|
| Status |
Public on Oct 09, 2018 |
| Title |
C2C12 H3K4me3 ChIP at 1k cells replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Immortal cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
antibody target: H3K4me3
primary antibody: mouse monoclonal anti-H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Libraries were prepared on the Illumina HiSeq1500 and 2500 platforms.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
The raw sequence reads were aligned to the mouse and human reference genomes (GRCm38 and GRCh38) using HISAT2 (version 2.0.4), and the uniquely mapped reads were retained.
The bigWig files were generated using bamCoverage command of deepTools (ver. 2.4.2) with the option: --smoothLength x --binSize y, where x and y are specified in the file names.
The csv countmatrix files were generated with multiBamSummary with the option bins -bs 4000 (or 10000).
ChILT peaks were generated with Homer findPeaks with the options -style histone -style histone -gsize 3e9 -size 4000 -regionRes 1 -minDist 1 -fdr 0.2.
ChIP peaks were generated with MACS2 (ver. 2.1.1) with the options -g hs -q 0.01 --nomodel --shift 0 --extsize 200 --keep-dup all.
Genome_build: GRCm38/mm10 and GRCh38/hg38
Supplementary_files_format_and_content: bigWig files contain signal data for visualization via tools such as the Integrative Genomics Viewer, csv files include comma-delimited matrices, the bed file contains the peak data for C2C12, MCF-7 and MDA-MB-231 data.
|
| |
|
| Submission date |
May 29, 2018 |
| Last update date |
Oct 09, 2018 |
| Contact name |
Yasuyuki Ohkawa |
| E-mail(s) |
yohkawa@bioreg.kyushu-u.ac.jp
|
| Organization name |
Medical Institute of Bioregulation
|
| Lab |
Division of Transcriptomics
|
| Street address |
3-1-1 Maidashi
|
| City |
Fukuoka |
| ZIP/Postal code |
8128582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE115047 |
A chromatin integration labeling method enables lower-input epigenomic profiling |
|
| Relations |
| BioSample |
SAMN09276604 |
| SRA |
SRX4137070 |
