|
| Status |
Public on May 04, 2024 |
| Title |
K562_i4_sgNTC1_DMSO_72_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
K562 dCas9-KRAB human CML cells (sgNTC-1)
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: DMSO 0.05%
treatment duration: 72h
genome build: hg38
|
| Growth protocol |
Cells were grown in RPMI (Corning, 15-040-CV) with 10% dialyzed fetal bovine serum (Sigma, F0392), 4mM glutamine, and 1% penicillin/streptomycin (Corning, 45000-652).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1 million live cells were sorted using a BD FACSAria and placed on ice. Immediately following the sort, cells were centrifuged, pelleted, and flash frozen in liquid nitrogen and placed at -80C. Pellets were processed in groups of 24 using the Zymo RNA Miniprep Kit and quantified using the Invitrogen Quant-it RNA kit. RNA was then diluted to a concentration of 2 ng/ul and 5ul of each sample was transferred to a 96 well plate.
Poly-A enrichment and cDNA synthesis were performed in parallel as described in Soumilion et al. 2014, followed by library preparation using the Nextera XT kit and paired-end sequencing on an Illumina NextSeq 500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
K562_i4_sgNTC1_DMSO_72_rep2
|
| Data processing |
Mouse and human data were mapped to mm10 and hg38 genomes, respectively, using STAR v2.7.8a and default parameters.
Reads that mapped to transcripts were counted using featureCounts v2.0.1 (with parameters -M -O --fraction --primary).
Supplementary files format and content: A tab-delimited file containing raw counts generated from featureCounts.
|
| |
|
| Submission date |
Aug 11, 2022 |
| Last update date |
May 04, 2024 |
| Contact name |
Brian Do |
| E-mail(s) |
bdo311@gmail.com
|
| Organization name |
MIT
|
| Department |
Biology
|
| Lab |
Vander Heiden
|
| Street address |
500 Main St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE172333 |
A myeloid maturation program initiated by nucleotide depletion during S phase [RNA-Seq] |
| GSE172335 |
Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress |
|
| Relations |
| BioSample |
SAMN30266370 |
| SRA |
SRX17035505 |
