|
| Status |
Public on Nov 17, 2019 |
| Title |
CTV1-RNA_woPU1_2 |
| Sample type |
SRA |
| |
|
| Source name |
CTV1-RNA_woPU1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CTV-1
cell type: T cell leukemia cell line
transfected ivt mrna: none
|
| 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 1000 |
| |
|
| 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 |
GPL15433 |
| 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 |
SAMN11252820 |
| SRA |
SRX5574420 |
