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| Status |
Public on Mar 15, 2023 |
| Title |
E0_2, egr-2_RNAi, 0_hr, biol_rep_2 |
| Sample type |
SRA |
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| Source name |
anterior third of tail fragments
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| Organism |
Schmidtea mediterranea |
| Characteristics |
strain/biotype: clonal line CIW4
tissue: anterior third of tail fragments
genotype: egr-2_RNAi
treatment: 0 hours post-amputation
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| Treatment protocol |
Planarians were fed twice per week (6 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 amputation.
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| Growth protocol |
Asexual Schmidtea mediterranea (clonal line CIW4) were maintained in Montjuic water and fed with beef liver paste. Planarians were starved 5-7 days prior to initiation of RNAi experiments.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the anterior third of 10 planarian tail fragments per biological replicate using Trizol as described (Forsthoefel et al., eLife, 2020).
Total RNA for 4 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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| Description |
E0_2
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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.
Assembly: 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 |
Mar 11, 2023 |
| Last update date |
Mar 15, 2023 |
| 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 (1) |
| GSE227155 |
Identification of dysregulated transcripts in egr-2(RNAi) planarians |
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| Relations |
| BioSample |
SAMN33725840 |
| SRA |
SRX19639394 |
| 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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