|
| Status |
Public on May 23, 2023 |
| Title |
Hybrid Pancreatic progenitor, Hybrid2 |
| Sample type |
SRA |
| |
|
| Source name |
Hybrid2
|
| Organisms |
Pan troglodytes; Homo sapiens |
| Characteristics |
cell line: Hybrid2
cell type: Pancreatic progenitor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Omni-ATAC protocol
Illumina Tagment DNA TDE1 Enzyme and Buffer Kits
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ATAC20_PP_Hyb2_total; ATAC20_PP_Hyb2_human; ATAC20_PP_Hyb2_chimp
ATACseq_ASCA_CM_HP_MN_PP_SKM_GRCh38.txt
ATACseq_ASCA_CM_HP_MN_PP_SKM_PanTro6.txt
|
| Data processing |
Remove sequencing adapters with SeqPrep version 1.2
Map reads to GRCh38 and PanTro6 with bowtie2
Remove duplicate reads with Picard 2.23.8 with randomized discarding of duplicates
Remove reads which exhibit mapping bias with WASP (Hornet)
Call peaks with MACS2 and count allele specific and total reads in peaks
Assembly: Human: GRCh38; Chimpanzee: PanTro6
Supplementary files format and content: Counts matrix with total and allele-specific raw read counts (rows are peaks, there are 3 columns per sample: total, human and chimpanzee read counts)
Supplementary files format and content: matrix text files are provided for samples mapped on both the human and chimpanzee genomes
|
| |
|
| Submission date |
May 19, 2023 |
| Last update date |
May 23, 2023 |
| Contact name |
Hunter Fraser |
| Organization name |
Stanford University
|
| Street address |
327 Campus Drive
|
| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL27803 |
| Series (2) |
| GSE232947 |
Cell type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells [ATAC-seq] |
| GSE232949 |
Cell type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells |
|
| Relations |
| BioSample |
SAMN35219300 |
| SRA |
SRX20452327 |
