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| Status |
Public on Sep 29, 2021 |
| Title |
ChIP-RPB1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| Sample type |
SRA |
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| Source name |
SPT5-dTAG DLD1
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| Organism |
Homo sapiens |
| Characteristics |
cell type: colorectal adenocarcinoma cell lines
chip antibody: RBP1
treatment: treated with dTAG13 for 3 hours
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| Treatment protocol |
One replicate was DMSO or dTAG treated for 3 hours.
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| Growth protocol |
Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated cells and INTAC-DNA complexes were isolated with antibody.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 with default parameters (Langmead and Salzberg, 2012).
All unmapped reads, low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9 (Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The number of spike-in mm10 reads was counted with SAMtools v1.9 and normalization factor alpha = 1e6/mm10_count was calculated (Li et al., 2009).
Normalized bigwig was generated with deeptools v3.5.0 and reads mapped to the ENCODE blacklist regions were removed using bedtools v2.29.2 (Amemiya et al., 2019; Quinlan and Hall, 2010; Ramirez et al., 2016).
Peaks were called using macs2 v2.2.6 with a q-value threshold of 0.05 and peak annotation was performed with ChIPseeker R package v1.24.0 (Yu et al., 2015; Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
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| Submission date |
Jul 26, 2021 |
| Last update date |
Sep 29, 2021 |
| Contact name |
Linna Peng |
| E-mail(s) |
[email protected]
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| Phone |
8618810567356
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| Organization name |
Fudan University
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| Street address |
Dong'an Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE180842 |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [ChIP-seq] |
| GSE180845 |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 |
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| Relations |
| BioSample |
SAMN20407876 |
| SRA |
SRX11555400 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5471920_ChIP-RPB1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1.bw |
236.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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