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Status |
Public on Mar 01, 2023 |
Title |
Kasumi-1_SMARCA5FKBP12_2hdTAG47_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: 2h
|
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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
2hr_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.
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|
|
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 |
SAMN16597492 |
SRA |
SRX9402616 |