|
| Status |
Public on Nov 18, 2017 |
| Title |
OBD-D9-H2Aub1(+BMP) (ChIP-seq) |
| Sample type |
SRA |
| |
|
| Source name |
reprogramming cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: reprogramming cells
treatment: BMP4(10ng/ml)
antibody: H2AK119ub(CST,#8240)
day of reprogramming: day 9
|
| Treatment protocol |
The cells treated with or without BMP4(10ng/ml) once we change the medium to iCD1 medium after two round infection.
|
| Growth protocol |
The cells infected with indicated factors were cultured in iCD1 reprogramming medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIP DNA library for NEXT Seq500 sequencing was constructed using VAHTS Turbo DNA Library Prep Kit for Illumina(Vazyme Biotech) according to the manufacturer's instruction. Briefly, 10ng ChIP DNA was end repaired and a dA was added. Then the DNA was ligated with adaptors. Adaptor-ligated DNA was purified using AMPure XP beads. The purified DNA was amplified by PCR for 15 cycles, followed by size selection using two round AMPure XP beads and eluted in 25 ul water. The library was quantified with VAHTS Library Quantification Kit for Illumina(Vazyme Biotech). The DNA was diluted to 10 nM before sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the mouse Genome mm9 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peak calling was performed by Dfilter (version 1.6 ).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file were generated with genomeCoverageBed and bedGraphToBigWig. Scores represent the number of fragments overlapping each genomic position.
|
| |
|
| Submission date |
Jan 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiangping He |
| E-mail(s) |
he_jiangping@grmh-gdl.cn
|
| Organization name |
Guangzhou Institutes of Biomedicine and Health (GIBH), CAS
|
| Street address |
Kai yuan avenue 190
|
| City |
GuangZhou |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE93972 |
Kdm2b regulates somatic reprogramming through variant PRC1 complex dependent function [ChIP-seq, MeDIP-seq] |
| GSE94160 |
Kdm2b regulates somatic reprogramming through variant PRC1 complex dependent function |
|
| Relations |
| BioSample |
SAMN06277195 |
| SRA |
SRX2523718 |
