|
| Status |
Public on Oct 21, 2019 |
| Title |
RNA-seq_ZT16 control REP2 |
| Sample type |
SRA |
| |
|
| Source name |
ZT16 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: BL52
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 |
SAMN08287099 |
| SRA |
SRX3527641 |
