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Sample GSM5225001 Query DataSets for GSM5225001
Status Public on Mar 30, 2022
Title EL4 T-bet + GATA3 rep1
Sample type SRA
 
Source name EL4 cell line
Organism Mus musculus
Characteristics cell line: EL4
treatment: PMA + inomomycin
ectopically expressed protein: FLAG-T-bet + HA-GATA3
Treatment protocol EL4 cells were stimulated with phorbol 12-myristate 13-acetate (50 ng/ml) and ionomycin (1 μM) for 4 hours prior to RNA extraction
Growth protocol EL4 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 4 mM L-alanyl-L-glutamine, 25 mM D-glucose, 1 mM sodium pyruvate, 10 mM HEPES, 100 U/ml penicillin and 100 µg/ml streptomycin
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated with TRIsure (Bioline)
Poly-adenylated RNA was purified from 1 mg of total RNA using the Qiagen Oliogtex kit and ribosomal RNA was depleted from total RNA using Ribo-Zero Gold (EpiCentre), as per manufacturers instructions. 5’ cap structures were removed with tobacco acid pyrophosphatase (TAP, Life Technologies) and RNA fragmented with potassium acetate (100mM) and magnesium acetate (30mM) at 94oC for 3 mins. RNA was then repaired with Antartic phosphatase and PNK, according to the instructions in the Illumina Directional mRNA-Seq Sample Prep Guide.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Raw reads were filtered for base quality using FastQC with default parameters and adapters sequences were removed with Trim Galore!
Transcript-level read abundances were created with kallisto using the Gencode M20 transcript models
Genome_build: mm10
Supplementary_files_format_and_content: kallisto transcript level abundaces tab-delimited text files
 
Submission date Apr 02, 2021
Last update date Mar 30, 2022
Contact name Arnulf Hertweck
E-mail(s) a.hertweck@ucl.ac.uk
Organization name University College London
Department UCL Cancer Institute
Street address Gower Street
City London
ZIP/Postal code WC1E 6BT
Country United Kingdom
 
Platform ID GPL17021
Series (2)
GSE171409 The TH1 cell lineage-determining transcription factor T-bet supresses TH2 gene expression by redistributing GATA3 away from TH2 genes [RNA-seq]
GSE171410 The TH1 cell lineage-determining transcription factor T-bet supresses TH2 gene expression by redistributing GATA3 away from TH2 genes
Relations
BioSample SAMN18605348
SRA SRX10505894

Supplementary file Size Download File type/resource
GSM5225001_EL4_T-bet_GATA3_rep1_kallisto_M18_abundance.tsv.gz 4.1 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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