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| Status |
Public on Dec 09, 2014 |
| Title |
Control Septic2 |
| Sample type |
SRA |
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| Source name |
eggs, Septic
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| Organism |
Tribolium castaneum |
| Characteristics |
tissue: eggs
genotype/variation: Control
replicate: 2
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| Treatment protocol |
Eggs were untreated (Naive), pricked with a sterile needle (Sterile) or pricked with a needle dipped in a concentrated mixture of E.coli and M.luteus (Septic).
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| Growth protocol |
Eggs were kept at 30°C before and after treatment. Control eggs were generated by parental RNAi using a non-Tribolium dsRNA sequence, serosa-less eggs were generated by parental RNAi with dsRNA of the Tczen1 gene.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Eggs were pooled in groups of approximately 300, these were rinsed in bleech to remove the chorion after which they were washed with water. Total RNA of eggs was extracted using trizol extraction (Invitrogen) after which the RNA was purified and DNA digested on column with the RNeasy kit (Qiagen).
Library was constructed by the ZFscreens sequencing company, Leiden, the Netherlands.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
paired-end experiment (R1,R2)
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| Data processing |
Adapter sequences were trimmed, sequences of quality 20 or lower were trimmed, bases below a quality of 3 from the 3'end were trimmed and we discarded reads shorter than 20bp all using CLC Genomics Workbench 6.
Sequences were mapped using CLC Genomics Workbench 6, 2 mismatches to the reference genome were allowed, seedlength was set to 28, mismatch quality to 100.
Minimum paired distance set to 180
Maximum paired distance set to 300
Genome_build: Tcas_3.0
Supplementary_files_format_and_content: The mapping results as output from CLC Genomics Workbench 6, expression data and all other available information is included in supplied data tables.
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| Submission date |
Jan 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris G.C. Jacobs |
| Phone |
+31715274882
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| Organization name |
Leiden University
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| Department |
Institute of Biology
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| Lab |
Evolutionary Biology
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| Street address |
Sylviusweg 72
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| City |
Leiden |
| State/province |
Zuid-Holland |
| ZIP/Postal code |
2333BE |
| Country |
Netherlands |
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| Platform ID |
GPL18162 |
| Series (1) |
| GSE54018 |
The extraembryonic serosa is a frontier epithelium providing the insect egg with a full-range innate immune response |
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| Relations |
| BioSample |
SAMN02582507 |
| SRA |
SRX425552 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1305926_Control_Septic_2.txt.gz |
434.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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