6707569d-ed02-47a9-81bf-310f7e24776a - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001008627 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The transcription factor IRF4 regulates immunoglobulin class switch recombination and plasma cell differentiation. Its differing concentrations appear to regulate mutually antagonistic programs of B and plasma cell gene expression. We show IRF4 to be also required for generation of germinal center (GC) B cells. Its transient expression in vivo induced the expression of key GC genes including Bcl6 and Aicda. In contrast, sustained and higher concentrations of IRF4 promoted the generation of plasma cells while antagonizing the GC fate. IRF4 cobound with the transcription factors PU.1 or BATF to Ets or AP-1 composite motifs, associated with genes involved in B cell activation and the GC response. At higher concentrations, IRF4 binding shifted to interferon sequence response motifs; these enriched for genes involved in plasma cell differentiation. Our results support a model of "kinetic control" in which signaling-induced dynamics of IRF4 in activated B cells control their cell-fate outcomes. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.
2013-05-04 | GSE46608 | GEO
Project description:Total RNA extracted from 15 knocking down treated 293T cells using siRNAs targeting transcription splicing factors and sequenced using Illumina Hiseq PE150 platform to generate RNA sequencing with 150bp in read length. Nearly 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and Ericscript software to detect fusion transcripts.
2018-12-14 | GSE113101 | GEO
Project description:This dataset contains spatial transcriptomics data of four lung neuroendocrine tumours (lung NETs), a rare and understudied type of lung cancer. The dataset consists of raw sequencing data, metadata, and gene expression matrices. It is part of the lungNENomics project. See https://doi.org/10.5281/zenodo.19366762 for processed data for the series, including downstream analyses data for the four samples in this dataset, such as inferred CNVs and aneuploidy status, and spatial domain and cell proportions for each spot. The lungNENomics project also generated other molecular data for a series of more than 200 samples. The raw sequencing data (fastq files for RNA-seq, cram files for WGS, and idat files for methylation arrays) is hosted on the European Genome-Phenome Archive website, study EGAS00001005979. Medical imaging data (Hematoxylin & Eosin stained whole-slide images) from the lungNENomics project is hosted in the EBI bioImage Archive (10.6019/S-BIAD3143).
2026-05-22 | E-MTAB-17055 | biostudies-arrayexpress
Project description:This dataset consists of miRNA expression in serum of 69 women. This data is the result of remapping raw sequencing FASTQ files being a part of the GSE226445 dataset and the SRA Bioproject PRJNA898621. MicroRNA abundance was quantified by sequencing. Data was analyzed together with plasma samples of those same patients with the aim of assessing the impact of blood processing steps on quantified miRNA abundance. Plasma data belongs to a separate submission (accession will be added when issued). Generation of this dataset was supported by The Gray Foundation grant “Circulating microRNAs for assessment of risk beyond the BRCA genes and early detection of breast cancer in high-risk families” awarded to Dipanjan Chowdhury and Polish National Research Center grant OPUS “Predictive Potential of Circulating MicroRNA Biomarkers in Patients with High Familial or Genetic Risk of Cancer” (2023/49/B/NZ5/03835) awarded to Wojciech Fendler.
2025-12-16 | GSE299846 | GEO
Project description:Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.
2013-05-04 | GSE46607 | GEO
Project description:Innate defense regulator (IDR) peptide-1002 is a synthetic host defense peptide derivative with strong anti-inflammatory properties.To investigate the anti-inflammatory mechanisms of IDR-1002 in vivo, the phorbol 12-myristate 13-acetate (PMA)-induced mouse ear inflammation model was used. Topical IDR-1002 treatment successfully dampened PMA-induced ear edema, proinflammatory cytokine production, reactive oxygen and nitrogen species release, and neutrophil recruitment in the ears of CD1 mice. Advanced RNA-Seq analysis on the mouse ear transcriptome revealed that IDR-1002 reduced sterile inflammation by suppressing the expression of transmembrane G-protein coupled receptors (Class A/1 rhodopsin-like), including receptors for chemokines, prostaglandins, histamine, platelet activating factor and anaphylatoxin. IDR-1002 also dampened IFNγ response and repressed the Interferon regulatory factor (Irf) 8-regulated network that controls central inflammatory pathways.
2018-01-31 | GSE100918 | GEO
Project description:This submission consists of processed single-cell RNA-seq data of knockout village samples, provided as filtered feature–barcode matrices generated using Cell Ranger v7.1.0 with default parameters. We previously deposited the same biological samples and data processed by STAR under GEO accession GSE288587. The corresponding raw FASTQ files are available in ENA under accession ERP168459. The supplementary file (reanalysis_samples.xlsx) provides a reference table linking each sample in this submission to its corresponding GSM in GSE288587, which contains the detailed experimental descriptions of culture information, genotypes, and differentiation stages.
2025-12-12 | GSE313516 | GEO
Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
2021-11-17 | E-MTAB-10548 | biostudies-arrayexpress
Project description:RNA sequencing paired-end data. This study involves Corallium rubrum, with data of two populations from contrasting environments (shallow vs mesophotic), exposed to a control and a temperature stress treatment in a common garden experiment. RNAseq samples were taken every 5 days from each individual. This experiment includes the following design: Shallow Population (15-18m): Shallow (N=3 individuals)x 3T (T0, T5, T10) = 9 replicates Deep Population (48m): Mesophotic (N=3 individuals)x 3T (T0, T5, T10) = 9 replicates N=18 replicates in each condition, for a total of N = 36 replicates for the total study.
2025-11-01 | E-MTAB-15157 | biostudies-arrayexpress
Project description:Raw fastq files from paired-end, Illumina-based sequencing on NovaSeq6000
2021-11-01 | GSE160791 | GEO