|
| Status |
Public on Sep 18, 2017 |
| Title |
PDX_TALL_dBET6_3 |
| Sample type |
SRA |
| |
|
| Source name |
T-ALL PDX
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T-ALL PDX
bar code: TATGCCAG
|
| Growth protocol |
Alpha-MEM with Glutamax-1, 10% FBS, 10% human AB serum, 1% L-glutamine, 1% penicillin/streptomycin, 1X Insulin-Transferrin-Selenium, 10 ng/mL recombinant mouse IL-7, and 10 ng/mL recombinant IL-2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.
RNA libraries were prepared for sequencing using SMARTer v4 Low Input RNA Kit from Clontech
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq after 6 hr dBET6 (250 nM) treatment
processed data file: PDX_TALL_all_fpkm_exprs_norm.txt
|
| Data processing |
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript
|
| |
|
| Submission date |
Oct 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE79253 |
BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment [RNA-seq] |
| GSE79290 |
BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment |
|
| Relations |
| BioSample |
SAMN05934759 |
| SRA |
SRX2264697 |
