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| Status |
Public on Jun 28, 2021 |
| Title |
Heterozygous rep3 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: embryo
age: embryonic day 11.5 (E11.5)
genotype: WWC2-/+
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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.
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| Submission date |
Jun 28, 2018 |
| Last update date |
Jun 28, 2021 |
| Contact name |
Anke Hermann |
| E-mail(s) |
a.hermann1301@gmail.com
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| Organization name |
University Hospital Münster
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| Department |
Internal Medicine D
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| Lab |
Molecular Nephrology
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| Street address |
Albert-Schweitzer-Campus 1
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| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE116382 |
Transcriptome analysis of WWC2-deficient E11.5 embryos |
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| Relations |
| BioSample |
SAMN09510586 |
| SRA |
SRX4318382 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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