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Three-dimensional arrangement of human bone marrow microvessels revealed by immunohistology in undecalcified sections - volume filtering verification

For each of the four ROIs (R1 to R4 in file names) we pick few sub-regions (annotated in R?_legend.png) and show the changes between sections (temporally encoded) from initial (registered) input, marked "1" in video to the final result of volume filtering, marked "5" in video. Subregion number j in ROI number i is bears the video file name "R_verification_volume_-_region_<j>_FullHD.mov".

Three-dimensional arrangement of human bone marrow microvessels revealed by immunohistology in undecalcified sections - registered sections (input data)

These are the 3500x3500 ROI data, selected from complete scans. Following procedure was applied: - Coarse registration (Ulrich et al, 2014) - ROI selection, 4k x 4k regions - Normalisation - Fine-grain registration (Lobachev et al, 2016) - Crop to the center to obtain 3500x3500 size. We estimated the slice thickness to be 7 µm.

Three-dimensional arrangement of human bone marrow microvessels revealed by immunohistology in undecalcified sections - overview videos

We reconstruct the 3D shape of the micro-vasculature in human bone marrow from serial sections. This upload shows three kinds of overview data. - R[n]_overview_... shows an overview of the mesh from ROI n as video - R[n]_input_animated_... shows a thumb cinema overlay of initial input data - R[n]_both.png shows a still with a frame from overview video (blue) and diameter measurement video (red).

opencc-by-sa-4.0Mar 2018View details →

Histopathology data of bone marrow biopsies (HistBMP or HistMNIST)

Data information We prepared a dataset basing on histopathological images freely available on-line (http://www.enjoypath.com/). We selected 16 patients (patient IDs: 272, 274, 283, 289, 290, 291, 292, 295, 297, 298, 299). Each histopathological image represents a bone marrow biopsy. Diagnoses of the chosen cases were associated with different kinds of cancer (e.g., lymphoma, leukemia) or anemia. All original images were taken using HE, 40×, and each image was of size 336 × 448. Data preparation The original RGB representation was transformed to gray scale. Further, we divided each image into small patches of size 28 × 28. Eventually, we picked 10 patients for training, 3 patients for validation and 3 patients for testing, which resulted in 6,800 training images, 2,000 validation images and 2,000 test images. The selection of patients was performed in such a fashion that each dataset contained representative images with different diagnoses and amount of fat. Since the small patches resemble a widely-used benchmark in machine learning/AI community called MNIST, the dataset is referred to as HistMNIST.  First usage The dataset was used to train deep generative models (VAEs): <ul> <li>Tomczak, J. M., & Welling, M. (2016). Improving variational auto-encoders using householder flow. arXiv preprint arXiv:1611.09630.</li> </ul>

Murine Bone Marrow Derived Macrophages (BMDM's) stimulated with LPS and treated with PBS, Epirubicin and Aclarubicin

This dataset was used in the analysis which composes the GitHub repository: <a href="https://github.com/andrebolerbarros/Chora_etal_2022">https://github.com/andrebolerbarros/Chora_etal_2022</a> The files presented here correspond to: gene_counts.tab: the table for the gene counts produced by the alignment of fastq files using STAR; sampleTable.csv: the treatment information for each sample produced.

opencc-by-4.0Aug 2020View details →

Single cell RNA-seq Data - Dissecting the functional reprogramming of the microenvironment in bone marrow fibrosis at the single cell level

We provide results regarding the bioinformatic analysis of scRNA-seq from distinct bone marrow fibrosis mouse models and human samples.   These include: Robjects&Markdown - R markdown and R objects with QC statistics, UMAP and final scRNA-seq data sets. Markers - Excel tables with cluster specific marker genes. DE Genes - Excel table with DE genes when comparing cells in control vs. disease condition per cluster. GO Analysis - Gene enrichment analysis of either DE genes. These are divided by either UP or down regulated genes.

Three-dimensional arrangement of human bone marrow microvessels revealed by immunohistology in undecalcified sections - methods

We reconstruct the 3D shape of microvasculature in human bone marrow specimen. <ul> <li> Files "2016-07-01_Methodenvideo_....mp4" detail on the novel embedding process of our specimen. The video details on material preparation, special embedding device and devised procedure, the sectioning and further processes. For convinience, a high-resolution ....FullHD.mp4 and low-resolution .....SD.mp4 versions are provided.</li> <li>Files "2016-07-27 Manual Quality Control - ...mp4" details on the computer-based verification of final mesh and initial (registered) image stack. We can observe some blind ends or interrruptions in the reconstruction, this tools allows us to evaluate the suspective areas. There is a FullHD encode, and a SD version.</li> </ul>

