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| Status |
Public on May 24, 2022 |
| Title |
3F_apob_severe_rep4 |
| 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
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| Treatment protocol |
Planarians were fed every 3-4 days (three feedings total) with 2 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 5-6 uninjured planarians per biological replicate using Trizol as described (Forsthoefel et al., eLife, 2020).
Total RNA for 4-6 biological replicates per condition was submitted to GENEWIZ (South Plainfield, NJ) for library generation from ~ 500 ng/sample using the NEB NEXT ULTRA Library Prep Kit and RNA sequencing with standard Illumina adapters.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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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 |
GPL30113 |
| Series (2) |
| GSE174227 |
Identification of dysregulated transcripts in apob-1(RNAi);apob-2(RNAi) planarians |
| GSE174246 |
Identification of dysregulated transcripts in planarians |
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| Relations |
| BioSample |
SAMN19106959 |
| SRA |
SRX10841836 |
| 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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