|
| Status |
Public on Aug 28, 2013 |
| Title |
CITH053_Beta_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
FACS-sorted pancreatic islet
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic islets
cell type: Beta
donor id: CITH053
chip-seq antibody: H3K4me3
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We performed FACS sorting on dispersed human islets using cell surface antibodies (1:20) and secondary antibodies (1:200; 115-116-075, 115-135-164, Jackson ImmunoResearch) as described before (Dorrell C, et al. Stem Cell Res 2008) to obtain cell populations highly enriched for alpha, beta, and exocrine (duct and acinar) cells. Total RNA was isolated from whole islets, and sorted alpha, beta, and exocrine cells using the Ambion mirVana miRNA Isolation Kit (AM1560) reverse transcribed to cDNA using SuperScript II reverse transcriptase (Invitrogen). ChIP and preparation of ChIP-Seq libraries was performed on individual cell sorts for each cell type and donor (H3K4me3: 8580, Abcam; H3K27me3: 07-449. Upstate).
DNA from ChIP or reverse transcription was treated by blunt end repair and ligation of sequencing adapters. Adapter-ligated fragments were size select to roughly 200bp and amplified by PCR. Final libraries were verified on an Agilent Technologies 2100 BioAnalyzer to check size, purity, and concentration of the library prior to sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample name: FGC0138_s_7
|
| Data processing |
Sequence reads and quality scores were extracted using Illumina CASAVA Pipeline v1.7
ChIP-seq reads were aligned to the human genome using ELAND, RNA-seq reads were aligned to the human genome/transcriptome using RUM
H3K4me3 ChIP-seq peak calling was performed with GLITR. H3K27me3 ChIP-seq peak calling was performed with STAR.
RNA-seq transcript quantification was performed with RUM.
Genome_build: hg18
Supplementary_files_format_and_content: Peak calls (ChIP-seq) and transcript quantification (RNA-seq), all in BED format.
|
| |
|
| Submission date |
Aug 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Logan J Everett |
| Organization name |
U.S. Environmental Protection Agency
|
| Department |
Office of Research and Development
|
| Lab |
Center for Computational Toxicology and Exposure
|
| Street address |
109 T.W. Alexander Dr
|
| City |
RTP |
| State/province |
North Carolina |
| ZIP/Postal code |
27711 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE50386 |
Epigenomic plasticity enables human pancreatic alpha to beta cell reprogramming |
|
| Relations |
| BioSample |
SAMN02338350 |
| SRA |
SRX340787 |
