|
| Status |
Public on Oct 28, 2022 |
| Title |
DMSO INTS11 ChIP-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: DMSO
chip antibody: INTS11 (Sigma, HPA029025)
|
| Treatment protocol |
WT cells were not treated. INTS11Halo cells were treated with DMSO or 500 nM PROTAC for 4 hours.
|
| Growth protocol |
INTS11Halo cells were maintained in SFES+2i/LIF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with formaldehyde for 10 minutes and quenched with glycine. After washing, cell pellets were resuspended in sonication buffer and sonicated using the Qsonica Q800R3 system. Chromatin was pre-cleared with Protein A agarose and incubated with the indicated antibody overnight. Protein A agarose beads were added and allowed to bind antibody-epitope complexes. IPs were washed extensively and eluted twice. DNA was purified using phenol/chloroform.
INTS11Halo eluates were spiked with Drosophila DNA. All libraries were constructed with the NEB NEBNext Ultra II DNA Library kit .
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing reads were filtered (requiring a mean quality score over 20) and trimmed to 50 bp.
Data from WT cells were mapped to a genome representing mm10 rRNA genes. Reads not mapping here were mapped to mm10 using Bowtie 1.2.2 (-v2 -k1 --best)
Data from INTS11Halo cells were first mapped to the Drosophila dm3 genome (spike) and reads not mapping here were subsequently mapped mm10 using Bowtie 1.2.2 (-v2 -k1 --best)
Mapped reads were converted to bedGraphs representing deduplicated fragment midpoints using extract_fragments.pl (DOI 10.5281/zenodo.5519914), which were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: INTS11Halo bigWigs represent deduplicated, background-subtracted, normalized fragment centers. WT bigWigs represent deduplicated fragment centers.
|
| |
|
| 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) |
| GSE200696 |
Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci (ChIP-Seq) |
| GSE200702 |
Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci |
|
| Relations |
| BioSample |
SAMN27549579 |
| SRA |
SRX14835817 |
