|
| Status |
Public on Mar 01, 2023 |
| Title |
Kasumi-1_SMARCA5FKBP12_24hdTAG47_2 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Kasumi-1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Kasumi-1
genotype/variation: SMARCA5-FKBP12F36V
treatment: dTAG47
time point: 24h
|
| Treatment protocol |
Cells were treated with 500 nM dTAG-47 for the indicated timepoints.
|
| Growth protocol |
Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted by Trizol according to the manufacturer's protocol and precipitated with isopropanol.
Libraries were constructed on polyA selected transcript using standard Illumina protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
24hr_500nM_dTAG47
|
| Data processing |
Adaptors were trimmed using TrimmomaticPE LLUMINACLIP:TruSeq3-PE-2.fa:2:30:7
Trimmed reads were aligned to the human genome (hg19) with TopHat v2.0.11.
Differential gene expression was determined using Cuffdiff v.2.1.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Cuffdiff differential gene expression output; tab-delimited text files.
|
| |
|
| Submission date |
Oct 29, 2020 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Scott W Hiebert |
| E-mail(s) |
mbomber92@gmail.com, scott.hiebert@vanderbilt.edu
|
| Organization name |
Vanderbilt University
|
| Department |
Biochemistry
|
| Lab |
Dr. Scott Hiebert
|
| Street address |
512 B Preston Research Building
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE160458 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing [RNA-seq] |
| GSE160470 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing |
|
| Relations |
| BioSample |
SAMN16597488 |
| SRA |
SRX9402620 |
