|
| Status |
Public on Aug 18, 2016 |
| Title |
nrg6_SR_28_6_4 |
| Sample type |
SRA |
| |
|
| Source name |
asexual CIW4 adult
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
tissue: Whole Worm
RNAi: nrg6
treatment: SR
gamma radiation (rads): 1250
days.post.sublethal.irradiation: 6
feedings: 6
days.post.feeding: 13
days: 28
replicate: 4
|
| Treatment protocol |
All genes were cloned into a pPR-T4P vector as described previously (Gurley et al., 2008). RNAi food was prepared by adding 125 µL of liver paste (9 parts of liver to 1 part of water) into a bacterial pellet obtained from a 50 mL overnight culture. Animals used in experiments were starved for 7-14 days. Animals in all RNAi experiments were fed 6 times with 3 days between feedings. 1,250 rads of irradiation was carried out 7 days after the last feeding using a GammaCell 40 Exactor irradiator. Day 0 represents the day of irradiation. X1 stem cells were isolated using a well-established method by Hoechst 33342 staining and flow cytometry.
|
| Growth protocol |
Asexual Schmidtea mediterranea strain (CIW4) animals were maintained in 1 x Montjuic water supplemented with 100 µg/mL gentamicin sulfate (Gemini Bioproducts, #400-100P) at 20ºC as previously described (Newmark and Sánchez Alvarado, 2000).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Worms and isolated cells were homogenized in Trizol reagent. Total RNA extraction was performed following the manufacturer-supplied protocol.
PolyA-selected, single stranded RNA-Sequencing libraries were prepared for four biological replicates per stage using the Illumina TruSeq RNA Sample V2 kit starting with 500 ng total RNA per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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 after removal of ribosomal RNAs (SMED30027845,SMED30032663,SMED30032887) 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 |
Jul 05, 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 (1) |
| GSE84025 |
Egf signaling directs neoblast repopulation by regulating asymmetric cell division in planarians |
|
| Relations |
| BioSample |
SAMN05359897 |
| SRA |
SRX1897805 |
