![](/coreweb/template1/pix/main_left_bg.gif) |
![](/coreweb/template1/pix/pixel.gif) |
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Aug 15, 2020 |
Title |
Mx3CT-11-3HD |
Sample type |
SRA |
|
|
Source name |
females, whole body
|
Organism |
Tribolium castaneum |
Characteristics |
strain: Cro1 selection regime: Control treatment: Hot-Dry
|
Treatment protocol |
Beetles were kept in climate chambers that could control temperature and air humidity. Conditions were: Control: 33°C, 70% relative humidity; Dry : 33°C and 30% r. h.; Hot : 37°C and 70% r. h.; Hot-Dry: 37°C and 30% r. h.
|
Growth protocol |
Beetles were kept in 24h darkness on sterilised organic wheat flour mixed with 10% organic baker's yeast. We sequenced adult reproducing females from different replicate selection lines (seven Control-lines, four Dry-lines, five Hot-lines, seven Hot-Dry lines) under different climate conditions (control, dry, hot, hot-dry). Selection lines had lived under these conditions for 20 generations. Before testing for adaptation, all lines stayed for one generation in control condition. Sequenced individuals were transferred to the respective condition in the egg stage and developed completely in treatment conditions.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA Mini Prep kit (Zimo Research, California, USA) LEXOGEN mRNA-Seq Library Kit (LEXOGEN GmbH, Vienne, Austria)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
reads were mapped against the reference genome(ftp://ftp.ensemblgenomes.org/pub/release30/metazoa/gtf/tribolium_castaneum/Tribolium_castaneum.Tcas3.30.gtf.gz) with STAR v.2.5 (adaptors were trimmed and the first 10 bases were hard trimmed, minimum average quality Q10, minimum tail quality 10, minimum read length 20). Number of reads per gene were counted with FeatureCounts (gtfFeatureType: exon, featureLevel: gene, allowMultiOverlap=TRUE, minFeatureOverlap=10, minMapQuality=10) Genome_build: Tcas3.30 Supplementary_files_format_and_content: tab-delimited text files: raw read counts data for each sample
|
|
|
Submission date |
Aug 14, 2020 |
Last update date |
Aug 16, 2020 |
Contact name |
Frederic Francois Guillaume |
Organization name |
University of Zurich
|
Department |
Evolutionary Biology and Environmental Studies
|
Street address |
Winterthurerstrasse 190
|
City |
Zurich |
ZIP/Postal code |
8057 |
Country |
Switzerland |
|
|
Platform ID |
GPL20193 |
Series (1) |
GSE156256 |
Transcriptome of Tribolium castaneum selection lines (control-, drought-, heat-, heat/drought-adapted) under different climatic conditions |
|
Relations |
BioSample |
SAMN15819280 |
SRA |
SRX8948500 |
Supplementary data files not provided |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
![](/coreweb/template1/pix/main_right_bg.gif) |