|
| Status |
Public on Apr 15, 2016 |
| Title |
H3K27me3 juvenile endocrine (EA46) |
| Sample type |
SRA |
| |
|
| Source name |
pancreas, juvenile, H3K27me3 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endocrine
age: juvenile
chip antibody: rabbit H3K27me3 (Diagenode, pAb-069-010)
tissue: pancreas
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Previously described ChIP-Seq methods were used (Rada-Iglesias et al. 2011 [PMID: 21160473]; Wapinski et al. 2013 [PMID: 24243019]).
Illumina HiSeq/TruSeq
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were aligned to hg19 using Bowtie.
A custom script was used to calculate ChIP-Seq read counts 2 kb upstream and downstream of transcription start site of age-dependent genes. The TSS coordinates were downloaded from the UCSC genome browser using RefSeq reference transcriptome list.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include tag counts normalized to the sequencing depth. 'adult_*.txt' and 'juv_*.txt' files include different gene loci that were categorized as adult or juvenile genes, respectively.
|
| |
|
| Submission date |
Apr 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Seung Kim |
| E-mail(s) |
seungkim@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Developmental Biology
|
| Lab |
Seung Kim Lab
|
| Street address |
279 Campus Dr B303
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE65793 |
Epigenomic landscapes of human primary pancreatic cell types |
| GSE79469 |
Age-dependent pancreatic gene regulation reveals mechanisms governing human β-cell function |
|
| Relations |
| BioSample |
SAMN04858629 |
| SRA |
SRX1707575 |
