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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 01, 2021 |
| Title |
EG1 DMSO Rep A input |
| Sample type |
SRA |
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| Source name |
iPSCs
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| Organism |
Mus musculus |
| Characteristics |
cell type: iPSCs reprogrammed from MEFs
strain: R26Fucci2aR (mixed C57BL/6, DBA/2, and CD1 background)
treatment: Early G1 cells were collected after: 6hr treatment with Nocodazole (200ng/ml) & 3hr simultaneous treatment with DMSO (1:2500), then mitotic shake off. Mitotic cells were released into fresh media for 1hr to enter early G1.
chip antibody: none
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| Treatment protocol |
see individual treatment descriptions
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| 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).
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
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| Description |
in_EG1da
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| 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.
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| Submission date |
Jan 06, 2021 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Effie Apostolou |
| E-mail(s) |
[email protected]
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| Organization name |
Weill Cornell Medicine
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| Street address |
1161 York Avenue, Apt 8A
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL30172 |
| 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] |
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| Relations |
| BioSample |
SAMN17227936 |
| SRA |
SRX9793866 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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