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Sample GSM1440536 Query DataSets for GSM1440536
Status Public on Nov 15, 2014
Title Acinar
Sample type SRA
 
Source name Acinar
Organism Mus musculus
Characteristics strain background: C57BL/6J
genotype/variation: Rag1-/-
tissue: Pancreas
tissue/cell type: Acinar cells
Treatment protocol Pancreata were perfused through the common bile duct. After removing endogenous islets, the acinar fraction was digested with liberase and Elastase (Roche) into single cells.
Growth protocol Rag1-/- were obtained from Jackson Labs (http://jaxmice.jax.org/strain/002216.html). For β- cell induction, 100ul (>1x 10^9 pfu) of purified adenovirus was directly injected into the splenic lobe of the dorsal pancreas.
Extracted molecule genomic DNA
Extraction protocol Cherry+ induced beta cells were isolated by fluorescent activated cell sorting (FACS) with FACSaria (BD Bioscience), RNA samples were extracted by Trizol
mRRBS libraries were prepared as previously described (Boyle et al. 2012). Briefly, genomic sequences were digested using the MspI restriction enzyme, which cuts at the sequence CCGG. Digested fragments were subjected to bisulfite treatment which converts unmethylated cytosine residues to uracil
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2500
 
Description Acinar.meth
Please note that the fastq files (for acinar, d10, d30, d60 samples) contain reads from both HiSeq 2000 and HiSeq 2500. The initial sequencing was performed on HiSeq 2000, but resequencing on HiSeq 2500. All the reads were merged into one fastq file for convenience.
Data processing Alignment: bisulfite-converted reads were aligned to a MspI-digested mm9 mouse genome using MAQ in bisulfite alignment mode using the following parameters: -D -s 0 -M c -e 100
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain methylation information for each CpG covered by mRRBS. For each CpG, the methylation is shown as the number of times the CpG was methylated over the total times the CpG was measured.
 
Submission date Jul 21, 2014
Last update date May 15, 2019
Contact name Kendell Clement
Organization name Harvard University
Lab Meissner Lab
Street address 7 Divinity Ave.
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platform ID GPL17021
Series (1)
GSE59615 Transcriptional and epigenetic program changes of induced beta cells over time [RRBS-seq]
Relations
BioSample SAMN02928565
SRA SRX658098

Supplementary file Size Download File type/resource
GSM1440536_acinar.bed.gz 11.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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