|
| Status |
Public on Oct 28, 2022 |
| Title |
PROTAC TT-seq Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Embryonic stem cell
cell line: F121-9
cell type: Embryonic stem cell
genotype: INTS11Halo
treatment: 500 nM PROTAC
|
| Treatment protocol |
Cells were treated with DMSO or 500 nM PROTAC for 4 hours and labled with 4sU for the final 20 minutes.
|
| Growth protocol |
INTS11Halo cells were maintained in SFES+2i/LIF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse. RNA was then fragmented. 4sU-containing RNA was biotinylated, pulled down, and washed. RNA was then eluted and purified.
4sU-labeled RNA was used as input to the Illumina TruSeq stranded totl RNA kit using the manufacturer's protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Other: 4sU RNA
|
| Data processing |
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 100 nt.
Samples were mapped to the Drosophila dm3 (spike) genome, and nonmapping reads subsequently mapped to mm10 using STAR 2.7.3a (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Assembly: mm10
Supplementary files format and content: bigWigs representing DEseq-normalized read coverage
Library strategy: TT-seq
|
| |
|
| Submission date |
Apr 12, 2022 |
| Last update date |
Oct 28, 2022 |
| Contact name |
Karen Adelman |
| E-mail(s) |
karen_adelman@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Biological Chemistry and Molecular Pharmacology
|
| Street address |
45 Shattuck St. LHRRB-201a
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE200701 |
Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci (TT-seq) |
| GSE200702 |
Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci |
|
| Relations |
| BioSample |
SAMN27549614 |
| SRA |
SRX14835830 |
