|
| Status |
Public on May 15, 2018 |
| Title |
50WtD |
| Sample type |
SRA |
| |
|
| Source name |
cardiac left ventricle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cardiac left ventricle
age: 12 weeks
gender: female
biological replicate: 2
genotype: wild type
experiment: diabetic pregnancy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol, libraries were prepared following manufacturer’s instructions at the Genomics Core Facility (EMBL Heidelberg, Germany) (KIT?)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Ribosomal RNA sequences were removed using sortmerna (version 2) and the SILVA rRNA database (version 119). Low quality reads and adaptor sequences were removed using Trimmomatic PE. Reads were aligned against the reference Mus musculus genome v GRCm38 using STAR (version 2.5.2b).
Annotated reads were counted using htseq-count with the reference model gencode.vM8.annotation.gtf
Normalized number of reads was generated by DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized and DESeq2 normalized number of reads for each Sample
|
| |
|
| Submission date |
Jan 25, 2018 |
| Last update date |
May 15, 2018 |
| Contact name |
Gabriela Pavlínková |
| Organization name |
Institute of Biotechnology, CAS, v.v.i
|
| Department |
Laboratory of Molecular Pathogenetics
|
| Street address |
Průmyslová 595
|
| City |
Vestec by Prague |
| ZIP/Postal code |
25250 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE109633 |
Effects of Hif1a mutation and maternal diabetes on the offspring heart |
|
| Relations |
| BioSample |
SAMN08395290 |
| SRA |
SRX3599513 |
