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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 20, 2019 |
| Title |
h3k36me3_norm3 |
| Sample type |
SRA |
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| Source name |
Normal liver_h3k36me3
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| Organism |
Mus musculus |
| Characteristics |
phenotype: Normal liver
tissue: Liver
background strain: B6
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Small liver pieces were incubated for 10 min at room temperature in 1× phosphate-buffered saline (PBS) containing 1% formaldehyde. The crosslinking reaction was quenched by adding glycine to a final concentration of 0.125 M. After a wash in 1× PBS, liver pieces were homogenized in lysis buffer and incubated for 10 min on ice. Nuclei were pelleted and resuspended in 1× TE buffer. Nuclei were sonicated using a Bioruptor (Diagenode, Liege, Belgium). Chromatin samples were diluted with 2× RIPA buffer to a final 1× concentration. IPs were performed with primary antibody and Dynabeads Protein A complex overnight at 4°C. Immune complexes were washed twice for 10 min in each of the following buffers: 1× RIPA buffer, 1× RIPA + 0.3 M NaCl, LiCl buffer, 1× TE + 0.2% Triton X-100, 1× TE. Then, immune complexes were in 100 μl 1× TE, protease K, and 0.3% sodium dodecyl sulfate (SDS) and incubated at 65°C overnight. Eluted DNA was purified using a QIAGEN PCR purification kit. Buffers were comprised of the following: lysis buffer (10 mM Tris [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1× TE; 10 mM Tris-HCl [pH 7.5], and 1 mM EDTA), 1× RIPA (1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and 10 mM Tris [pH 7.5], 1 mM EDTA), LiCl buffer (0.25 M LiCl, 0.5% NP40, and 0.5% sodium deoxycholate). Every buffer included 1× protease inhibitor cocktail (Roche Molecular Biochemicals, Indianapolis, IN). The following antibodies were used: H3Ace (06-599, Upstate/Millipore, Temecula, CA), H3K36me3 (ab9050, abcam), H3K27me3 (07-449, Upstate/Millipore, Temecula, CA), H3K4me3 (07-473, Upstate/Millipore, Temecula, CA), RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody (abcam, ab5131). RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody (abcam, ab5095), Anti-H3 (millipore 06-755).
Illumina ChIP library prep (Part # 11251892 Rev. A)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
We extended the 34-bp reads toward the 3’ end to cover DNA fragments bound by the specific modified histone proteins. The readout was converted to browser extensible data (BED) files for visualization in the UCSC genome browser (http://genome.ucsc.edu).
Genome_build: mm9
Supplementary_files_format_and_content: BED
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| Submission date |
Jan 20, 2016 |
| Last update date |
Jan 20, 2019 |
| Contact name |
Young-Joon Kim |
| E-mail(s) |
yjkim@yonsei.ac.kr
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| Organization name |
Yonsei university
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| Street address |
Yonsei-ro 50
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| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE77023 |
ChIP-seq analysis of normal and HBx transgenic mouse liver |
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| Relations |
| BioSample |
SAMN04430431 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2042667_h3k36me3_norm3_eland.txt.gz |
232.4 Mb |
(ftp)(http) |
TXT |
| GSM2042667_h3k36me3_norm3n.bed.gz |
38.7 Mb |
(ftp)(http) |
BED |
| Raw data provided as supplementary file |
| Processed data provided as supplementary file |
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