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Sample GSM2911212 Query DataSets for GSM2911212
Status Public on Oct 21, 2019
Title RNA-seq_ZT8 control REP1
Sample type SRA
 
Source name ZT8 control_liver
Organism Mus musculus
Characteristics strain: C57BL/6J
treatment: 12 wk control Diet (Research Diet, D12329)
tissue: liver
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from 50 mg of liver using QIAZOL reagent. Quality of the RNA was assayed by using Agilent RNA 6000 Nano Kit (Agilent) in a 2100 Bioanalyzer (Agilent).
Libraries were prepped from 1 µg RNA by Illumina TruSeq RNA library prep kit v2 chemistry in an automated system (Agilents Bravo liquid handling platform). Libraries run in a HighSeq2500 sequencer (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description sample code: BL31
processed data file:
table_featureCounts.txt
table_filtered_VST.txt
Data processing Reads were aligned to the mm9 genome with STAR v2.4.2a and the output SAM files were converted to BAM using samtools v1.3.1
Feature counting: counting all reads which were located within an exon, do not overlap multiple features, are not chimeric, and have a minimum mapping quality of 4. Using featureCounts v1.4.6: featureCounts -p -C -F GTF -t exon -Q 4 -a gencode.vM1.annotation.gtf -g gene_id -o $output $input -T 16 However for further processing steps, the count matrix was filtered (0 count rows and those where the average was less then 50 were left out). These filtered tables were than the input tables for DESeq2 and for the normalization step.
Finding differentially expressed genes using DESeq2 v1.15.51
Finding oscillating genes with JTK_Cycle v3.1
Genome_build: mm9
Supplementary_files_format_and_content: .txt tables. Those with the name table_featureCounts*.txt are the count matrices, where the rows are the genes and the columns the samples. A cell in the matrix contains the count number for gene i in sample j. The table table_filtered_featureCounts_DL-DH-BL-BH.txt is a combined count table, which is formed from the table table_featureCounts_DL-DH.txt and some columns of the table_featureCounts.txt matrix. Tables named table_filtered_VST*.txt are the prefiltered, VST normalized tables. The file table_filtered_VST_DL-DH-BL-BH.txt is the filtered, VST normalized table_filtered_featureCounts_DL-DH-BL-BH.txt table.
 
Submission date Jan 03, 2018
Last update date Oct 21, 2019
Contact name Nina Henriette Uhlenhaut
E-mail(s) henriette.uhlenhaut@helmholtz-muenchen.de
Organization name HelmholtzZentrum München - IDC
Department Molecular Endocrinology
Lab Uhlenhaut IDC
Street address Ingolstädter Landstraße 1, Neuherberg
City Munich
State/province Bavaria
ZIP/Postal code D-85764
Country Germany
 
Platform ID GPL17021
Series (2)
GSE108688 GR cistromes reprogramming by High Fat Diet [RNA-seq]
GSE108690 Cistromic reprogramming of the diurnal glucocorticoid hormone response by high fat diet
Relations
BioSample SAMN08287081
SRA SRX3527634

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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