Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TNF-alpha–induced transcriptomic changes in three-dimensional engineered skeletal muscle (C2C12)

ABSTRACT: Three-dimensional engineered skeletal muscle (C2C12) was used to examine transcriptomic changes induced by sustained TNF-α. Constructs received TNF-α (100 ng/mL, 72 h) or vehicle (n = 3/group), during which electrically evoked force declined under TNF-α. RNA-seq libraries were prepared with TruSeq Stranded mRNA and sequenced on an Illumina NovaSeq 6000 (PE 2×151 bp). Processed data include a gene-by-sample raw count matrix (raw_counts.tsv); raw FASTQ files are linked via SRA.

ORGANISM(S): Mus musculus

PROVIDER: GSE309438 | GEO | 2026/02/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-sequencing of C2C12 myotubes after electrical stimulation under 5% O2 and 1% O2 and their non-stimulated controls

Project description:To investigate the effect of acute hypoxic exposure on the response of transcripts to electrically-evoked contractions in C2C12 myotubes

2024-01-01 | GSE225927 | GEO

CpG island mediated linear and spatial gene partitioning (RNA-seq)

Project description:We reanalyzed published RNA-seq data to study 1) the genomic landscapes near surrounding regions of transcriptional start sites with regard to the gene expression activities and 2) the gene expression change upon transcription factor (MYBL1, ATF4) depletion. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009).

2018-02-15 | GSE80793 | GEO

CpG island mediated linear and spatial gene partitioning (ChIP-seq)

Project description:In order to elucidate the general rules for gene localization and regulation mediated by CpG islands, we reanalyzed published ChIP-seq data of CXXC domain, H3K9me3, KDM2A, SUV39H1, ATF4, MYBL1, MYOD1, SPI1, and CTCF. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using Bowtie 2.2.5 onto the mouse and human genome (mm9 and hg19, respectively). For the identification of factor binding sites, model-based analysis for ChIP-seq peak caller (MACS 1.4.2) was used with a p-value cutoff of 1e-5.

2018-02-15 | GSE80791 | GEO

Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4 (ChIP-seq)

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

RNA-seq profiling of gene expression in mock-infected and human cytomegalovirus (HCMV)–infected human embryonic lung fibroblasts (HELF) at 72 hours post infection (two biological replicates per condition)

Project description:RNA-seq was performed to quantify host gene-expression changes in human embryonic lung fibroblast (HELF) cells following infection with the human cytomegalovirus (HCMV) HAN strain. HELF cells harvested at 72 hours post infection and mock-infected controls were profiled, with two biological replicates per condition (HELF_1/2 for mock; HCMV_HELF_1/2 for infected). Libraries were sequenced on an Illumina platform with paired-end 150-bp reads, and reads were aligned to the human reference genome (GRCh38) for gene-level quantification. The submission includes a cross-sample expression matrix (raw counts and FPKM) and a differential-expression results table comparing infected versus mock conditions, enabling reuse of the dataset for downstream analyses. Raw FASTQ files are deposited in SRA under the corresponding BioProject and BioSample accessions.

2025-10-01 | GSE307100 | GEO

CpG island mediated linear and spatial gene partitioning (pA+ RNA-seq profile)

Project description:In order to test the global effects of CpG island-centered gene regulation on global gene expression profile, pA+ RNA-seq data of diverse tissues and cell lines were gathered and profiled. All available mouse poly-A positive RNA-seq data (3,818 samples) were summarized and downloaded at May, 5th, 2015. Among them, excluding single cell RNA-seq or experiments whose expression verified gene counts are small (less than 5,000 genes with RPKM 0.5 or higher), 1,524 high quality RNA-seq data were used. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009).

2018-02-15 | GSE80797 | GEO

AmpliSeq transcriptome profiling of human adipose tissue senescent progenitor cells

Project description:Transcriptomic profile of human adipose tissue progenitor cells was performed as follows. For AmpliSeq transcriptome sequencing library construction, AmpliSeq™ Library PLUS, AmpliSeq Transcriptome Human Gene Expression Panel and AmpliSeq CD indexes SetA kits were purchased from Illumina and sequencing libraries were constructed as described in AmpliSeq for Illumina Transcriptome Human Gene Expression Panel reference guide (Illumina). Equimolar concentrations of libraries were pooled at 4 nM and denatured and diluted as described in Denature and Dilute Libraries Guide (Illumina) and adjusted to final concentration of 1.4 pM. Resulting library was sequenced on NextSeq 500 using NextSeq 500/550 High Output v2 kit with 2 X 151 bp cycle. Generated raw files were converted to FASTQ files and used for data analysis. AmpliSeq transcriptome FASTQ files were analyzed on Array studio V10.0 (Omicsoft, Qiagen). Following raw read QC, first and last 10 bases were trimmed and mapped to reference genome Human.B38. The read count data was generated using GeneModel RefGene20170606. Resulting data was normalized by DESeq package, transformed to log2 value and used for ANOVA analyses.

2023-01-12 | GSE222749 | GEO

Next generation sequencing of the transcriptome in MCF-7 cells with/without SRA knockdown

Project description:We employed next generation sequencing to examine whether knocking down the steroid receptor RNA activator (SRA) gene significantly affect the expression levels of certain genes in MCF-7 cells. MCF-7 cells were transfected with either a pool of four non-target control siRNAs or a pool of four SRA siRNAs for 32 hrs. 157 million reads were generated from triplicate samples of the control group; 151 million reads were generated from triplicate samples of the SRA knockdown group. Six genes were identified as significantly changed in the expression levels with the cutoff of q value ≤ 0.05, fold change ≤ 0.5 or ≥ 2, and reads per kilobase per million mapped reads (RPKM) ≥ 1. However, except for SRA itself, the other five genes were shown by real-time PCR to be only affected by one siRNA in the SRA siRNA pool. Further analysis of this dataset with different cuttoff setting may reveal true SRA-regulated genes in MCF-7.

2014-01-23 | GSE52385 | GEO

Transcription profiling by array of mouse C2C12 myoblasts were treated with TNF alpha

Project description:C2C12 Myoblasts were treated with TNF alpha (10ng/ml) and differentially expressed genes were identified by oligo-nucleotide microarray

2010-03-06 | E-MEXP-2592 | biostudies-arrayexpress

Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [RNA-seq]

Project description:The involvement of m6A modification in macrophage activation has been validated in our study that the expression of TNF-α in Mettl3-depleted Raw 264.7 cells stimulated with LPS were markedly reduced in comparison to control cells. To further explore the biological effects of m6A deficiency macrophages, we performed RNA sequencing analysis of Mettl3-KO and WT control Raw 264.7 cells upon LPS treatment. The GO enrichment analysis documented that the downregulated transcripts in Mettl3-KO Raw 264.7 cells were enriched in innate immune response related to defense and external stimulus. Notably, transcripts of the downstream components of the TLR4 signaling pathway, such as proinflammatory cytokines (Tnf-α, Il-6, Il-1β, Il-18,and Il-23) and co-stimulation molecules (Cd86), were downregulated in Mettl3-deficient cells, suggesting that METTL3 has a critical function in controlling the innate immune response of Raw 264.7 macrophages.

2021-04-30 | GSE162248 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data