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| Status |
Public on May 17, 2019 |
| Title |
Female carcass S8 |
| Sample type |
SRA |
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| Source name |
Female carcass lack ovary
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| Organism |
Tribolium castaneum |
| Characteristics |
strain: GA2
tissue: Female carcass
genotype: Wild type
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| Growth protocol |
Beetles were reared on flour medium (95% flour, 5% yeast by weight), and caged in glass jars with tight-fitting fine mesh closures. Beetles were housed in a growth chamber at 25°C with 60-80% relative humidity and 12/12 hour light cycling
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Embryos were collected at 0-5 hours and 6-11 hours respectively in three replicates (each replicate has 80-100 Embryos). Similarly, ovary, testis and carcasses from adult beetles at four days post eclosion (30 beetles in each replicate) were collected to evaluate transcriptional activity. Total RNA from these tissues was extracted with Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. After total RNA extraction, RNA was treated with Turbo DNase (Ambion/Applied Biosystems, Austin, TX).
RNAseq library was prepared using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490) for mRNA isolation and NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB #E7530S) for library preparation according to the manufacturing instructions. Each library had a peak size of approximately 300 base pairs. cDNA library quality was assessed on an Agilent 2200 TapeStation using a High Sensitivity D1000 tape. Libraries were quantified using the Invitrogen Qubit 2.0 Fluorometer High Sensitivity dsDNA assay. All libraries were normalized to a 4 nM concentration and then pooled in equal volumes for denaturing and diluting for sequencing. The library pool was denatured and diluted to a final concentration of 1.8 pM following the Illumina NextSeq Denature and Dilution protocol including a 1% PhiX DNA spike in
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
HiSat2 software version 2.0.5 (Kim et al. 2015) was used to align reads to the Tribolium genome (GCA_000002335.3_Tcas5.2_genomic_RefSeqIDs.gff, obtained from www.ncbi.nlm.nih.gov) using default parameters. Edge R software (McCarthy 2012) in “R” package was used to normalized the libraries using the trimmed mean of M-values method and for differential gene expression analysis. Lowly expressed transcripts were removed from the analysis if the counts per million (CPM) was less than five in 3 samples.
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| Submission date |
Sep 10, 2018 |
| Last update date |
May 17, 2019 |
| Contact name |
SHER AFZAL KHAN |
| E-mail(s) |
sher-afzal-khan@tamu.edu
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| Phone |
979-458-3106
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| Organization name |
Texas A&M University
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| Department |
Entomology
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| Street address |
370 Olsen Blvd
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| City |
COLLEGE STATION |
| State/province |
TX |
| ZIP/Postal code |
77843 |
| Country |
USA |
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| Platform ID |
GPL20193 |
| Series (1) |
| GSE119739 |
Differentially and co-expressed genes in embryo, germ-line and somatic tissues of Tribolium castaneum |
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| Relations |
| BioSample |
SAMN10026665 |
| SRA |
SRX4666282 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3382022_Female_Carcase_S8_fastqc.tar.gz |
684.1 Kb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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