 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 01, 2015 |
| Title |
sample_F_head_3 |
| Sample type |
SRA |
| |
|
| Source name |
sample F head 3
|
| Organism |
Tribolium castaneum |
| Characteristics |
strain: San Bernardino
tissue: head
Sex: female
developmental stage: adult
|
| Treatment protocol |
Sex seperation and dissection of the different bodyparts
|
| Growth protocol |
Beatles were reared at 28 °C on full grain flour supplemented with 5% dry yeast, defined ages ranging from 0 to 21 days old were equaly pooled
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using ZR Tissue & Insect RNA MicroPrep™ (Zymo, #R2030) according to the manufacturers protocol.
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 400 ng of total RNA . Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (PairedRead; 2x100 bp).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
whole heads excluding the antennae, but with mouthparts
|
| Data processing |
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics).
Reference transcriptome: The preliminary au3.cds gene set supplemented with not covered genes from the OGS and manually curated candidates involved in olfaction (OR, GR, IR, SNMP, ODE, OBP...) was used as the mapping reference. Isoforms were removed to avoid multiple mappings. The final transcriptome contained only t1 isoforms.
Reads were mapped to the reference using bowtie2 (version 2.1.0) with the these settings: -q -D 20 -R 3 -N 1 -L 20 -i S,1,0.50
Raw count tables were obtained with samtools (version 0.1.18).
Gene prediction set au3: http://bioinf.uni-greifswald.de/tcas/genes/au3/ supplemented with gene models of the OGS and manually curated genes involved in olfaction
FastQC A Quality Control tool for High Throughput Sequence Data http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ by S. Andrews
Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and Subgroup, 1000 Genome Project Data Processing (2009). The Sequence Alignment/Map format and SAMtools. Bioinforma. Oxf. Engl. 25, 2078–2079.
Supplementary_files_format_and_content: raw and normalized counts
|
| |
|
| Submission date |
Nov 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Georg Oberhofer |
| E-mail(s) |
goberho@gwdg.de
|
| Phone |
+49 176 877 87615
|
| Organization name |
University Göttingen
|
| Department |
Developmental Biology
|
| Lab |
Bucher
|
| Street address |
Justus von Liebig Weg 11
|
| City |
Göttingen |
| State/province |
Lower Saxony |
| ZIP/Postal code |
37077 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18255 |
| Series (1) |
| GSE63162 |
Tissue-specific transcriptomics, chromosomal localization, and phylogeny of chemosensory and odorant binding proteins from the red flour beetle Tribolium castaneum reveal subgroup specificities for olfaction or more general functions |
|
| Relations |
| BioSample |
SAMN03174806 |
| SRA |
SRX757117 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1542481_sample13.counts.txt.gz |
98.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
