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| Status |
Public on Sep 24, 2014 |
| Title |
H3K4me3_ChIPSeq_Nickel |
| Sample type |
SRA |
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| Source name |
BEAS-2B cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: NiCl2
time point (hours): 72
chip antibody: H3K4me3 (Millipore, 07-473)
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| Treatment protocol |
For exposing cells to nickel, NiCl2 (Sigma N6136) was added to the media at a concentration of 500 mM and the cells were cultured for 72 hours.
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| Growth protocol |
Immortalized human Bronchial Epithelial Cells (Beas-2B) were cultured in Dulbecco’s Modified Eagle’s Medium (Cellgro) supplemented with 1% Penicillin Streptomycin and 10% Fetal Bovine Serum (Atlanta Biologicals) at 37° C and 5 % CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP, untreated and NiCl2 exposed BEAS-2B cells were crosslinked with 1% formaldehyde for 10 minutes at 25°C and sonicated to obtain 200-500 base pair fragments. ChIP was performed using ChIP grade antibodies against H3K9me2 (Abcam, ab1220), H3K27me3 (Millipore, 07-449), H3K4me3 (Millipore, 07-473), H3K9ac (Abcam, ab4441) and CTCF (Active Motif, 61311).
ChIP-Seq libraries were prepared using Illumina TruSeq ChIP sample preparation Kit (IP-202-1024), according to manufacturer’s protocol.
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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 |
basecalling have been done by CASAVA-1.8.2
Histone modification ChIP-seq data have been aligned to human hg19 by bowtie ( version 1.0.0 "–strata –best –n 1 –m 1 -3 10" for sequence by Illumina HiSeq 2500 because Fastqc checked last 10 bases are not good in quality, otherwise "–strata –best –n 1 –m 1"). CTCF ChIP-seq data have been aligned to human hg19 by bowtie ( version 1.0.0 –strata –best –n 1 –m 1 )
H3K4me3, H3K9ac, CTCF peaks have been called by MACS (1.4.2 version 20120305, default parameters) take correspond input sequence as control.
H3K9me2 and H3K27me3 domains have been called by RSEG (version 0.4.8-rc) with binsize 10kb and 5kb respectively
Genome_build: hg19
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| Submission date |
Mar 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Dustin E Schones |
| E-mail(s) |
schoneslab@gmail.com
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| Phone |
+1-626-471-9319
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| Organization name |
City of Hope
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| Department |
Cancer Biology
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| Lab |
Schones
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| Street address |
1500 Duarte Rd
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| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE56051 |
Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption [ChIP-Seq] |
| GSE56053 |
Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption |
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| Relations |
| BioSample |
SAMN02692741 |
| SRA |
SRX497248 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1354431_geo_H3K4me3_3d_peaks.bed.gz |
280.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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