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Sample GSM4727907

Query DataSets for GSM4727907

Status

Public on Aug 15, 2020

Title

Mx3CT-11-1HD

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