|
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 |