|
| Status |
Public on Sep 01, 2016 |
| Title |
zfp1_9_4 [X1 cells] |
| Sample type |
SRA |
| |
|
| Source name |
X1 cells
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
RNAi: zfp1
time point (days): 9
replicate: 4
|
| 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 |
To isolate stem cells, we used a well-established method to isolate planarian stem cells by Hoechst blue staining and flow cytometry. Sorted cells were homogenized in Trizol reagent and RNA was isolated per the manufacturer-supplied 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 2500 |
| |
|
| Description |
zfp1_9_4
|
| Data processing |
Base calls were performed using CASAVA-1.8.2
Prior to alignment, fastx_trimmer was used to retain only bases 11 to 80 of each read.
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. One of the samples yielded very few reads and was discarded as an outlier (unc22 day 13 replicate2), thus 35 data sets remain.
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) |
| GSE80544 |
RNA Seq analysis of neoblasts from Schmidtea mediterranea treated with RNAi against zfp1, p53, or unc22 to identify factors involved in neoblast differentiation. |
| GSE80562 |
The cell type and dynamic complexity of the planarian epidermis is determined by both conserved and derived transcriptional regulators. |
|
| Relations |
| BioSample |
SAMN04883231 |
| SRA |
SRX1717895 |
