|
| Status |
Public on May 01, 2024 |
| Title |
H60_ctrl_02 |
| Sample type |
SRA |
| |
|
| Source name |
HL-60
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HL-60
cell type: human leukemia
treatment: no treatment
|
| Treatment protocol |
Molm 14 cells were cultured in growth media and treated with low (11.1 pM) and high (100 pM) concentrations of DSA for 36 hours. HL-60 cells were cultured in growth media with low (112.7 pM) and high (500 pM) concentrations of DSA for 36 hours.
|
| Growth protocol |
Molm 14 cells were cultured in RPMI with 10% heat-inactivated FBS, L-glutamine and penn strep. HL-60 cells were cultured in IMDM with 20% heat-inactivated FBS, L-glutamine and penn strep. Both cell lines were maintained in 5% CO2 at 37oC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction from cells and tumor tissues was performed using the RNeasy Mini Kit according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60) and were mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation ( human release 31).
Assembly: GRCh38 (hg38)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files
|
| |
|
| Submission date |
Oct 12, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Hongjian Jin |
| E-mail(s) |
hongjian.jin@STJUDE.ORG
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38015 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE245161 |
Gene expression profile of Duocarmycin SA-treated human AML cell lines in vitro |
|
| Relations |
| BioSample |
SAMN37799786 |
| SRA |
SRX22080086 |
