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| Status |
Public on May 24, 2022 |
| Title |
1F_ctrl_rep3 |
| Sample type |
SRA |
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| Source name |
Whole animal
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| Organism |
Schmidtea mediterranea |
| Characteristics |
strain: clonal line CIW4
tissue: live uninjured whole planarians
developmental stage: starved 7 days
RNAi: egfp(RNAi) (control)
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| Treatment protocol |
Planarians were fed once with 1 µg dsRNA mixed with 1 µl blue food coloring, 8 µl water, and 40 µl 2:1 liver:water homogenate, then starved seven days prior to RNA extraction.
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| Growth protocol |
Asexual Schmidtea mediterranea (clonal line CIW4) were maintained in 0.5 g/L Instant Ocean salts with 0.0167 g/L sodium bicarbonate dissolved in Type I water, and fed with beef liver paste. For all experiments, planarians were starved seven days prior to fixation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 6-10 uninjured planarians per biological replicate using Trizol as described (Forsthoefel et al., eLife, 2020).
mRNA was enriched from 1 µg total RNA/sample using oligo-dT homopolymer beads, and libraries were generated using the Illumina Truseq Stranded mRNA Library Prep Kit according to the manufacturer's protocol. Final libraries were assayed on the Agilent TapeStation for appropriate size and quantity. Libraries were pooled in equimolar amounts as ascertained by fluorometric analysis, then final pools were absolutely quantified using qPCR on a Roche LightCycler 480 with Kapa Biosystems Illumina Library Quantification Reagents.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Read quality was assessed with FastQC (v0.11.5) before and after trimming with BBDuk (v36.99) for paired end reads: k=13 ktrim=r mink=11 qtrim=rl trimq=10 minlength=35 tbo tpe.
Reads were mapped to the dd_Smed_v6 transcriptome restricted to 28,069 unique transcripts as in (Forsthoefel et al., eLife, 2020) using Bowtie2 (v2.3.1) for paired end reads, with "-a" multi-mapping and "--local" soft-clipping allowed.
Read summarization was conducted with the "featureCounts" utility in the Subread package (v1.6.3) (Liao et al., Nuc. Acids Res., 2019), using a custom ".SAF" file and options "-p -M -O -F SAF" to include multi-mapping and multi-overlapping reads.
Genome_build: Dresden S. mediterranea transcriptome dd_Smed_v6 (http://planmine.mpi-cbg.de/) (Brandl et al., Nuc. Acids Res., 2016)
Supplementary_files_format_and_content: Processed data are in a tab-delimited .txt file, wich includes geneID, transcript length, log2 Fold Changes, logCPM,and FDR-adjusted P value.
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| Submission date |
May 11, 2021 |
| Last update date |
May 24, 2022 |
| Contact name |
David J Forsthoefel |
| E-mail(s) |
david-forsthoefel@omrf.org
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| Phone |
405-271-4047
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| Organization name |
Oklahoma Medical Research Foundation
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| Department |
Genes and Human Disease Research Program
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| Lab |
S-314
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| Street address |
825 NE 13th St
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| City |
Oklahoma |
| State/province |
OK |
| ZIP/Postal code |
73104 |
| Country |
USA |
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| Platform ID |
GPL29967 |
| Series (2) |
| GSE174228 |
Identification of dysregulated transcripts in nkx2.2(RNAi) planarians. |
| GSE174246 |
Identification of dysregulated transcripts in planarians |
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| Relations |
| BioSample |
SAMN19106976 |
| SRA |
SRX10841932 |
| 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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