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| Status |
Public on Aug 16, 2023 |
| Title |
KATOIII H3K4me1 |
| Sample type |
SRA |
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| Source name |
Gastric Cancer Line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: KATOIII
chip antibody: H3K4me1
treatment: Untreated
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, sheared chromatin were subjected to immunoprecipitation with 2 μg antibody against H3K27ac (ab4729, Abcam), H3K4me1 (ab8895, Abcam) or 5 μg antibody against TEAD1 (610923, BD Biosciences). For RNA-seq, total RNA was extracted following manufacturer’s protocols (Qiagen)
For Nano histone ChIP-seq, ChIP and input DNA were subjected to whole-genome amplification using the WGA4 kit (Sigma-Aldrich) and a universal primer linked to BpmI restriction site (Qiagen). 30ng of BpmI-digested DNA was used for ChIP-seq library preparation according to manufacturer’s protocols (New England Biolabs). For TF ChIP-seq, 30ng of ChIP and input DNA was used for library preparation. For RNA-seq, libraries were prepared accordingly using Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit (Illumina), with an input of 1 μg total RNA.
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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 |
For Nano ChIP-seq, sequenced reads were first trimmed to remove the first and last ten bases. No trimming was required for TF ChIP-seq. Sequenced reads were mapped to the human genome assembly (hg19) using Burrows-Wheeler Aligner (BWA-MEM, version 0.7.10). Only reads with MAPQ value of at least 10 were retained, and PCR duplicates were removed using SAMtools (version 0.1.19). Significant ChIP enrichment peaks relative to input were identified using MACS2 callpeak function. Wiggle track visualizations were generated using MEDIPS (version 1.20.1).
For RNA-seq, sequenced reads were aligned to hg19 using STAR mapper and gene expression abundance was estimated with RSEM as fragments per kilobase per million (FPKM) using default parameters (pipeline available at https://github.com/gis-rpd/pipelines/tree/master/rnaseq/star-rsem).
Genome_build: hg19 for ChIP-seq and RNA-seq
Supplementary_files_format_and_content: wig/bigwig files for ChIP-seq, RSEM gene count files for RNA-seq
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| Submission date |
Oct 25, 2021 |
| Last update date |
Aug 16, 2023 |
| Contact name |
Shamaine Ho |
| E-mail(s) |
e0223167@u.nus.edu
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| Organization name |
Genome Institute of Singapore
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| Street address |
60 Biopolis Street
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| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE186521 |
Regulatory Enhancer Profiling of Mesenchymal-type Gastric Cancer Reveals Subtype-Specific Epigenomic Landscapes and Targetable Vulnerabilities |
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| Relations |
| BioSample |
SAMN22561396 |
| SRA |
SRX12764675 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5655135_KATOIII-H3K4me1-replicate.wig.gz |
19.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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