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Status |
Public on Mar 30, 2022 |
Title |
EL4 T-bet + Plum rep2 |
Sample type |
SRA |
|
|
Source name |
EL4 cell line
|
Organism |
Mus musculus |
Characteristics |
cell line: EL4 treatment: PMA + inomomycin ectopically expressed protein: FLAG-T-bet
|
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.
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|
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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
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|
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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 |
SAMN18605346 |
SRA |
SRX10505896 |