Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNASeq of RNA from blasted CD4+ T cells from individuals with TCF3 mutations and healthy controls

ABSTRACT: RNA-seq was performed using RNA extracted from blasted CD4+ T cells from individuals with TCF3 (haploinsufficiency [HI], null, or dominant negative [DN] mutations and healthy controls for the following study groups: healthy controls (HC, n=4) and patients with TCF3 mutations (HI=4, null=1, DN=1 ). Libraries were prepared using the AmpliSeq for Illumina Transcriptome Human Gene Expression panel. RNA-seq was performed on the Illumina HiSeq 2500 (Illumina; AmpliSeq for Illumina/HiSeq 2500). Demultiplexed reads were mapped to the hg19 genome using the splice-aware aligner Tophat (Trapnell et al., 2009). Gene-level counts data were generated using the Rsubread feature counts a read summarization program that counts mapped reads for genomic features such as genes (Liao et al., 2019). Differential expression analysis was performed using R (v.3.5.3) and DESeq2 (v.1.22.2)(Love et al., 2014).

ORGANISM(S): Homo sapiens

PROVIDER: GSE218787 | GEO | 2022/12/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNASeq of RNA from naïve B cells and T cell blasts from individuals with AIOLOS N160S mutation and healthy controls

Project description:RNA-seq was performed using RNA extracted from enriched T cell blasts (CD3 T cells were enriched from the T-cell blasts, purity >90%, Stemcell Technologies, 19051) or naïve B cells (purity >90%, Stemcell technologies, 19254) for the following study groups: healthy controls (HC, n=3-4) and patients with AIOLOS N160S (n=1 for naïve B cells [A.III.1] and n=2 for T cell blasts [A.II.2 and A.III.1]). Libraries were prepared using the AmpliSeq for Illumina Transcriptome Human Gene Expression panel, which captures 20,802 genes (>95% of human RefSeq genes). RNA-seq was performed on the Illumina HiSeq 2500 (Illumina; AmpliSeq for Illumina/HiSeq 2500). Demultiplexed reads were mapped to the hg19 genome using the splice-aware aligner Tophat (Trapnell et al., 2009). Gene-level counts data were generated using the Rsubread feature counts a read summarization program that counts mapped reads for genomic features such as genes(Liao et al., 2019). Differential expression analysis was performed using R (v.3.5.3) and DESeq2 (v.1.22.2)(Love et al., 2014).

2021-09-14 | GSE183966 | GEO

Sox2 suppresses gastric tumorigenesis in mice [RNA-seq]

Project description:Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach. Methods: mRNA profiles of Sox2 WT and Sox2 KO gastric glands were generated by RNA-sequencing, in triplicate, using a Illumina HiSeq 2500 instrument, resulting in 36 million single-end 50bp reads per smaple. Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR (Dobin et al., 2013). Read counts over transcripts were calculated using HTSeq v.0.6.0 (Anders et al., 2015) based on a current Ensembl annotation file for mm10/GRCm38 (release 75). Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of cancer and intestinal related genes. mRNA profiles of stomachs from 10 week old Sox2 WT and Sox2 KO mice were generated by sequencing, in triplicate, using a Illumina HiSeq 2500.

2016-08-04 | E-GEOD-83964 | biostudies-arrayexpress

Sox2 suppresses gastric tumorigenesis in mice [RNA-seq]

2016-08-04 | GSE83964 | GEO

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis [RNA-Seq]

Project description:Analysis of the changes in gene expression during in vitro cardiomyocyte differentiation due to the lack of Tbx5, Nkx2-5 or both. We performed RNA-seq in WT, Tbx5KO (TKO), Nkx2-5KO (NKO) and Tbx5KO;Nkx2-5KO (DKO) cells at the cardiac precursor (CP) and cardiomyocyte (CM) differentiation stages. Total RNA was isolated from 3 mill cells using TRizol Reagent. RNA-seq libraries were prepared according to NuGEN Ultralow V2 kit and paired-end 100bp sequenced on an Illumina HiSeq 2500 instrument. Reads were trimmed using the fastq-mcf program (Aronesty, 2011), and then aligned to the mm9 mouse genome assembly using tophat2 (RNA-seq) (Kim et al., 2013). For each gene, reads were counted, and counts-per-million (CPM) calculated using featureCounts (Liao et al., 2014). Finally, edgeR was used to perform differential expression analyses (Robinson et al., 2010).