Three-dimensional arrangement of human bone marrow microvessels revealed by immunohistology in undecalcified sections - final data

These are the meshes used to render the videos in 10.5281/zenodo.57834 and 10.5281/zenodo.57754 The file names are: R[n]_[kind].ply where n is the ROI number, 1-4 kind is the diameter mesh or the overview mesh. The diameter meshes have additionally removed inner components and also other small non-connected components, as described in the paper.

opencc-by-4.0Oct 2016View details →

Three-dimensional arrangement of human bone marrow microvessels revealed by immunohistology in undecalcified sections - difference between meshes

The difference between the overview mesh and mesh used for SDF for all ROI. Black is no difference, i.e. baseline, objects removed for SDF processing are red.

Three-dimensional arrangement of human bone marrow microvessels revealed by immunohistology in undecalcified sections - diameters

We reconstruct blood vessels in human bone marrow specimen. These videos show the diameters of blood vessels. Red is under 12 µm, green is over 30 µm, in-between is the gradient from red to green. The coloring is based on the SDF computation and the accompanying MeshLab Quality Mapper file.

opencc-by-4.0Sep 2022View details →

Full-length, single-cell RNA-sequencing of human bone marrow subpopulations reveals hidden complexity

<a href="http://www.biorxiv.org/content/10.1101/2021.07.28.454226v2">Full-length, single-cell RNA-sequencing of human bone marrow subpopulations reveals hidden complexity</a> Bone marrow progenitor cell differentiation has frequently been used as a model for studying cellular plasticity and cell-fate decisions. Recent analysis at the level of single-cells has expanded knowledge of the transcriptional landscape of human hematopoietic cell lineages. Using single-molecule real-time (SMRT) full-length RNA sequencing, we have previously shown that human bone marrow lineage-negative (Lin-neg) cell populations contain a surprisingly diverse set of mRNA isoforms. Here, we report from single cell, full-length RNA sequencing that this diversity is also reflected at the single-cell level. From fresh human bone marrow unselected and lineage-negative progenitor cells were isolated by droplet-based single-cell selection (10xGenomics). The single cell-derived mRNAs were analyzed by full-length SMRT and short-read sequencing. In both samples we detected an average of 8000 different genes using short-read sequencing. Differential expression analysis arranged the single-cells of the total bone marrow into only four clusters whereas the Lin-neg population was much more diverse with nine clusters. mRNA isoform analysis of the single-cell populations using full-length sequencing revealed that Lin-neg cells contain on average 24% more novel splice variants than the total bone marrow cells. Interestingly, among the most frequent genes expressing novel isoforms were members of the spliceosome, e.g. HNRNPs, DEAD box helicases and SRSFs. Mapping the isoforms from all genes to the cell type clusters revealed that total bone marrow cells express novel isoforms only in a small subset of clusters. On the other hand, lineage-negative progenitor cells expressing novel isoforms were present in nearly all subpopulations. In conclusion, on a single-cell level lineage-negative cells express a higher diversity of genes and more alternatively spliced novel isoforms suggesting that cells in this subpopulation are poised for different fates.

opencc-by-4.0Apr 2024View details →

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-4.0Nov 2024View details →

scGeneAI bone marrow fine-tune dataset

<div>The input bone marrow fine-tune dataset used in the full-size examples in scGenAI is uploaded here</div> <div> <div>   </div> </div>

opencc-by-4.0Aug 2021View details →

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging

MELC (Multi-epitope ligand cartography) multiplex imaging data of our neuroblastoma cohort supporting the publication " Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging". The zip folders contain raw image data of one to four fields of view (FoV). The folder "RoI" contains the masks of user-selected regions. "marker_status.csv" is used for normalization with RESTORE. "MELC_single_cell_data.csv" contains the normalized single-cell data with cell type assignments.

Figure 7 in Inflammation reduction potential of nanostructured lipid carriers encapsulated with rat's bone marrow cells' lysate

Figure 7. In-vivo Gene Expression Analysis: (A) represents apoptotic markers; BAX and Caspase-3, expression in treated nanostructured lipid carriers (T-NLC), treated bone marrow-derived mesenchymal stromal cells (BMSCs) lysate (C-I-BMSCs-L) and NLC loaded BMSCs lysate (C-I-NLC-BMSCs-L) groups as compared to normal (N) and carrageenan injected injury (C) groups (B) shows proinflammatory markers (IL-6 and IL-8) expression levels in treated C-I-BMSCs-L and treated C-I-NLC-BMSCs-L groups as compared to N and C groups (C) shows Proliferative markers (Ki-67, PCNA and TOP2A) expression in treated C-I-BMSCs-L and treated C-INLC-BMSCs-L group as compared to N and C groups. Whereas N-NS represents normal rats injected with normal saline, C-NS represents carrageenan-injected normal saline, C-I-DFS represents carrageenan-injected diclofenac sodium. Where; the* sign shows significance between untreated and treated groups while α and ss sign shows significance between carrageenan injury and other treatment groups. Where, ns is non-significant, * & α represents P<0.05, ** & ss represents P<0.001, *** & αss represents P<0.0001.

