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Status |
Public on Jun 30, 2020 |
Title |
SW480_H3K36me3 |
Sample type |
SRA |
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Source name |
SW480 cell line
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Organism |
Homo sapiens |
Characteristics |
chip antibody: H3K36me3 (Abcam Cat. No. ab9050) tumor stage: Dukes' type B, colorectal adenocarcinoma treatment: none
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Growth protocol |
SW480 and SW620 cell lines were obtained from China Infrastruture of Cell Line Resources and cultured as described37. Briefly, SW480 and SW620 cells were cultured in DMEM (Gibco Cat. No. C11995500BT) supplemented with 10% fetal bovine serum (Gemini Cat. No. 900-108) and 1% penicillin/streptomycin (Gibco Cat. No. 15140-122). Cells were cultured at 37°C with 5% CO2. Cells used to inject mice were stably transfected with luciferase.
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Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP-sequencing libraries were prepared by using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB Cat. No. E7370), according to the manufacturer’s instructions. The sequencing was performed by Hiseq1500 (Illumina).
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 1500 |
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Data processing |
Fastq files from ChIP-seq experiments were mapped to the human genomes (hg19) by using STAR41 with parameters --outFilterMismatchNoverLmax 0.05. For the ChIP-seq of histone modification, enriched loci were identified by using the findPeaks command from HOMER (http://homer.salk.edu/homer/) with the option –style histone, 4-fold enrichment over the input sample, 4-fold enrichment over local background, at FDR = 0.001, and normalization to 10 million mapped reads per experiment. Genomic binding peaks for transcription factor FOXA2 were identified with option -style factor, 2-fold enrichment over the input sample, 2-fold enrichment over local background, at the false discovery rate of 0.001. Genome_build: hg19 Supplementary_files_format_and_content: bigwig files and peaks were generated using HOMER.
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Submission date |
Nov 15, 2017 |
Last update date |
Jun 30, 2020 |
Contact name |
Yang Eric Li |
E-mail(s) |
liyang01133@gmail.com
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Phone |
+1-8589222580
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Organization name |
Tsinghua University
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Department |
School of Life Sciences
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Lab |
Zhi John Lu
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Street address |
Room 2-110, Biotechnology Building, School of Life Sciences, Tsinghua University
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City |
Beijing |
State/province |
Beijing |
ZIP/Postal code |
100084 |
Country |
China |
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Platform ID |
GPL18460 |
Series (2) |
GSE106921 |
Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer (ChIP-Seq) |
GSE106923 |
Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer |
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Relations |
BioSample |
SAMN08027769 |
SRA |
SRX3394269 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2857644_SW480_H3K36me3.regions.bed.gz |
736.6 Kb |
(ftp)(http) |
BED |
GSM2857644_SW480_H3K36me3.ucsc.bigWig |
365.1 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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