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Status |
Public on Aug 09, 2022 |
Title |
ChIP-seq-18-RPB1N-SPT6PAF1AID-Veh-2h |
Sample type |
SRA |
|
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Source name |
DLD-1
|
Organism |
Homo sapiens |
Characteristics |
cell line: DLD-1 cell type: Colorectal adenocarcinoma genotype: SPT6-AID/PAF1-AID OsTIR1 treatment: Vehcle 2h chip antibody: RPB1 NTD (Cell signaling # 14958S)
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Treatment protocol |
To induce degradation of AID-tagged proteins, 500 µM auxin was added to culture.
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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).
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
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|
Description |
ChIP-seq Pol II (total)
|
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.
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|
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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 |
SAMN28088018 |
SRA |
SRX15147199 |