|
| Status |
Public on Sep 01, 2016 |
| Title |
IR72_1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Worm Tissue
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
time point: 72 hours
gamma radiation: 6000 rads
replicate: 1
|
| Treatment protocol |
Planarians 2-3 mm in length were starved for at least 1 week before use. Irradiation was done with a GammaCell 40 Exactor irradiator at a dose rate of 85 Rad/minute.
|
| 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 |
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 2000 |
| |
|
| 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 |
GPL15553 |
| Series (2) |
| GSE80540 |
RNA Seq analysis of gene expression in Planaria at 24, 48, 72, and 96 hours after exposure to 6k rad of gamma irradiation. |
| GSE80562 |
The cell type and dynamic complexity of the planarian epidermis is determined by both conserved and derived transcriptional regulators. |
|
| Relations |
| BioSample |
SAMN04883187 |
| SRA |
SRX1717816 |
