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| Status |
Public on Nov 01, 2017 |
| Title |
MTA2_ChIPSeq |
| Sample type |
SRA |
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| Source name |
Colon cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
chip antibody: MTA2 (Santa Cruz, sc-28731)
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| Treatment protocol |
In EsiM group, HCT116 cells were treated with MTA2 RNAi oligonucleotides. The RNAi oligonucleotides were transfected into cells by using the Lipofectamine 2000 transfection kit (Invitrogen) according to the manufacturer’s instructions. The final concentration of the siRNA molecules is 10 nM and cells were harvested 48 hours later. There is no treatment in other three groups.
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| Growth protocol |
human colon cancer cell line HCT116 was maintained in DMEM medium supplemented with 10% FBS in a humidified incubator containing 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries of ChIP samples were prepared according to a modified version of the Illumina Genomic DNA protocol, as described previously (Mikkelsen et al., 2007).
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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 |
read alignment software: Bowtie with -v 2 -m 1 --best --strata
peak calling: MACS with pvalue cutoff 1e-3 and model fold 4,30
Genome_build: hg19
Supplementary_files_format_and_content: *.clean_hg19.bed files are mapping results by Bowtie. The six lines are: chromosome, start, end, number of mismatch, 0 and strand.
Supplementary_files_format_and_content: *_VS_I_p-3_mfold4_peaks.bed files are peaks got by MACS. The five lines are: chromosome, start, end,name and -10*log10(pvalue) for the peak region.
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| Submission date |
Jul 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tingting Li |
| E-mail(s) |
litt@hsc.pku.edu.cn
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| Phone |
+86-10-82801585
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| Organization name |
Peking University
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| Department |
Medical informatics
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| Street address |
38 Xueyuan Rd
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| City |
Beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE39467 |
Profiling the target genes for MTA2 and EZH2 in HCT116 |
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| Relations |
| SRA |
SRX160744 |
| BioSample |
SAMN01091328 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM969795_M.clean_hg19.bed.gz |
192.4 Mb |
(ftp)(http) |
BED |
| GSM969795_M_VS_I_p-3_mfold4_peaks.bed.gz |
207.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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