|
| Status |
Public on Feb 23, 2017 |
| Title |
mv411_dTAG13_24h_r3 |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF4 rearranged acute myeloid leukemia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MV4;11 (Cas9; ENL-FKBP(F36V); ENL-/-)
bar code: ACAGTG
|
| Treatment protocol |
Cell were treated with 500 nM dTAG-13 (0.1% DMSO final concentration) for 8, 24, or 96 hours; 500 nM EPZ-5676 (0.1% DMSO final concentration) for 96 hours; or DMSO (0.1%) for 24 or 96 hours
|
| Growth protocol |
MV4;11 (Cas9; ENL-FKBP(F36V); ENL -/-) cells (MV4;11 parent cell line obtained from the laboratory of Prof. Scott A. Armstrong) were cultured in RPMI supplemented with 10% FBS, penecillin, and streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Prior to RNA isolation, cell were counted and total RNA isolation was performed using the miRvana miRNA total RNA isolation kit (ThermoFisher Scientific, AM1560) according to manufacturers instructions. Following isolation, RNA was digested with DNase (Ambion). During isolation, external RNA spike-ins (ERCC, Ambion) were added at the time of cell lysis.
Total RNA was subject to polyA selection and adapter ligation in preparation for next-generation sequencing (Illumina stranded mRNA library prep)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq after 24 hr dTAG-13 (500 nM) treatment
|
| 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: ENL_all_fpkm_exprs_norm.txt: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript
|
| |
|
| Submission date |
Jun 01, 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) |
| GSE82117 |
Transcription control by the ENL YEATS domain in acute leukemia [RNA-seq] |
| GSE82118 |
Transcription control by the ENL YEATS domain in acute leukemia |
|
| Relations |
| BioSample |
SAMN05194767 |
| SRA |
SRX1813457 |
