|
| Status |
Public on Sep 01, 2015 |
| Title |
OldBeta_Rep1_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic Beta Cells
|
| Organism |
Mus musculus |
| Characteristics |
age: 15 months
strain: MIP-GFP/Bl6
antibody: N/A
|
| Extracted molecule |
total RNA |
| Extraction 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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RawReadCounts.txt, TrancriptFPKMCounts.txt
|
| Data processing |
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq: Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
ChIP-Seq: Reads were aligned to mm9 genome using bowtie version 0.12.7 with parameters -v 3 -k 1 -m 1 --best --strata. Redundant reads were discarded before creating bedgraph profiles.
Peak calling was done using HOMER for H3K4me1 and H3K27Ac marks at FDR=0.01 with respect to corresponding Input. Peak calling using STAR was done for H3K27me3 marks at FDR=0.01.
BIS-Seq: DNA sequencing data was aligned to mouse genome (mm9) with the BS Seeker program. Data was reported as the fraction of reads that were methylated, calculated as the ratio of cytosine bases (indicating methylated CpGs) to total reads for each CpG coordinate. Unmethylated cytosines are ultimately converted to thymine bases during the bisulfite conversion process.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited file of transcript raw read counts.
Supplementary_files_format_and_content: Tab delimited file of transcript FPKM counts.
Supplementary_files_format_and_content: Peak files are tab-delimited listing genomic coordinates and their respective scores and p-values. Scores represent fold-change with respect to Input.
Supplementary_files_format_and_content: Tab-delimited files of loci, fraction of methylated cytosines and total read count.
Supplementary_files_format_and_content: RawReadCounts.txt: Raw transcript counts
Supplementary_files_format_and_content: TrancriptFPKMCounts.txt: Transcript FPKM counts
Supplementary_files_format_and_content: Old_H3K4me1.peaks.txt: peak
Supplementary_files_format_and_content: Old_H3K27me3.peaks.txt: peak
Supplementary_files_format_and_content: Young_H3K4me1.peaks.txt: peak
Supplementary_files_format_and_content: Young_H3K27me3.peaks.txt: peak
Supplementary_files_format_and_content: Young_H3K27Ac.peaks.txt: peak
Supplementary_files_format_and_content: OldBeta_bs_seeker-CG.tab: Percent methylated cytosines
Supplementary_files_format_and_content: YoungBeta_bs_seeker-CG.tab: Percent methylated cytosines
|
| |
|
| Submission date |
May 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Dana Avrahami Tzfati |
| E-mail(s) |
dana.tzfati@mail.huji.ac.il
|
| Organization name |
Hadassah Hebrew University School of medicine
|
| Department |
Developmental Biology and cancer research
|
| Lab |
Dor and Glaser
|
| Street address |
Ein-Kerem
|
| City |
Jerusalem |
| ZIP/Postal code |
91120 |
| Country |
Israel |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE68618 |
Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved insulin secretion by pancreatic β cells |
|
| Relations |
| BioSample |
SAMN03703607 |
| SRA |
SRX1035135 |
