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Sample GSM3687051 Query DataSets for GSM3687051
Status Public on Nov 17, 2019
Title CTV1-RNA_PU1_rep_3
Sample type SRA
Source name CTV1-RNA_PU1
Organism Homo sapiens
Characteristics cell line: CTV-1
cell type: T cell leukemia cell line
transfected ivt mrna: PU1
Treatment protocol Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA) daily for seven days prior to RNA isolation
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 and subjected to 7 cycles of PU.1 mRNA transfection delivering one dose a day for a total of 7 days prior to total RNA isolation.
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
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
BioSample SAMN11252819
SRA SRX5574421

Supplementary file Size Download File type/resource
GSM3687051.txt.gz 368.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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