|
| Status |
Public on Oct 10, 2016 |
| Title |
GHZ-41 |
| Sample type |
SRA |
| |
|
| Source name |
Intact adult females, replicate 3
|
| Organism |
Tetranychus urticae |
| Characteristics |
strain: London
tissue: Whole body
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted with Qiagen RNeasy RNA extraction kit from intact adult females and dissected proterosoma of adult females.
RNA-Seq libraries were prepared for sequencing using the Illumina strand specific protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA from 100 intact adult females
|
| Data processing |
Illumina reads generated by Fasteris (Switzerland) on a HiSeq instrument with standard base calling were aligned to T. urticae reference genome (September 29, 2009) with STAR 2.5.0b in two-pass alginment mode; a maximum intron size of 20 kb was used (information from the refrerence annotation was not used for read alignment).
Read counts for genes in the October 29, 2015 annotation were obtained with HTSeq 0.6.0 with "--stranded=yes" and "--feature=exon."
Differential expression evaluated with DESeq2 1.6.3 with "ddsminReplicatesForReplace" set to "Inf", "cooksCutoff" set to "FALSE" and "independentFiltering" set to "FALSE."
Genome_build: September 29, 2009 (genome sequence) and October 29, 2015 (genome annotation). The genome sequence and annotations are publically available from ORCAE (http://bioinformatics.psb.ugent.be/orcae/).
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts and DESeq2 output.
|
| |
|
| Submission date |
May 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard M Clark |
| Organization name |
University of Utah
|
| Department |
Department of Biology
|
| Lab |
Clark Laboratory
|
| Street address |
257 So. 1400 East, RM 204 SB
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL21813 |
| Series (1) |
| GSE81128 |
Gene expression data for body versus head samples for detection of genes with enriched expression in salivary glands of the spider mite Tetranychus urticae |
|
| Relations |
| BioSample |
SAMN04954982 |
| SRA |
SRX1743287 |
