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| Status |
Public on Jan 21, 2021 |
| Title |
iPSC_160-2_H3K27ac_rep1 |
| Sample type |
SRA |
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| Source name |
iPS line 160-2
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| Organism |
Papio anubis |
| Characteristics |
cell type: Induced pluripotent stem cells
antibody: H3K27ac
cell line: iPS line 160-2
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| Growth protocol |
Baboon (Papio anubis) ES (B4, B15) and iPS (160-2, M14939#3) cells used in this study were previously derived (Navara et al., 2013) and grown on feeder cells at 37°C/5% CO2 in PluriSTEM™ Human ES/iPS Medium as described (Navara et al., 2018).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-Seq libraries were prepared with antibodies for H3K4me3 (abcam8580), H3K9me3 (abcam8898), H3K27me3 (abcam6002), and H3K27ac (39133, Active Motif, Carlsbad, CA). Each library was prepared from 50,000 cells with inclusion of PEG in samples during MNase digestion, adapter ligation with NEB adapters (E7535S, New England Biolabs, Ipswich, MA) and adapter cleavage by incubation with USER enzyme (M5505S, New England Biolabs) at 37°C for 15 min.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Baboon ChIP-seq reads files were mapping to UCSC papAnu4 by Rsubread with default parameters.
After mapping to the reference genome, bam files of repicates were merged by samtools-1.10. Duplicated reads were marked by Picard-2.239, then removed from the downstream analysis by samtools. Uniquely mapped reads were sorted by samtools-1.10.
MACS2 was used for reads filteration, fragments length prediction and peak calling.
Deeptools bamcoverage was used for making bigwig files and heatmap analysis.
Genome_build: papAnu4
Supplementary_files_format_and_content: peak filles generated by MACS2
Supplementary_files_format_and_content: bigwig files, generated by Deeptools
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| Submission date |
Jan 20, 2021 |
| Last update date |
Jan 22, 2021 |
| Contact name |
keren cheng |
| E-mail(s) |
keren.cheng@outlook.com
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| Organization name |
University of Pennsylvania
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| Department |
Biomedical Sciences
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| Street address |
3800 Spruce Street
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL29629 |
| Series (2) |
| GSE165186 |
Validation of Baboon Pluripotent Cells as a Model for Translational Stem Cell Research [ChIP-Seq] |
| GSE165191 |
Validation of Baboon Pluripotent Cells as a Model for Translational Stem Cell Research |
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| Relations |
| BioSample |
SAMN17389680 |
| SRA |
SRX9903347 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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