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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 18, 2021 |
| Title |
CUL4B-ChIPseq |
| Sample type |
SRA |
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| Source name |
PANC-1 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell treatment method: untreated
chip antibody: CUL4B
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 5 x 107 cells were used for each ChIP-Seq assay. The chromatin DNA precipitated by polyclonal antibodies against SIRT1 and CUL4B. The DNA was purified with a Qiagen PCR purification kit.
A Vazyme TruePrep DNA Library Prep Kit V2 for Illumina ® (Vazyme Biotech) was used for DNA library construction. Briefly,the kit uses a new-type transposasea for DNA fragmentation and ligation of Illumina's adapters. 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 Genome Analyzer following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using CASAVA version 1.4
The high quality reads were mapped to the Human genome of Ensembl by using Bowtie(version 0.12.8) with the default parameter.
Data were filtered using the following specification:A Perl program was used to filter of low quality sequences from raw sequencing data. The quality of each base was checked from the first base of each read. Once a low-quality base (quality<10) was found, it was removed together with following sequences. For paired-end reads, if one read was less than 30 bases after the trimming of low quality bases, the whole paired-end reads were removed."
The expression peaks were detected by MACS(Model-based Analysis for ChIP-Seq) using the parameter:-f BOWTIE -g hs -n C_Ip -w.
Genome_build: hg 19
Supplementary_files_format_and_content: tab-delimited text files were generated using MACS2 and The R programming language-ChIPseeker
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| Submission date |
Dec 16, 2020 |
| Last update date |
Jun 20, 2021 |
| Contact name |
yan wang |
| E-mail(s) |
yanwang@tmu.edu.cn
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| Organization name |
National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
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| Street address |
17 panjiayuan nanli, chaoyang district, Beijing, China
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| City |
beijing |
| ZIP/Postal code |
100021 |
| Country |
Zimbabwe |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE163337 |
Genome-wide maps of chromatin state in PANC-1 cells. |
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| Relations |
| BioSample |
SAMN17092659 |
| SRA |
SRX9690616 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4977254_C4_Anno_peak.txt.gz |
734.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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