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Sample GSM3230372 Query DataSets for GSM3230372
Status Public on Jun 28, 2021
Title WT rep3
Sample type SRA
Source name embryo
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: embryo
age: embryonic day 11.5 (E11.5)
genotype: wild type
Extracted molecule total RNA
Extraction protocol Embryos were isolated and washed with PBS at 4°C. Embryos were homogenized and RNA was isolated using the GenEluteTM Mammalian total RNA Miniprep Kit according to the manufacturer’s instructions.
After determination of the concentration and RNA integrity number, the library was constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina and the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Using a molecular barcode, the samples were demultiplexed (bcl2fastq2) to fastq data and quality controlled (FastQC)
Trimmomatic (Version 0.33) was used for adapter trimming and read filtering
Reads were aligned to the mouse reference genome (mm10) using Hisat2 and SAMtools (Kim et al., 2015 and Li et al., 2011).
The sorted and aligned reads were counted into genes using HTSeq-counts and differential expression was performed using the r-package deseq2 (Anders et al., 2015 and Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing basemeans, log2(FC) and padj values of all determined genes from comparison of wildtype versus homozygous or wildtype versus heterozygous.
Submission date Jun 28, 2018
Last update date Jun 28, 2021
Contact name Anke Hermann
Organization name University Hospital Münster
Department Internal Medicine D
Lab Molecular Nephrology
Street address Albert-Schweitzer-Campus 1
City Münster
ZIP/Postal code 48149
Country Germany
Platform ID GPL19057
Series (1)
GSE116382 Transcriptome analysis of WWC2-deficient E11.5 embryos
BioSample SAMN09510589
SRA SRX4318379

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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