|
| Status |
Public on Jun 30, 2022 |
| Title |
human MPCs H3K27ac WT – rep2 |
| Sample type |
SRA |
| |
|
| Source name |
human pancreatic MPCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HPSCs-derived MPCs (stage 4)
antibody: H3K27ac (Abcam, ab4729)
genotype: PTF1A+/+
|
| Growth protocol |
Human embryonic stem cell line H1 (Wicell) was cultured in E8 medium (Thermo Fisher). Differentiation to pancreatic progenitors was performed following protocols published by Balboa et al 2018 and Rezania et al 2014.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MPCs were crosslinked with 1% PFA, lysed and sonicated with Covaris S220. DNA-protein complexes were isolated with antibodies, as described in Miguel-Escalada et al 2019.
NEBNext Ultra II DNA library Prep Kit (New England Biolabs)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adaptors were trimmed from ChIP-Seq raw reads using cutadapt v1.9.1 (options -m 20)
Trimmed ChIP-Seq reads were aligned to hg19 using bowtie2 v2.1.0 (options –no-unal)
ChIP-Seq peaks were called using MACS2 using options –bw=300 –keep-dup all -q 0.01 (H3K27ac) and -q 0.05 (PTF1A and MED1).
Consistent peaks between 2 biological samples were defined by overlapping MACS2 called peaks from each replicate with bedtools intersectBed v2.27.1
Genome_build: hg19
Supplementary_files_format_and_content: peak text files are broadPeak or narrowPeak text files outputs from MACS2
Supplementary_files_format_and_content: Bigwig files were created using bedGraphToBigWig from UCSC tools.
|
| |
|
| Submission date |
Sep 08, 2021 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Irene Miguel-Escalada |
| E-mail(s) |
irene.miguelescalada@crg.eu
|
| Organization name |
CRG
|
| Street address |
Dr Aiguader 88
|
| City |
BArcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE183672 |
Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster |
| GSE183674 |
Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster |
|
| Relations |
| BioSample |
SAMN21356642 |
| SRA |
SRX12101857 |
