|
| Status |
Public on Mar 01, 2023 |
| Title |
Kasumi-1_SMARCA5FKBP12_0hdTAG47_4 [PRO-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Kasumi-1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: untreated
cell line: Kasumi-1 cells
|
| 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 |
total RNA |
| Extraction protocol |
following nuclear run-on, total RNA was isolated by Trizol extraction and biotinylated RNA isolated by streptavidin bead binding
follwing hydrolysis of RNA, 3'adaptors were ligated to biotinylated RNA fragments. After 5'Cap removal and end repair, 5' adaptors were also ligated. Adaptor-ligated RNA fragments were reverse transcribed and cDNA libraries amplified using indexed primers.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
biotinylated RNA
|
| Data processing |
Adaptors were trimmed and short/low quality sequence filtered by Trimmomatic-0.32: ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15 MINLEN:15
Reverse complement sequence was generated using fastx_reverse_complement from the FASTX toolkit(v 0.0.13)
Reverse complement sequences were aligned to the human genome (hg19)+ S2 genome using bowtie2 (v2.2.2)
Raw Counts tables for promoter proximal counts and gene body counts were calculated with Nascent RNA Sequencing Analysis (NRSA) pipeline - pause_PROseq.pl. The counts tables were normalized with DESeq2 and differential analysis was performed
Assembly: hg19
Supplementary files format and content: differential gene transcription analysis generated by NRSA and DESeq2
Library strategy: PRO-seq
|
| |
|
| Submission date |
Dec 06, 2022 |
| 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 |
GPL18573 |
| Series (2) |
| GSE160459 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing [PRO-seq] |
| GSE160470 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing |
|
| Relations |
| BioSample |
SAMN32075005 |
| SRA |
SRX18512589 |
