|
| Status |
Public on Apr 05, 2017 |
| Title |
MV411.shENL_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MV411
|
| Organism |
Homo sapiens |
| Characteristics |
cell: MV411 cells
treatment: shENL Knock Down
batch: 4
|
| Treatment protocol |
ICas9-MOLM-13 Cells were treated with doxycyline for indicated time before RNA collection; MV411 cells were transduced with shRNA followed by drug selection, and RNA was collected at 6 days post infection for RNA-seq
|
| Growth protocol |
Cells were cultured in RPMI with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from iCas9-MOLM-13 and MV411 cells using the RNeasy Mini Kit (Qiagen, Gaithersburg, MD).
Samples were prepared as instructed using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles, DNA fragments were sequenced using single-end sequencing technology on Illumina NextSeq 500 platform (MOLM-13) or pair sequencing technology on Illumina HiSeq 2000 platform (MOLM-13)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MV411.RNAseq_pool.htseq.txt
|
| Data processing |
Basecalls performed by Illumina CASAVA 1.8.2
Raw reads were mapped to human reference genome (hg19) and transcriptome using the the TopHat2 package. Transcript abundances were quantified using htseq-count v0.6.0
Differentially expressed genes were determined using DESeq2 for MOLM13 RNA-seq samples, and EdgeR for MV411 RNAseq-samples.
Genome_build: hg19
Supplementary_files_format_and_content: raw count files were generated using htseq-count v0.6.0
|
| |
|
| Submission date |
Apr 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Liling Wan |
| E-mail(s) |
lwan@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Lab |
Laboratory of Chromatin Biology and Epigenetics
|
| Street address |
1230 York Avenue, Box 78
|
| City |
NEW YORK |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE80774 |
ENL Links Histone Acetylation to Oncogenic Gene Expression in AML |
|
| Relations |
| BioSample |
SAMN04913663 |
| SRA |
SRX1735688 |
