|
| Status |
Public on Oct 11, 2018 |
| Title |
Pvir#6_hep [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
P.virginalis_Heidelberg laboratory strain
|
| Organism |
Procambarus virginalis |
| Characteristics |
strain: Heidelberg laboratory strain
tissue: hepatopancreas
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 20-60 mg frozen tissues. Thawed tissues were homogenized in 1 ml Trizol (Ambion), precipitated with isopropanol and resuspended in 20-100 µl RNase-free water (Gibco Life Technologies). Total RNA was treated with DNase using the RNeasy Mini Kit (Qiagen) following the manufacturer's RNeasy Mini Protocol for RNA Cleanup in combination with the On-Column DNase Digestion Protocol.
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
RNA mapping: hisat2 2.0.4
calculating expression levels: RSEM-1.2.30
Genome_build: Pvir0.4
Supplementary_files_format_and_content: rsem genes.results files
|
| |
|
| Submission date |
Mar 27, 2018 |
| Last update date |
Oct 11, 2018 |
| Contact name |
Fanny Gatzmann |
| E-mail(s) |
f.gatzmann@dkfz.de
|
| Organization name |
DKFZ
|
| Department |
A130 Epigenetics
|
| Street address |
Im Neuenheimer Feld 580
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24771 |
| Series (2) |
| GSE112410 |
Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [RNA-seq] |
| GSE112411 |
Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish |
|
| Relations |
| BioSample |
SAMN08802952 |
| SRA |
SRX3854634 |
