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| Status |
Public on Oct 09, 2013 |
| Title |
H3K4me3 |
| Sample type |
SRA |
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| Source name |
human colon carcinoma
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| Organism |
Homo sapiens |
| Characteristics |
ChIP: H3K4me3
cell line: RKO
growth conditions: untreated cells, normal growth conditions
antibody vendor/catalog: abcam, ab8580
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| Treatment protocol |
no treatment
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| Growth protocol |
DMEM, 10% FBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the Illumina Genome analyzer or HiSeq2000 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 |
Raw reads were mapped on the human genome build hg18 using Burrows-Wheeler Aligner (bwa http://bio-bwa.sourceforge.net/). Uniquely mapped reads were kept for further analysis. Samtools and the script genomeCoverageBed were used to produce bedgraph files.
Genome_build: hg18
Supplementary_files_format_and_content: bw or bed
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| Submission date |
May 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Marie-Eve Lalonde |
| Organization name |
CHUQ
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| Street address |
9 McMahon street
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| City |
Quebec city |
| State/province |
Qc |
| ZIP/Postal code |
G1R 2J6 |
| Country |
Canada |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE47190 |
ChIP-seq of MYST acetyltransferases |
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| Relations |
| BioSample |
SAMN02169383 |
| SRA |
SRX286204 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1146450_H3K4me3RKO_hg18.bw |
228.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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