|
| Status |
Public on Sep 01, 2016 |
| Title |
sox8_6_3 [Whole Worm Tissue] |
| Sample type |
SRA |
| |
|
| Source name |
Whole Worm Tissue
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
RNAi: sox8
time point (days): 6
replicate: 3
|
| Treatment protocol |
Cloned gene vectors were transformed into bacterial strain HT115, induced to express dsRNA at O.D.= 0.8 with 1mM (final) IPTG, and incubated for 2 hours at 37 C with shaking. Bacterial pellets were rinsed once with Milli-Q water, and mixed with an equal weight of calf liver paste. dsRNA food was given to the animals every 3 days for three feedings.
|
| Growth protocol |
The CIW4 clonal line of S. mediterranea was maintained at 20 C in 1X Montjuic salts (Cebrià and Newmark, 2005) supplemented with 50 ug/mL gentamicin sulfate, and fed homogenized calf liver paste once per week.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole worms or sorted cells were homogenized in TRIzol reagent (Sigma) and RNA was isolated as described in the manufacturer’s manual. Isolated RNA from whole worm tissue was treated with RNase-free DNase on QIagen RNeasy columns and eluted in nuclease-free water.
500ng-1μg RNA per whole worm sample or 100ng of sorted cell RNA was used for generation of RNAseq libraries using the Illumina TruSeq kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
sox8_6_3
|
| Data processing |
Base calls were performed using CASAVA-1.8.2
Reads were aligned using bowtie with the following parameters: --best --strata -v 2 -m 5 against transcriptome smed_20140614 defined in GEO submission: GSE72389
Read counts to genes were tallied from the SAM files with a custom script. RPKM values were generated using the rpkm function from the edgeR library from Bioconductor in R.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: rpkm.txt contains tab-delimited RPKM vales for each sample.
|
| |
|
| Submission date |
Apr 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris W Seidel |
| E-mail(s) |
seidel@phageT4.org
|
| Phone |
816 926 9054
|
| Organization name |
Stowers Institute
|
| Department |
Genomics
|
| Lab |
Seidel
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL20150 |
| Series (2) |
| GSE80543 |
RNA Seq analysis in flatworm following 6, 12, or 18 day treatment with RNAi against Pax5, Sox8, or Zfp1, relative to unc22 to identify transcriptional targets. |
| GSE80562 |
The cell type and dynamic complexity of the planarian epidermis is determined by both conserved and derived transcriptional regulators. |
|
| Relations |
| BioSample |
SAMN04883254 |
| SRA |
SRX1717839 |
