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1,090 results for “Bulk RNA-seq”
Bulk RNA-Seq PBMC data of SLE patients and healthy volunteers/ profiling of 29 individual immune cell types as well as PBMCs of healthy donors
<p>This Zenodo project contains processed gene expression data from two publicly available data sets. It includes the gene expression data of peripheral blood mononuclear cells (PBMCs) of systemic lupus erythematosus (SLE) patients as well as healthy volunteers (GSE122459). The project also comprises the bulk RNA-Seq profiling of 29 immune cell types as well as PBMCs of healthy individuals (GSE107011). In both cases, the raw RNA-Seq data was downloaded, aligned and processed. The gene expression data is available in form of a count matrix (GSE107011) or count matrix and transcript-per-million (TPM) values (GSE122459). For the latter, an annotation file is attached. Further details are provided in the information file. </p>
Bulk RNA-seq dataset of human embryonic stem cells (hESCs) differentiation
<p>The dataset consists of 31 bulk samples obtained from human embryonic stem cells undergoing undirected differentiation. The samples were collected at 16 time points on days 0 and 7-21 of differentiation. The file contains the raw read counts.</p> <p>More details can be found in:</p> <p>SPIRAL: Significant Process InfeRence ALgorithm for single cell RNA-sequencing and spatial transcriptomics\<br> Hadas Biran, Tamar Hashimshony, Tamar Lahav, Or Efrat, Yael Mandel-Gutfreund, and Zohar Yakhini</p> <p> <a href="https://doi.org/10.1101/2022.05.24.493189">https://doi.org/10.1101/2022.05.24.493189</a></p>
Synthetic bulk RNA-Seq transcriptomic profiles representing 10 Cancer hallmarks
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Isosceles paper simulated ovarian cell line ONT data (bulk RNA-Seq)
<div> <p>Simulated ovarian cell line ONT data (bulk RNA-Seq) for the Isosceles paper - more details can be found in the <a href="https://github.com/Genentech/Isosceles_Paper" target="_blank" rel="noopener">Isosceles_Paper</a> repository.</p> </div>
Jagodinsky et al 2024 bulk RNA-seq counts
<p>On day 3 following BT, tumors were collected and tissue samples were taken from the high, moderate, and low dose regions. The samples were homogenized in Trizol reagent (ThermoFisher) using a Bead Ruptor Elite (OMNI). RNA was isolated using Qiagen’s RNeasy Mini Kit according to the manufacturer’s instructions. 1 µg of RNA was used for library preparation (Illumina) with UD indexing (Illumina) according to manufacturer’s instructions. The prepared libraries were sequenced on an Illumina NOVAseq 6000. Skewer was used to trim adapter sequences from reads and to remove low quality bases from read 3’ ends before aligning to GRCm38.p6 using STAR.<br> <br> RSEM was used to calculate expected gene counts from aligned reads. Principal component analysis and Pearson correlation between vectors of gene counts that belong to biological replicates was employed to detect outlier libraries. Any samples with inter-replicate Pearson correlation less than 0.9 or which did not cluster with replicates by PCA were dropped from downstream analyses.</p>
Bulk and single-cell RNA-seq of human fetal pancreatic organoids
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Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data
<p>ConDecon is a clustering-independent method for inferring the likelihood for each cell in a single-cell dataset to be present in a bulk tissue. This repository contains the raw data of the benchmarking analyses presented in the original publication using the pipeline of Avila-Cobos et al. (10.1038/s41467-020-19015-1). We used this pipeline to evaluate the ability of ConDecon and 17 other deconvolution methods to infer discrete cell type abundances in bulk tissues. The compressed file in this repository contains the synthetic bulk data, ground truth cell type proportions, and the predicted cell type proportions for each method and dataset associated with these analyses. Additional details can be found in the Methods section of the ConDecon publication.</p>
Gene-level read counts from bulk RNA-seq data for 38 follicular lymphoma diagnostic biopsies
<p>Conventional (bulk) RNA-sequencing was performed on unfractionated cell suspension or snap frozen whole tissue material. Total RNA was isolated with TRIzol reagent followed by purification over PureLink RNA Mini Kit columns (Invitrogen). RNA-seq was performed using a polyA-enriched strand-specific library construction protocol (doi: 10.1016/j.ccell.2016.02.009) and paired-end 75bp sequencing on an Illumina HiSeq 2500 instrument.</p> <p>Raw reads were aligned to the reference human genome assembly GRCh37 (hg19) using STAR (v2.5.2.a). To improve spliced alignment, STAR was provided with exon junction coordinates from the reference annotations (Gencode v19). We applied a modified version of a bioinformatics workflow for normalization of raw read counts and differential gene expression analysis<span> (</span>doi: 10.12688/f1000research.9005.3). Gene-level read counts were quantified using HTSEQ-count (v0.11.0; intersection-strict, reverse mode) (doi: 10.1093/bioinformatics/btu638). Genes showing low read counts (i.e., genes not showing counts per million (cpm) > 1.0 in at least 10% of samples) were removed from further analysis. Raw counts from expressed genes were then TMM-normalized and scaled to counts per million (CPM) using the edgeR (v3.22.2) package (doi: 10.1093/bioinformatics/btp616).</p> <p>Sample IDs correspond to those referenced in Wang X et al, Nature Communications (2022).</p>
Bulk RNA-seq of macrophages isolated from Salmonella Typhimurium infected zebrafish embryos
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Global transcriptional profiles of primary and secondary cellular senescence in vivo by oncogene-induced senescence (OIS) and stress-induced senescence (SIS) [Bulk RNA-seq]
GEO Series GSE242704. Mus musculus. 70 samples. Type: Expression profiling by high throughput sequencing.
Amino acid primed mTOR activity is essential for heart regeneration [bulk RNA-seq]
GEO Series GSE188243. Danio rerio. 8 samples. Type: Expression profiling by high throughput sequencing.
Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor [bulk RNA-seq]
GEO Series GSE238252. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
Bulk RNA-seq of aplastic anemia (AA) and healthy donors
GEO Series GSE165870. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Bulk RNA-seq of neuromuscular system models generated from human induced pluripotent stem cells (hiPSCs)
GEO Series GSE226477. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Regional specialization and fate specification of mesenchymal stromal cells in skeletal development [bulk RNA-seq]
GEO Series GSE156634. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
SCD inhibition reverses immune, synaptic and behavioral deficits in an animal model of Alzheimer’s disease [bulk RNA-Seq]
GEO Series GSE167601. Mus musculus. 23 samples. Type: Expression profiling by high throughput sequencing.
APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition [bulk RNA-seq]
GEO Series GSE297743. Mus musculus. 28 samples. Type: Expression profiling by high throughput sequencing.
An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [bulk RNA-seq]
GEO Series GSE182672. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[bulk RNA-seq]
GEO Series GSE272410. Homo sapiens. 73 samples. Type: Expression profiling by high throughput sequencing.
Blockade of PF4-induced Th1-Treg polarization enhances anti-tumor immunity (Bulk RNA-Seq)
GEO Series GSE252052. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.