|
| Status |
Public on Mar 01, 2023 |
| Title |
Kasumi-1_SMARCA5FKBP12_6hdTAG47_2 [PRO-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: 6hr
|
| 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.
Following 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 |
6hr_500nM_dTAG47
biotinylated RNA
|
| Data processing |
Library strategy: PRO-seq
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).
samtools -view generated .bam file with hg19 chromosomes.
Differential transcript analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - pause_PROseq.pl with DESeq normalization.
Differential eRNA analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - eRNA.pl
Bedgraph files were generated by Homer makeUCSCfile.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Homer-generated bedgraph files. neg.bedGraph: negative strand, plus.bedGraph: positive strand.
Supplementary_files_format_and_content: Differential gene transcription analysis generated by NRSA; tab-delimited text files. gb_change.txt: gene body changes, Enhancer_change: eRNA changes.
|
| |
|
| 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 |
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 |
SAMN16597500 |
| SRA |
SRX9402629 |