Figure 6 in Inflammation reduction potential of nanostructured lipid carriers encapsulated with rat's bone marrow cells' lysate

Figure 6. Percentage inhibition of inflammation at a time interval (hr) in carrageenan-induced rat's hind paw oedema model. The effect of different treatment groups, i.e., normal (N), normal rat paw injected with normal saline (N-NS), carrageenan injected group (C), carrageenan injected with normal saline group (C-NS), carrageenan injected with diclofenac sodium group (C-I-DFS), carrageenan injected with nanostructured lipid carriers group (C-I-NLC), carrageenan injected with bone marrow-derived mesenchymal stromal cells (BMSCs) lysate group (C-I-BMSCs-L) and Carrageenan injected with NLC loaded BMSCs lysate group (C-I-NLC-BMSCs-L); on hind paw oedema at different hours (0, 1 2, 3, 6 & 24 hours). Where; the* sign shows significance between normal and carrageenan-induced treated groups while α and ss sign shows significance between carrageenan injected and carrageenaninduced treatment groups. Where; ns is non-significant, ** & ss denotes P<0.001, *** & αss denotes P<0.0001.

Figure 4 in Inflammation reduction potential of nanostructured lipid carriers encapsulated with rat's bone marrow cells' lysate

Figure 4. (A) Expression analysis of angiogenesis marker vascular endothelial growth factor (VEGF) via immunocytochemistry; (B) Expression analysis of apoptotic marker p53 via immunocytochemistry; (C) Expression analysis of apoptotic marker p53 via immunocytochemistry. Where: Untreated (UT), H 2 O 2 injury (I-H 2 O 2), treated NLC (T-NLC), treated BMSCs lysate (T-BMSCs-L), and treated NLC loaded bone marrow-derived mesenchymal stromal cells lysate (T-NLC-BMSCs-L). Stained cells are red, and blue denotes the nuclei counterstained with 4′,6-diamidine-2′-phenylindole dihydrochloride (DAPI,) while arrows show the positive cells expressing the protein. Scale bar: 200µm.

Figure 2 in Inflammation reduction potential of nanostructured lipid carriers encapsulated with rat's bone marrow cells' lysate

Figure 2. Represents cytotoxicity analysis/percentage cell viability and standardized viability concentration (SVC) values of different treatment groups on NIH 3T3 Cells (A) Represents the percentage of NIH 3T3 cells viability treated with different concentrations of nanostructured lipid carriers (NLC), bone marrow-derived mesenchymal stromal cells lysate (BMSCs-L), and NLC loaded BMSCs lysate (NLC-BMSCs-L). N represents % age viability of normal cells that receive no treatment and no H 2O2 injury; (B) Cytotoxicity analysis of various concentrations (500µg/µL, 1mg/mL, 2mg/mL, and 3mg/mL) of BMSCs lysate (C) SVC of BMSCslysate on NIH 3T3 cells; (D) Cytotoxicity analysis of various concentrations (500µg/µL, 1mg/mL, 2mg/mL, and 3mg/mL) of NLC loaded BMSCs lysate (E) shows SVC of NLC loaded BMSCs lysate on cells. Where; ***P<0.0001, *shows significance between untreated and treated groups while α and ss sign shows significance between H 2O2 injury and other treatment groups, αss shows P<0.0001, and ns is non-significant.

Figure 1 in Inflammation reduction potential of nanostructured lipid carriers encapsulated with rat's bone marrow cells' lysate

Figure 1. (A) Scanning Electron Micrograph of NLC and (B) Scanning Electron Micrograph of NLC-BMSCs-L; (B) Characterization of nanostructured lipid carriers (NLC) loaded bone marrow-derived mesenchymal stromal cells (BMSCs) lysate via enzyme-linked immunosorbent assay (ELISA):vascular endothelial growth factor (VEGF) and interleukin-6 (IL-6) expression in NLC, BMSCs-L, and NLC loaded bone marrow-derived mesenchymal stromal cells lysate (NLC-BMSCs-L).Where; *P<0.05, **P<0.01, ***P<0.0001, ns is non-significant.