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Sample GSM2299179 Query DataSets for GSM2299179
Status Public on Sep 01, 2016
Title 6d_cKO1
Sample type SRA
 
Source name pancreas
Organism Mus musculus
Characteristics tissue: pancreas
genotype: Ptf1a(CreER/fl)
Treatment protocol Tamoxifen treatment: On day 0, 1, 2, mice received 0.25 mg tamoxifen/g mouse at 50 mg/ml in corn oil by gavage. Mice were sacrificed on day 6.
Extracted molecule total RNA
Extraction protocol RNA preparation: pancreas was homogenized in 4 M Guanidine Thiocyanate, 0.1 M Tris HCl pH 7.5, 1% 2-mercaptoethanol with a Tekmar Tissuemizer. RNA was isolated from an aliquot of the homogenate by addition of N-Lauroylsarcosine sodium salt to 0.5%, Potassium Acetate pH 5.5 to 0.1 M, and Acetic Acid to 0.08 M, followed by addition of 0.75 volume ethanol while vortexing. RNA was allowed to precipitate from the solution at -20 C for at least 1 hour, collected by centrifugation at 12,000 g for 5', and the RNA pellet resuspended in Trizol (equal volume to starting homogenate). Subsequent steps were as per manufacturer's protocol (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina True-seq protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina HiSeq Control Software version 2.0.10.0 used for basecalling
Sequences were mapped to mm9 mouse genome using TopHat v2.0.4 (by use of Bowtie v0.12.7.0) with parameters --no-novel-juncs --segment -length 25 --segment-mismatches 3
Sequences per gene were counted using Samtools ( v0.1.18.0) /HTSeq (v0.6.0)
Counts-per-million (CPM) were calculated using TMM normalization according to Robinson et al., Bioinformatics, 2010. Data set was filtered for minimal expression by "keep <- rowSums(cpm(d)) >= 3"
Differential gene expression analysis was performed with edgeR v3.0.8 (FDR < 0.05)
Genome_build: mm9
Supplementary_files_format_and_content: Normalized counts-per-million (CPM) for each sample in tab-delimited text file
Supplementary_files_format_and_content: EdgeR results as .xlxs spreadsheets, all results as DE_Ptf1a_cKO 6-day, and fdr < 0.05.
 
Submission date Aug 31, 2016
Last update date May 15, 2019
Contact name Galvin Swift
E-mail(s) galvin.swift@utsouthwestern.edu
Organization name U TX Southwestern Medical Center
Department Molecular Biology
Lab Ray MacDonald
Street address 6000 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75390-9148
Country USA
 
Platform ID GPL17021
Series (2)
GSE86261 Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation and Homeostasis by PTF1A [6-day RNA-Seq]
GSE86263 Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation and Homeostasis by PTF1A
Relations
BioSample SAMN05717693
SRA SRX2069625

Supplementary file Size Download File type/resource
GSM2299179_Ptf1a_KO1_Htseq.txt.gz 89.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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