the major heme-binding protein produced by P. gingivalis, especially in iron- and heme-depleted conditions, typical for healthy periodontium and the initial stages of infection. The HusA protein could play a supporting role in P. gingivalis heme uptake.  The Word document (Data description.docx) contains a description of files.

opencc-by-4.0Oct 2024View details →

zenodo36/100

Analysis of heme and iron influence on Porphyromonas gingivalis A7436 and ATCC 33277 strains genes expression (microarray results)

The aim of this study was to analyze phenotypic differences between P. gingivalis more virulent A7436 and less virulent ATCC 33277 (33277) strains. The analysis comprised the influence of heme and iron on P. gingivalis gene expression. P. gingivalis A7436 and 33277 strains were cultured in basal medium (3% trypticase soy broth and 0.5% yeast extract), supplemented with 3.6 mM L-cysteine hydrochloride, and 0.5 mg/l menadione, in anaerobic conditions (80% N2, 10% H2 and 10% CO2). To generate heme and iron-limited conditions, the medium was supplemented with 0.16 mM of the iron chelator 2,2-dipyridyl (DIP conditions). To generate heme and iron-rich conditions, the medium was supplemented with 0.0077mM hemin chloride (Hm conditions). Three sample replicates of A7436 and 33277 strains were grown in Hm or DIP conditions for 20 hours. RNA isolation and microarray analysis were performed in IMGM laboratories (Martinsried, Germany), as described by Śmiga et al. (2023).The online tool eArray (http://earray.chem.agilent.com/; Agilent Technologies, Santa Clara, CA, USA) was used to design an Agilent Custom Porphyromonas gingivalis A7436 Gene Expression Microarray (8×15K format). Probes were prepared based on P. gingivalis transcriptome information derived from the NCBI reference sequence NZ_CP011995.1. Total RNA isolation, RNA quantity, and quality were determined as described by Curaszkiewicz et al. 2014. For internal labeling control, the total RNA was spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix; Agilent Technologies). Subsequently, samples were reverse transcribed into cDNA and then converted into cyanine-3-labeled complementary RNA (cRNA) with Low Input Quick-Amp Labeling Kit One-Color (Agilent Technologies). For microarray hybridization, a Gene Expression Hybridization Kit (Agilent Technologies) was used. Labeled cRNA was hybridized for 17 hours at 65℃ on Agilent Custom GE 8×15K Microarrays, washed according to the manufacturer's protocol, and dried with acetonitrile (Sigma-Aldrich). The fluorescence of samples was detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner (Agilent Technologies) and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies). For data analysis, Feature Extraction 10.7.3.1 (Agilent Technologies), GeneSpring GX 13.1.1 (Agilent Technologies), and Excel 2010 (Microsoft, Redmond, WA, USA) were used. For statistical analysis, Welch's approximate t-test was used. Differences in gene expression are shown as fold change values (FC). The average was calculated from the normalized signal values and they were transformed from the log2 to the linear scale. Increases and decreases in gene expression are shown as positive and negative numbers, respectively. The fold change in gene expression was considered significant for FC ≥ 2 or FC ≤ -2 and P-value ≤ 0.05<ul><li>Ciuraszkiewicz J, Śmiga M, Mackiewicz P, Gmiterek A, Bielecki M, Olczak M, Olczak T. 2014. Fur homolog regulates Porphyromonas gingivalis virulence under low-iron/heme conditions through a complex regulatory network. Mol Oral Microbiol 29:333-353. doi: 10.1111/omi.12077.</li><li>Śmiga M, Ślęzak P, Olczak T. 2023. Comparative analysis of Porphyromonas gingivalis A7436 and ATCC 33277 strains reveals differences in the expression of heme acquisition systems. Microbiol Spectr (revised manuscript under revision).</li></ul>

opencc-by-4.0Nov 2023View details →

zenodo36/100

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS livers injected or not with heme

The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease. Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease. All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. The results of livers (indicated foie) from HbSS mice injected or not with heme are presented here.  The results of livers (indicated foie) from HbAA mice injected or not with heme can be found at number 10.5281/zenodo.10963640.  Thirty μm-thick frozen tissue sections of livers were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.

opencc-by-4.0Apr 2024View details →

zenodo36/100

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA heart injected or not with heme

The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. The results of heart (indicated coeur) from HbAA mice injected or not with heme are presented here .  The results of heart (indicated coeur) from HbSS mice injected or not with heme can be found at number 10.5281/zenodo.10964159 Thirty μm-thick frozen tissue sections of kidneys were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.

opencc-by-4.0Apr 2024View details →

zenodo36/100

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS kidneys injected or not with heme

The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. The results of kidney (indicated rein) from HbSS mice injected or not with heme are presented here .  The results of kidney (indicated rein) from HbAA mice injected or not with heme can be found at number 10.5281/zenodo.10963926. Thirty μm-thick frozen tissue sections of kidneys were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.

