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| Status |
Public on Oct 21, 2015 |
| Title |
p53_3_2 |
| Sample type |
SRA |
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| Source name |
whole worm_3 days after p53 RNAi
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| Organism |
Schmidtea mediterranea |
| Characteristics |
time after rnai treatment: 3 days
RNAi: p53
tissue: Whole Worm Tissue
replicate: 2
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| Treatment protocol |
Animals were given RNAi food every 3 days, with the first day designated as Day 0. For RNA Seq analysis, control (unc 22 RNAi), chd4(RNAi) and p53(RNAi) animals were fed RNAi food 3 times.
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| Growth protocol |
Schmidtea mediterranea CIW4 asexual strain was maintained in 1X Montjuic salts supplemented with 50 ug/ml Gentamicin and fed homogenized calf liver paste as previously described (Gurley at al., Science 2008, PMID: 18063757; Reddien et al., Dev. Cell 2005, PMID: 15866156).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Three biological replicates of 10 worms each were collected for RNA isolation. Replicates for each time point were stored in Trizol (Life Technologies) at –80C until ready for chloroform extraction. RNA was precipitated with isopropanol and washed with 75% ethanol. Pellet was air-dried and resuspended in nuclease-free water.
Libraries were prepared for RNA Seq analysis from 500ng-1ug per whole worm sample or 100ng of sorted cell Total RNA by polyA selection and conversion to strand-specific libraries using the Illumina TruSeq kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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 to a set of 36,035 S. mediterranea transcripts assembled from various sources including a previous transcriptome used in microarrays studies (Adler et al.,2014), trinity assemblies from lab generated data involving whole animals, embryos, and sorted X1 cells, a transcriptome from the Bartscherer lab (Boser et al., 2013), and the Dresden transcriptome assembly from PlanMine (http://planmine.mpi-cbg.de), reduced as a collection to unique representations of loci via CD-HIT (Fu et al., 2012).
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.
smed_20140614.fa contains the sequences of the 36,035 alignment targets described above. Each sequence defline contains a unique identifier for the sequence, the originating transcriptome identifier, and the source of the sequence.
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| Submission date |
Aug 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris W Seidel |
| E-mail(s) |
seidel@phageT4.org
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| Phone |
816 926 9054
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| Organization name |
Stowers Institute
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| Department |
Genomics
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| Lab |
Seidel
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| Street address |
1000 E 50th St
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| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platform ID |
GPL20150 |
| Series (1) |
| GSE72389 |
RNA Seq analysis of Schmidtea mediterranea treated with RNAi against chd4, p53, or unc22 to identify factors involved in neoblast differentiation. |
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| Relations |
| BioSample |
SAMN04012451 |
| SRA |
SRX1164636 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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