Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pancreas
Cell type
Pancreatic beta cells
NA
NA

Attributes by original data submitter

Sample

source_name
Pancreatic Beta Cells
age
16-18 months
strain
C57BL6
antibody
N/A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA-Seq: Flow cytometry sorting was performed on live β cells from isolated pancreatic islets of young and old MIP-GFP mice. Total RNA were isolated using the RNeasy kit (Qiagen). ChIP-Seq: ChIP was performed on sonicated chromatin obtained from sorted old and young mouse β cells using antibody against H3K27ac (39685, Active Motif), H3K4me1 (ab8895, Abcam) and H3K27me3 (07-449, upstate). Input and bound DNA fractions were purified using PCR purification kit (Qiagen) for library preparation. BIS-Seq: Genomic DNA was extracted from FACS sorted old and young beta cells using FFPE AllPrep kit (Ambion), sonicated and bisulfite converted by Qiagen Epitect Bisulfite Kit and used for preparation of libraries. RNA-Seq:Libraries were constructed from 200ng of total RNA using the standard TruSeq RNA sample prep kit (Illumina) using manufacturer's protocols. ChIP-Seq: Libraries were prepared using NEBNext ChIP-seq library prep reagent kit according to Illumina's instructions. BIS-Seq: Libraries were prepared following manufacturer's instructions using NEBNext ChIP-seq library prep reagent kit with methylated adapters (NEB).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
65226664
Reads aligned (%)
94.2
Duplicates removed (%)
52.1
Number of peaks
558 (qval < 1E-05)

mm9

Number of total reads
65226664
Reads aligned (%)
93.9
Duplicates removed (%)
52.1
Number of peaks
607 (qval < 1E-05)

Base call quality data from DBCLS SRA