opencc-by-4.0Apr 2024View details →

zenodo36/100

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA livers injected or not with heme

The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. The results of livers (indicated foie) from HbAA mice injected or not with heme are presented here .  The results of livers (indicated foie) from HbSS mice injected or not with heme can be found at number <a href="https://doi.org/10.5281/zenodo.10962971">10.5281/zenodo.10962971</a>.  Thirty μm-thick frozen tissue sections of livers were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.

opencc-by-4.0Apr 2024View details →

zenodo36/100

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA kidneys injected or not with heme

The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. The results of kidney (indicated rein) from HbAA mice injected or not with heme are presented here .  The results of kidney (indicated rein) from HbSS mice injected or not with heme can be found at number  Thirty μm-thick frozen tissue sections of kidneys were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.

opencc-by-4.0Apr 2024View details →

zenodo36/100

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS lung injected or not with heme

The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. The results of lung (indicated poumon) from HbSS mice injected or not with heme are presented here .  The results of lung (indicated poumon) from HbAA mice injected or not with heme can be found at number  10.5281/zenodo.10965912 Thirty μm-thick frozen tissue sections of lungs were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.

opencc-by-4.0Apr 2024View details →

zenodo36/100

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA lung injected or not with heme

<div> <div> The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. The results of lung (indicated poumon) from HbAA mice injected or not with heme are presented here .  The results of lung (indicated poumon) from HbSS mice injected or not with heme can be found at number 10.5281/zenodo.10966094 Thirty μm-thick frozen tissue sections of lungs were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.  </div> </div>

opencc-by-4.0Apr 2024View details →

zenodo36/100

Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS heart injected or not with heme

<div> The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection. The results of heart (indicated coeur) from HbSS mice injected or not with heme are presented here .  The results of heart (indicated coeur) from HbAA mice injected or not with heme can be found at number 10.5281/zenodo.10964042 Thirty μm-thick frozen tissue sections of kidneys were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters. Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme.  </div>

opencc-by-4.0Apr 2024View details →

zenodo36/100

Dataset of the research article "Choline Oxidase and Choline Ionic Liquids in Biocatalytic Heme Peroxidase Cascades"

The dataset contains primary data related to the article entitled "Choline Oxidase and Choline Ionic Liquids in Biocatalytic Heme Peroxidase Cascades", published in ChemCatChem. The dataset contains spreadsheet data detailing kinetic measurements and calculations.

opencc-by-4.0Sep 2024View details →

zenodo36/100

Spectroscopic data and DFT coordinates for "The three-spin intermediate at the O–O cleavage and proton pumping junction in heme–Cu oxidases"

This dataset includes spectroscopic data and atomic coordinates of DFT structures in the manuscript titled "The three-spin intermediate at the O–O cleavage and proton pumping junction in heme–Cu oxidases". Spectroscopic data included are from magnetic circular dichroism (MCD), variable-temperature variable-field MCD, absorption and resonance Raman spectroscopies.

opencc-by-4.0Aug 2021View details →

dryad36/100

Thiol catalyzed NO-ferro-heme signaling

Nitric oxide (NO) is an endogenously produced signaling molecule that regulates blood flow and platelet activation. However, intracellular and intravascular diffusion of NO are severely limited by scavenging reactions with hemoglobin, myoglobin, and other hemoproteins, raising unanswered questions as to how free NO can signal in hemoprotein-rich environments. We explored the hypothesis that NO could be stabilized as a ferrous heme-nitrosyl complex (Fe2+-NO, NO-ferroheme. Unexpectedly, we observed a rapid reaction of NO with labile ferric heme (Fe3+) and a reduced thiol to yield NO-ferroheme and a thiyl radical. This thiol-catalyzed reductive nitrosylation reaction occurs readily when hemin is solubilized in lipophilic environments, such as red blood cell membranes or bound to serum albumin. The resulting NO-ferroheme is stable, even in the presence of oxyhemoglobin, and potently inhibits platelet activation. NO-ferroheme albumin administered intravenously to mice results in dose-dependent vasodilation at low- to mid-nanomolar concentrations. In conclusion, we report the fastest rate of reductive nitrosylation observed to date to generate a NO-ferroheme molecule that resists oxidative inactivation, is soluble in cell membranes, and is transported intravascularly by albumin to promote potent vasodilation.

opencc-zeroJun 2023View details →

ClinicalTrials.gov36/100

Heme Iron Polypeptide for Iron Deficiency Anemia in Chronic Renal Failure

ClinicalTrials.gov study NCT00318812. IPD Sharing: Not stated. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

ClinicalTrials.gov36/100

Hospital at Home at EOL in Heme Malignancies

ClinicalTrials.gov study NCT04690205. IPD Sharing: YES. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →

ScienceDex guides

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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.

Compare curated datasets

Allen Brain Atlas

Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

DANDI Archive for NWB datasets

DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

OpenNeuro

OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record