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2,556
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Dataset results
2,556 results for “RNAseq”
IgSeqR RNAseq tutorial dataset
<p>Data hosted for IgSeqR tutorial. A tutorial relating to sample 822 is hosted in our github repo: https://github.com/ForconiLab/IgSeqR/tree/main</p> <p>Data is derived from Biostudies dataset E-MTAB-12017.</p> <p>IgSeqR preprint: https://www.biorxiv.org/content/10.1101/2024.09.03.611002v1</p> <p>IgSeqR publication: TBC</p> <p> </p> <p> </p> <p> </p>
Single Cell RNAseq Pancreatic Cancer Atlas
<p>Complete object for scRNAseq PDAC atlas.</p> <p> </p> <p>Please cite: Loveless IM, Kemp SB, Hartway KM, Mitchell JT, Wu Y, Zwernik SD, Salas-Escabillas DJ, Brender S, George M, Makinwa Y, Stockdale T, Gartrelle K, Reddy RG, Long DW, Wombwell A, Clark JM, Levin AM, Kwon D, Huang L, Francescone R, Vendramini-Costa DB, Stanger B, Alessio A, Waters AM, Cui Y, Fertig EJ, Kagohara LT, Theisen B, Crawford HC, Steele NG. Human pancreatic cancer single cell atlas reveals association of CXCL10+ fibroblasts and basal subtype tumor cells. Clin Cancer Res. 2024 Dec 5. doi: 10.1158/1078-0432.CCR-24-2183. Epub ahead of print. PMID: 39636224.. </p>
Quantification of RNAseq and CUT&RUN from MeCP2 adult knockout hippocampus
Open the record for dataset details and reuse information.
Xena TCGA TARGET TCGx RNAseq Data
<p>TCGA, TARGET and TGx RNA-seq data downloaded from XenaBrowser.</p> <p>The data is formatted into a MultiAssayExperiment object, and compressed with R's qs package. </p>
Tumor RNAseq and nCounter for ERY974 monotherapy and/or combination with chemotherapy
<p>We examined pharmacodynamic (PD) of ERY974, CD3 and GPC3-targeting T cell bispecific antibody (TRAB), in tumors of huminized/NOG mice administered with ERY974 and/or chemotherapy. First, we examined the RNAsea data of ERY974 monothrapy for tumors of PC10, NCI-H446, MKN45, and MKN74 of humanized/NOG mice. We found that gene expression related with immune cells at baseline is correlated with efficacy of ERY974. Then,we examined the PD of ERY974 combined with chemotherapy (paclitaxel, cisplatin and capecitabine). In NCI-H446, a representative of non-inflamed-tumor, we examined the tumor RNA of huminized/NOG mice administered with ERY974 and/or paclitaxel, or cisplatin. In MKN45, a representative of non-inflamed-tumor, we examined the tumor RNA of huminized/NOG mice administered with ERY974 and/or capecitabine. For capecitabine combination, we firstly examined the suitable timing among day 3,7,and 14 when combination effect was cleary observed, and found that day 14 is the most suitable timing. From all the data, we found that combination of chemotherpay increased ERY974-induced gene expression related with T cell marker and T cell activation. To examine if our findings are observed in other TRABs in common, we parepred for the EGFR-TRAB, and examined the RNA analysis of MKN45 tumor of huminized/NOG mice administred with EGFR-TRAB and/or paclitaxel. We confirmed that paclitaxel increased EGFR-TRAB-induced gene expression related with T cell marker and T cell activation. We concluded that combination of TRABs with chemotharpy is suitable strategy to erradicate non-inflamed tumors.</p>
ICB_Hugo_RNAseq
<p>Processed RNAseq data used for ICB_Hugo data object.</p> <p>Publication: <a href="https://pubmed.ncbi.nlm.nih.gov/26997480/">https://pubmed.ncbi.nlm.nih.gov/26997480/</a>.</p> <p>Raw data obtained from <a href="https://www.ebi.ac.uk/ena/browser/view/PRJNA312948?show=reads">https://www.ebi.ac.uk/ena/browser/view/PRJNA312948?show=reads</a>.</p> <p>Processed with <a href="https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto">https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto</a></p> <p>Dataset details: <a href="https://predictio.ca/dataset/5">https://predictio.ca/dataset/5</a>.</p>
ICB_Jung_RNAseq
<p>Processed RNAseq data used for ICB_Jung data object.</p> <p>Publication: <a href="https://pubmed.ncbi.nlm.nih.gov/31537801/">https://pubmed.ncbi.nlm.nih.gov/31537801/</a>.</p> <p>Raw data obtained from <a href="https://www.ebi.ac.uk/ena/browser/view/PRJNA557841?show=reads">https://www.ebi.ac.uk/ena/browser/view/PRJNA557841?show=reads</a>.</p> <p>Processed with <a href="https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto">https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto</a></p> <p>Dataset details: <a href="https://predictio.ca/dataset/23">https://predictio.ca/dataset/23</a>.</p>
ICB_Gide_RNAseq
<p>Processed RNAseq data used for ICB_Gide data object.</p> <p>Publication <a href="https://pubmed.ncbi.nlm.nih.gov/30753825/">https://pubmed.ncbi.nlm.nih.gov/30753825/</a>.</p> <p>Raw data obtained from :<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB23709?show=reads">https://www.ebi.ac.uk/ena/browser/view/PRJEB23709?show=reads</a>.</p> <p>Processed with <a href="https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto">https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto</a></p> <p>Dataset details: <a href="https://predictio.ca/dataset/20">https://predictio.ca/dataset/20</a>.</p>
ICB_Riaz_RNAseq
