NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4035261 Query DataSets for GSM4035261
Status Public on Oct 21, 2019
Title RNA-Seq_LFD Dex treated at ZT0 and sac. at ZT4 REP 2
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics treatment: 12 wk control Diet (Research Diet, D12329)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from >50mg of liver using QIAZOL (QIAGEN). Quality of the RNA was assayed using the Agilent RNA 6000 Nano Kit in a 2100 Bioanalyzer (Agilent).
Libraries were prepped from 1µg total RNA with the Illumina TruSeq RNA library prep kit v2 chemistry in an automated system (Agilent Bravo liquid handling platform). Libraries were run on Illumina sequencers.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description LFD Dex treated at ZT0 and sac. at ZT4 REP 2
sample code: GSE108690-DL_5
table_featureCounts_ZT04.txt
table_filtered_VST_ZT04.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 v1.23.10
Finding oscillating genes with JTK from MetaCycle v1.2.0, period was set to 24 hours.
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. Tables named table_filtered_*.txt are the prefiltered, normalized tables.
Supplementary_files_format_and_content: table_featureCounts_noBL41.txt: txt file which contains the count matrix
Supplementary_files_format_and_content: table_filtered_noBL41_rlog.txt: the rlog normalized count matrix
Supplementary_files_format_and_content: table_filtered_noBL41_VST.txt: the VST normalized count matrix
Supplementary_files_format_and_content: table_featureCounts_KO-WT_AlbCre.txt: txt file which contains the count matrix
Supplementary_files_format_and_content: table_filtered_KO-WT_AlbCre_rlog.txt: the rlog normalized count matrix
Supplementary_files_format_and_content: table_filtered_KO-WT_AlbCre_VST.txt: the VST normalized count matrix
Supplementary_files_format_and_content: table_featureCounts_ZT04.txt: txt file which contains the count matrix (mice were injected with Dex at ZT0 and sacrificed at ZT4)
Supplementary_files_format_and_content: table_featureCounts_ZT1216.txt: txt file which contains the count matrix (mice were injected with Dex at ZT12 and sacrificed at ZT16)
Supplementary_files_format_and_content: table_filtered_VST_ZT1216.txt: the VST normalized count matrix
Supplementary_files_format_and_content: table_filtered_VST_ZT04.txt: the VST normalized count matrix
 
Submission date Aug 14, 2019
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 SAMN12573700
SRA SRX6716656

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap