|
| Status |
Public on Apr 30, 2021 |
| Title |
SMS.Etoposide_6h |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: chronic myelogenous leukemia cell line
treatment: treated with Etoposide for 6 hours
|
| Treatment protocol |
For drug treatments, 1.5 million cells were seeded in 3 ml of the medium without antibiotic per well in 6-well plates. After 16 hours, various drugs or DMSO/water controls were added and incubated for 3 or 6 hr. All drugs were obtained from Abmole Bioscience Inc and dissolved in DMSO (with the exception of YM-155 and cytarabine that were dissolved in water). The concentration of DMSO was kept at 0.1% in all treatments.
|
| Growth protocol |
Human CML leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRNzol Universal (Tiangen, DP424) and Total RNA kit I (Omega, R6834-02) according to the manufacturer’s protocols and quantified using Qubit 3.0 Fluorometer (Life technologies). Total RNA (5 μg) was treated with 5 U of TURBO DNase (Thermo Fisher Scientific, AM2238) in 1× TURBO DNase buffer (Thermo Fisher Scientific, AM2238) at 37°C for 30 min to remove genomic DNA, and then purified with 2× volumes of VAHTS RNA Clean Beads (Vazyme, N412).
Total RNA samples were used for cDNA synthesis performed with a modified version of the not-so-random hexamer method to avoid synthesis of rRNA. The cDNA samples were polyA−tailed with TdT, blocked and used directly for sequencing on the Helicos/SeqLL SMS platform.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Helicos HeliScope |
| |
|
| Data processing |
The raw SMS reads were filtered for length (≥25 bases) and sequence quality using Helisphere package. The remaining reads were then aligned to the GRCh37/hg19 assembly of the human genome using indexDPgenomic software
Genome_build: GRCh37
Supplementary_files_format_and_content: BED files containing coordinates of aligned SMS reads
|
| |
|
| Submission date |
Apr 23, 2021 |
| Last update date |
Apr 30, 2021 |
| Contact name |
Huifen Cao |
| E-mail(s) |
hfcao_bnu@163.com, hfcao@hqu.edu.cn
|
| Phone |
+86 05926167250
|
| Organization name |
Huaqiao University
|
| Department |
School of Biomedical Sciences
|
| Lab |
Institute of Genomics
|
| Street address |
668 Jimei Road
|
| City |
Xiamen |
| State/province |
Fujian |
| ZIP/Postal code |
361021 |
| Country |
China |
| |
|
| Platform ID |
GPL14761 |
| Series (1) |
| GSE173221 |
Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans |
|
| Relations |
| BioSample |
SAMN18849367 |
| SRA |
SRX10666034 |
