|
| Status |
Public on Jul 11, 2019 |
| Title |
P300_500_it_rep2_ESC |
| Sample type |
SRA |
| |
|
| Source name |
cultured mESC (V6.5)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: cultured mESC (V6.5)
fixed by: formaldehyde
molecule subtype: ChIP-DNA
ip reagent: bio-ChIP with SA beads
|
| Growth protocol |
Mouse embryonic stem cells were cultured in DMEM/F12 and neurobasal with 2i or 15% fetal bovine serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked cells were treated with 0.3% SDS at 37°C and followed by gentle sonication. Transposition was set up by incubation at 37°C for 1 h, followed by addition of stopping buffer. Soluble chromatin was used for following ChIP experiments. DNA was eluted from beads, reverse crosslinked and treated with proteinase K. Finally, DNA was extracted by pheno-chloroform.
After PCR enrichment using NEBNext Q5 Ultra II master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "-N 1".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files. Bigwig files of replicates data could show the stability. Similarity among data of different cell magnitude reflected the applicability of itChIP-seq. H3K27me3-data and H3K4me4-data showed that signals could be detected in both active regions and repressed regions by itChIP.
|
| |
|
| Submission date |
Feb 15, 2019 |
| Last update date |
Jul 11, 2019 |
| Contact name |
Chen Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Peking University
|
| Department |
Institute of Molecular Medicine
|
| Lab |
Aibin He Lab
|
| Street address |
Yihe Yuan Road No.5
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE109757 |
Profiling chromatin state by single-cell itChIP-seq [itChIP-seq] |
| GSE109762 |
Profiling chromatin state by single-cell itChIP-seq |
|
| Relations |
| BioSample |
SAMN10948933 |
| SRA |
SRX5382173 |
