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Sample GSM3687047 Query DataSets for GSM3687047
Status Public on Nov 17, 2019
Title CTV1-RNA_PU1mut_1
Sample type SRA
 
Source name CTV1-RNA_PU1mut
Organism Homo sapiens
Characteristics cell line: CTV-1
cell type: T cell leukemia cell line
transfected ivt mrna: PU1mut
Treatment protocol Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA) and total RNA was isolated after 24 h
Growth protocol CTV-1 were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with the RNeasy Mini Kit (Qiagen).
RNAseq was carried out using the using the ScriptSeq Complete Kit (Illumina) according to manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Sequence reads were trimmed to 75bp if longer using HOMER (homerTools trim)
Sequencing reads were mapped to the human genome using STAR v2.5.3a (Dobin et al., 2013). The human hg19 genome index incorporated gene annotation from GENCODE ((Frankish et al., 2019), release 19) was used to aid in spliced alignment
Tables of raw uniquely mapped read counts per human gene were generated during mapping using the built-in --quantMode GeneCounts option in STAR.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing the raw count values for each sample.
 
Submission date Mar 25, 2019
Last update date Nov 19, 2019
Contact name Michael Rehli
E-mail(s) michael.rehli@klinik.uni-r.de
Organization name University Hospital Regensburg
Department Internal Med III
Street address F.-J.-Strauss-Allee 11
City Regensburg
ZIP/Postal code 93042
Country Germany
 
Platform ID GPL21290
Series (2)
GSE128836 The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo [RNA-seq]
GSE128837 The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo
Relations
BioSample SAMN11252822
SRA SRX5574417

Supplementary file Size Download File type/resource
GSM3687047.txt.gz 358.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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