|
| Status |
Public on Nov 26, 2019 |
| Title |
3_ATRA+GSK-LSD1 |
| Sample type |
SRA |
| |
|
| Source name |
acute myeloid leukemia
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HL-60
perturbation: ATRA (100 nM)
|
| Treatment protocol |
1.5 x 10^6 cells were treated with respective compounds for 3 hours.
|
| Growth protocol |
Cells were cultured in humidified incubator at 37°C and 5% CO2 in RPMI 1640 (supplemented: 1 mM sodium pyruvate, 10% FCS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and purified using Direct-zol™ RNA Kit (Zymo Research)
Library preparation was done using Illumina's TruSeq Stranded mRNA Library Preparation Kit following the manufacturer's instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using bcl2FastQ v1.8.4.
Reads were aligned to the hg19 genome assembly using HISAT2.
Gene counts were quantified using htseq-count.
Genome_build: GRCh37/hg19 and respective gene annotation.
Supplementary_files_format_and_content: The Excel file includes raw counts of all genes for each sample.
|
| |
|
| Submission date |
Dec 27, 2018 |
| Last update date |
Nov 26, 2019 |
| Contact name |
Marco Groth |
| E-mail(s) |
dnaseq@leibniz-fli.de
|
| Organization name |
Leibniz Institute on Aging - FLI
|
| Department |
Core Facility - Next Generation Sequencing
|
| Street address |
Beutenbergstraße 11
|
| City |
Jena |
| ZIP/Postal code |
07747 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE124422 |
RNA-seq of HL-60 cells following treatment with different compounds |
| GSE124423 |
HL-60 cells following treatment with different compounds |
|
| Relations |
| BioSample |
SAMN10655790 |
| SRA |
SRX5184923 |
