Status
Public on Mar 01, 2021
Title
Mit p300i Rep A input
Sample type
SRA
Source name
iPSCs
Characteristics
cell type: iPSCs reprogrammed from MEFs
strain: R26Fucci2aR (mixed C57BL/6, DBA/2, and CD1 background)
treatment: Mitotic cells were collected after: 6hr treatment with Nocodazole (200ng/ml) then mitotic shake-off. Cells were also treated with p300i (20uM A485) for 3hrs prior to mitotic shake-off.
chip antibody: none
Treatment protocol
see individual treatment descriptions
Growth protocol
Mouse FUCCI2a clonal iPSCs were cultured on irradiated feeder cells in KO-DMEM media with FBS, LIF, and 2i (MEK inhibitor & GSK3 inhibitor).
Extracted molecule
genomic DNA
Extraction protocol
5 million cells were cross-linked with 1% formaldehyde, quenched, and snap frozen until ready to proceed. 5 million formaldehyde-fixed Drosophila nuclei were added to each sample prior to sonication for normalization. After fragmentation, inputs were set aside, and remaining chromatin was immunoprecipitated using H3K27ac antibody and stringent washes. After elution, DNA was reverse-crosslinked and then purified using ZYMO kit.
25ng of immunoprecipitated (ChIP) or input (input) material were used for library prep. Libraries were preared using KAPA HyperPrep kit according to manufacturer's instructions.
Library strategy
ChIP-Seq
Library source
genomic
Library selection
ChIP
Instrument model
NextSeq 2000
Description
in_MITpa
Data processing
Fastq files were first aligned to the Drosophila genome (version DM6) and unaligned reads were mapped to mm10.
All low quality reads were filtered out (Q<20) with the use of samtools
Duplicate reads were removed with the use of picard tools
Additional filtering of reads from chrM and blacklisted regions ws performed with the use of bedtools
Filtered reads from Drosophila were used to normalize each sample and bedgraph and/or BigWig files were generated with the use of bedtools and kentUtils
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files. All files were normalized based on Drosophila spike-in and ratio of Chip/Input was generated with the use of deepTools for each replicate.
Submission date
Jan 06, 2021
Last update date
Oct 10, 2023
Contact name
Effie Apostolou
Organization name
Weill Cornell Medicine
Street address
1161 York Avenue, Apt 8A
City
New York
State/province
NY
ZIP/Postal code
10065
Country
USA
Series (2)
GSE138965
The transcriptional and architectural resetting of stem cell identity during G1 entry
GSE164341
Mitotic bookmarking by H3K27 acetylation is critical for rapid transcriptional, but not architectural, resetting of stem cell-related genes and enhancers upon G1 entry [ChIP-seq]
Relations
Supplementary data files not provided
Raw data are available in SRA
Processed data provided as supplementary file