2016-02-11 | E-GEOD-77547 | biostudies-arrayexpress

Variation in transcriptional responses to salt stress in rice

Project description:The aim of this study is to assess natural variation in transcriptional responses to salt stress in rice. We utilized a diversity panel (RDP1) described in Zhao et al 2011. Eight day old rice seedlings were subjected to a gradual 6 dS·m-1 salt stress for a period of 24h. RNA seqeuncing was performed on shoot tissue using Illumina HiSeq 2500.

2018-01-01 | GSE98455 | GEO

CARD9-associated Dectin-1 and Dectin-2 are Required for Protective Immunity of a Multivalent Vaccine Against Coccidioides posadasii Infection

Project description:Preparation of sequencing libraries and sequencing analysis using Illumina HiSeq 3000 platform (50 bp single-read module) were conducted at the Genomics Core of UT Health San Antonio. Sequencing reads were preprocessed by Trim Sequences tools in CLC Genomics workbench. Remaining reads were then aligned to mouse GRCm38(mm10) reference genome using RNA-Seq Analysis module in CLC Genomics workbench. To determine differentially expressed genes, exact test were performed after filtering lowly expressed gene (counts per million < 1 in more than three samples across the dataset) using edgeR package (Robinson, McCarthy et al. 2010). Gene Ontology (GO) analysis were performed using DAVID (Dennis, Sherman et al. 2003) and then visualized by GOplot (Walter, Sanchez-Cabo et al. 2015).

2020-04-16 | GSE133140 | GEO

Genome wide CRISPR screen for Sorafenib resistance in MOLM13 and MV411 cells using Y. Kosuke library

Project description:MOLM13 or MV411 cells were generated to express Cas9, infected with CRISPR library (Tzelepis et al 2016) , selected for puromycin resistance and exposed to Sorafenib (50nM), Crenolanib (20nM) or vehicle, DMSO. Cells were collected at time 0 (post puromycin selection), day 7 and 14 for Sorafenib as well as 14 and 21 for Crenolanib. DNA was extracted and sgRNA barcodes were amplified. The resulting PCR library was deep sequenced using the Illumina HiSeq 2500 using 6 samples per lane.

2021-05-19 | GSE138343 | GEO

Transcriptome profiling of purified mouse platelets

Project description:Purpose: The aim of this study is to determine the relative expresson levels of mRNA transcripts in wild type platelets Methods: Total RNA was extracted and purified from purified platelets from BALB/c male mice (3 independent samples). Platelet purification was performed as described in Josefsson EC et al, Journal of Experimental Medicine (2011) 208:2017-31. Total RNA (100 ng) was used to generate sequencing libraries for whole transcriptome analysis following Illumina’s TruSeq RNA v2 sample preparation protocol. Completed libraries were sequenced on HiSeq 2000 with TruSeq SBS Kit v3- HS reagents (Illumina) as 100 bp paired-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Reads were aligned to the mouse reference genome mm10 and counts for known genes were obtained using the Rsubread package (version 1.18.0) (Liao et al. 2013; Liao et al. 2014).

2016-04-16 | GSE75896 | GEO

Project description:Transcriptome Sequencing and Analysis of Eggplant samples Using Illumina Hiseq 2500/4000

| PRJNA750594 | ENA

Quantitative Analysis of hippocampal transcriptomes form wild-type, control and Kdm5c mutant mice (KO and ifKO) through Next Generation Sequencing (RNA-Seq)

Project description:RNA preparation for sequencing was performed as described in (Fiorenza et al., 2016). Hippocampi derived from three different animals were pooled together for each sample and three independent samples were sequenced. RNA-seq datasets from Kdm5c null mice and control littermates at their home cages (HC) and after 1 h of novelty exploration (NE) were generated by next-generation sequencing (RNA-seq) using Illumina HiSeq 2500 apparatus, where the configuration was in conditional samples paired-end and in conventional samples single-end. RNA-Seq libraries were prepared from total RNA using poly(A) enrichment of the mRNA (mRNA-Seq). The libraries were stranded and multiplexed. Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Library sizes can be found in Suppl Table 9 of the manuscript. RNA-Seq libraries were mapped to reference genome (Ensembl GRCm38) using STAR v2.5.0c (Dobin A. et al. 2013), and with corresponding gene model annotation (Mus_musculus.GRCm38.83.gtf). Samtools (v1.3) was used to further process BAM files (Li et al., 2009). For calling of differentially expressed genes (DEG), mapped reads were counted with HTSeq v0.6.1 (Anders et al., 2014) at gene level and count tables were analysed using DeSeq2 (v1.10.0) R-package (Love et al., 2014) and bioconductor v3.2. For consideration of differentially regulated genes between conditions, we used adjusted p-value < 0.1 as indicated in the manuscript.

2017-08-18 | GSE85874 | 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