|
| Status |
Public on Aug 09, 2022 |
| Title |
ChIP-seq-15-CDC73-SPT6AID-Aux-2h |
| Sample type |
SRA |
| |
|
| Source name |
DLD-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD-1
cell type: Colorectal adenocarcinoma
genotype: SPT6-AID OsTIR1
treatment: Auxin 2h
chip antibody: CDC73 (Bethyl # A300-170A)
|
| Treatment protocol |
To induce degradation of AID-tagged proteins, 500 µM auxin was added to culture.
|
| Growth protocol |
Human DLD-1 cells that constitutively express OsTIR1 were cultured at 37°C in DMEM (Sigma #D6429) supplemented with 10% FBS (Sigma #F2442), 1% Pen-Strep (Gibco #15140-122) in CO2 incubators.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq in human DLD1 cells, ~30 million cells were crosslinked with 1% paraformaldehyde in PBS for 10 min at r.t. Spike-in mouse embryonic fibroblast fixed cells were added to samples. Chromatin was sonicated with the Covaris E220. Immunoprecipitations were carried out with antibodies and Dynabeads Protein G.
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ChIP-seq CDC73
|
| Data processing |
For ChIP-seq, single-end raw reads trimmed by cutadapt 1.14 (Martin, 2011) were aligned to a concatenated genome comprised of human hg38 and mouse mm10 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. The bigwig files with normalized counts were generated using deepTools 3.1.1 bamCoverage (Ramírez et al., 2016).
Assembly: hg38
Supplementary files format and content: bigWig files contain spike-in normalized ChIP-seq signal.
Supplementary files format and content: bed files contain coordinates of genes or pause sites that were used in this study.
|
| |
|
| Submission date |
May 04, 2022 |
| Last update date |
Aug 09, 2022 |
| Contact name |
Yuki Aoi |
| E-mail(s) |
yuki.aoi@northwestern.edu
|
| Organization name |
Northwestern Univ
|
| Department |
Biochemistry & Molecular Genetics
|
| Lab |
Ali Shilatifard
|
| Street address |
303 E Superior St. SQBRC 7-300
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE202184 |
SPT6 functions in transcriptional pause-release via PAF1C recruitment [ChIP-seq] |
| GSE202190 |
SPT6 functions in transcriptional pause-release via PAF1C recruitment |
|
| Relations |
| BioSample |
SAMN28088023 |
| SRA |
SRX15147194 |