<p>Processed RNAseq data used for ICB_Riaz data object.</p> <p>Publication: <a href="https://pubmed.ncbi.nlm.nih.gov/29033130/">https://pubmed.ncbi.nlm.nih.gov/29033130/</a>.</p> <p>Raw data obtained from <a href="https://www.ebi.ac.uk/ena/browser/view/PRJNA356761?show=reads">https://www.ebi.ac.uk/ena/browser/view/PRJNA356761?show=reads</a>.</p> <p>Processed with <a href="https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto">https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto</a></p> <p>Dataset details: <a href="https://predictio.ca/dataset/12">https://predictio.ca/dataset/12</a>.</p>
single-nucleus RNAseq data from female Aedes aegypti antenna
<p>Single-nucleus RNA sequencing data accompanying Herre*, Goldman* et al. (2022), "Non-Canonical Odor Coding in the Mosquito" (https://doi.org/10.1016/j.cell.2022.07.024)</p> <p>For further analysis see: https://github.com/VosshallLab/Younger_Herre_Vosshall2020/tree/main/snRNAseq_SupplementaryData</p> <p>For raw sequencing files see NCBI BioProject: PRJNA794050</p>
ICB_Fumet2_RNAseq
<p>Processed RNAseq data used for ICB_Fumet2 data object.</p> <p>Publication: <a href="https://pubmed.ncbi.nlm.nih.gov/30753825/">https://www.ncbi.nlm.nih.gov/pubmed/35051357</a>.</p> <p>Raw data obtained from: <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB23709?show=reads">https://www.ebi.ac.uk/ena/browser/view/PRJNA786565?show=reads</a>. (Sample Title column corresponds to the sample id)</p> <p>Sample metadata to map between run accession and sample title: <a href="http://ftp.ncbi.nlm.nih.gov/geo/series/GSE190nnn/GSE190266/matrix%C2%A0">https://ftp.ncbi.nlm.nih.gov/geo/series/GSE190nnn/GSE190265/matrix/</a></p> <p>Processed with <a href="https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto">https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto</a>.</p>
ICB_Fumet1_RNAseq
<p>Processed RNAseq data used for ICB_Fumet1 data object.</p> <p>Publication: <a href="https://pubmed.ncbi.nlm.nih.gov/30753825/">https://pubmed.ncbi.nlm.nih.gov/35051357/</a>.</p> <p>Raw data obtained from: <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB23709?show=reads">https://www.ebi.ac.uk/ena/browser/view/PRJNA786567?show=reads</a>. (Sample Title column corresponds to the sample id)</p> <p>Sample metadata to map between run accession and sample title: <a href="http://ftp.ncbi.nlm.nih.gov/geo/series/GSE190nnn/GSE190266/matrix ">https://ftp.ncbi.nlm.nih.gov/geo/series/GSE190nnn/GSE190266/matrix </a></p> <p>Processed with <a href="https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto">https://github.com/LupienLab/kallisto_snakemake/tree/main/Run_Kallisto</a>.</p> <p>Dataset details: <a href="https://predictio.ca/dataset/20">https://www.predictio.ca/dataset/8</a>.</p>
RNAseq of partially paralyzed zebrafish embryos at 5 days post-fertilization compared to normal siblings
<p>Sofa potato (sop) is a mutant zebrafish line, whose synaptic transmission at the neuromuscular junction is absent due to a point mutation in the δ subunit gene of the acetylcholine receptor (AChR), leading to paralysis of its skeletal muscles. To explore genetic changes in embryos caused by the lack of synaptic transmission, we performed RNA-seq analysis of normal siblings (<em>sop</em><sup>+/?</sup>) and <em>sop </em>homozygous embryos<em> (sop<sup>-/-</sup>) </em>at 5 days post-fertilization.</p>
Mouse RNASeq data for "The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer", part 1
Open the record for dataset details and reuse information.
Mouse RNASeq data for "The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer", part 2
Open the record for dataset details and reuse information.
CRUK ACRCelerate CRC GEMM bulk RNAseq
<p>A comprehensive dataset comprising transcriptomic analysis of a world-leading collection of preclinical genetically engineered mouse models (GEMMs) of colorectal cancer (CRC). These patient-relevant models are driven by the mutation of key genes, or aberrant regulation of pathways central to human disease, including, but not limited to APC, TP53, KRAS, BRAF, TGFBR1 and NOTCH. Models within this cohort represent all stages of CRC, spanning from early lesion to late-stage metastatic disease; organoid, tumouroid, orthotopic engrafted disease and ultimately autochthonous primary and disseminated tumours. Moreover, models which discriminate key clinical features such as mismatch repair deficiency and proficiency (MMRd/MMRp), colitis association and anatomical location (right-sided/left-sided) are included.</p> <p>A schematic of available models appears as Figure 1, with further details found in Table 1.</p> <p>For access to the data set please contact: <a>gemmdata@crukscotlandinstitute.ac.uk</a></p> <p> </p> <p> </p> <p> </p> <p> </p>
Fishbook_RNAseq_3
<p>Fishbook RNAseq dataset 3</p>
Fishbook_RNAseq_2
<p>Fishbook RNAseq dataset 2</p>
Fishbook_RNAseq_4
<p>Fishbook RNAseq dataset 4</p>
Fishbook_RNAseq_1
<p>Fishbook RNAseq dataset 1</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research 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.
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.
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.
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.
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.