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168 results for “bulk RNAseq”
Introduction to bulk RNAseq analysis: supplementary material
<p><strong>Vampirium setup</strong></p><p>This archive contains materials (datasets, exercises and slides, etc) used for the Introduction to bulk RNAseq analysis workshop taught at the University of Copenhagen by the Center for Health Data Science (HeaDS). The course repo can be found on <a href="https://github.com/hds-sandbox/bulk_RNAseq_course">Github</a>:</p><p>Assignments.zip contains exercises for the preprocessing part of the course, like fastqc and multiqc examples of bulk RNAseq experiments</p><p>Data.zip contains count matrices (both traditional counts and salmon pseudocounts), as well as sample metadata (samplesheet.csv) and backup results from the preprocessing pipeline.</p><p>Notes.zip contains supplementary materials such as extra pdfs for more information on bulk RNAseq technology.</p><p>Slides.zip contains all the slides used in the workshop.</p><p>raw_reads.zip contains the raw reads from the bulk RNAseq experiment (<a href="https://doi.org/10.1016/j.celrep.2014.10.054">10.1016/j.celrep.2014.10.054</a>) used in this course.</p>
Bulk RNAseq of chronic LPS treated female mouse pituitary across doses
<p>To investigate the mechanisms of chronic inflammation on gonadotropin secretion we performed bulk RNA-seq on pituitaries from female mice chronically exposed to lipopolysaccharide for 6 weeks.</p>
AD_bulk_RNAseq_review
<p>Supplementary files for the Systematic review and meta-analysis for bulk RNAseq studies comparing brain tissue from Alzheimer's disease patients and controls. </p>
Discretized bulk data by the discretization step of rFASTCORMICS used in in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>Bulk data RNAseq data were downloaded from GEO, GTEX, and other sources (see below) and discretized by the discretization step of rFASTCORMICS (Pacheco et al, 2019) used in the optimization step in scFASTCORMICS:</p> <p>CRC bulk RNAseq data were obtained from Lee et al(2020) <br> CRC control (NM) was downloaded from GSE81861 (GTEX, Healthy colon from)</p> <p>Pancreatic Human islet bulk RNAseq data was downloaded from EBI Expression Atlas (Pancreatic islet cells)</p> <p>Immune cells in pancreatic carcinoma bulk data were obtained from GEO (GSE156278)</p> <p>liver and breast cancer bulk RNAseq data were obtained from the TCGA (GSE62944)</p> <p> </p> <p>rFASTCORMICS and tutorial on rFASTCORMICS can be found: https://github.com/sysbiolux</p> <p> </p> <p> </p> <p> </p> <p><br> </p>
Generating VISA scores on glioma bulk RNAseq and single cell RNAseq glioma
<p>Tissue stiffness is collectively determined by the stiffness of ECM and cells. Gliomas are characterized by dysregulated expression of ECM proteins, ECM crosslinking enzymes, and aberrant cellular contractility.While The RNA sequencing datasets have been comprehensively analyzed to interrogate tumor genomes, epigenomes, and transcriptomes, we realized an untapped potential: using transcriptomic data coupled with analysis of gene expression associated with ECM and actomyosin contractility to establish a bioinformatic tool, which we named VIrtual Stiffness Algorithm (VISA), capable of inferring tissue stiffness.</p> <p>This data repository is for reproducing VISA scores on glioma bulk RNAseq and single cell RNAseq glioma.</p>
Bulk RNAseq of K7M2 osteosarcoma cells in engineered bone marrow treated with Doxorubicin
Open the record for dataset details and reuse information.
Bulk RNAseq of chronic LPS treated female mouse pituitary across doses
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>
Bulk RNAseq parietal bone PND9-Isotype VS aCSF1R
GEO Series GSE305410. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Bulk RNAseq of Basal Cell Carcinoma (BCC) mouse models
GEO Series GSE290008. Mus musculus. 21 samples. Type: Expression profiling by high throughput sequencing.
HMGN3 ChIP-seq in AC16 cells and Bulk-RNAseq in AC16 cell with and without HMGN3 knockdown
GEO Series GSE306626. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Rbfox contributes to a conservative program of self-antigen splicing in thymic epithelial cells [mTEC_bulk_RNAseq]
GEO Series GSE145930. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing; Third-party reanalysis.
Proneural-Mesenchymal hybrid glioblastoma cells are resistant to therapy and dependent on nuclear import-bulk RNAseq
GEO Series GSE256064. Homo sapiens. 56 samples. Type: Expression profiling by high throughput sequencing.
Single cell and bulk RNAseq profiles of thymic pro-T cells
GEO Series GSE130812. Mus musculus. 241 samples. Type: Expression profiling by high throughput sequencing.
Bulk RNAseq of C1Q knockout TauP301S hippocampi
GEO Series GSE186414. Mus musculus. 17 samples. Type: Expression profiling by high throughput sequencing.
Bulk RNAseq profiling of Streptococcus pneumoniae EF3030 and Influenza A virus (A/California/07/2009(H1N1)) mono/coinfection in the mouse lungs.
GEO Series GSE294560. Mus musculus. 60 samples. Type: Expression profiling by high throughput sequencing.
Bulk RNAseq of AB1-HA murine mesothelioma tumors from complete responders and partial responders to cyclophosphamide chemotherapy
GEO Series GSE182674. Mus musculus. 46 samples. Type: Expression profiling by high throughput sequencing.
Comparative bulk RNAseq analysis of cultured single-clone WT (P23) and p53-deleted (cKO, P28 and P4M) skeletal cells in bone marrow
GEO Series GSE185793. Mus musculus. 14 samples. Type: Expression profiling by high throughput sequencing.
antigenic KPC model_bulk pancreas RNASeq
GEO Series GSE131602. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Comparative bulk RNAseq analysis of CXCL12-abundant retiucular (CAR) cells, fetal perichondrium-derived CAR cells and chondrocyte-derived CAR cells.
GEO Series GSE197933. Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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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.