|
| Status |
Public on Aug 21, 2017 |
| Title |
HL60-0-hrs-2 |
| Sample type |
SRA |
| |
|
| Source name |
Myeloid leukemia cell
|
| Organism |
Homo sapiens |
| Characteristics |
cancer type: Leukemia
cell type: Human myeloid cell
time: 0h
dox: N/A
|
| Treatment protocol |
Human cell lines were treated with vitamin C in culture for 0, 12 and 72hrs. Mouse progenitors were treated with 1ug/ml Doxycycline to turn off Tet2 shRNA expression for 14 days
|
| Growth protocol |
Human cell lines were grown in RPMI media with 10-20% FBS, mouse progenitors were cultured in Optimem media supplemented with 10%FBS and SCF, IL3 and IL6 cytokines
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells according to the RNeasy Qiagen Kit protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the human and mouse genomes (build hg19/GRCh37 and mm10/GRCm38, respectively) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.
|
| |
|
| Submission date |
Apr 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Igor Dolgalev |
| Organization name |
NYU Grossman School of Medicine
|
| Street address |
550 1st Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE97440 |
RNA-sequencing of human leukemia cells and mouse hematopoietic progenitors |
| GSE97442 |
Genetic and pharmacological restoration of TET2 function blocks stem cell self-renewal and progression of leukemia |
|
| Relations |
| BioSample |
SAMN06689198 |
| SRA |
SRX2711371 |
