 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 15, 2023 |
| Title |
E2_4, egr-2_RNAi, 2_dpa, biol_rep_4 |
| Sample type |
SRA |
| |
|
| Source name |
anterior third of tail fragments
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
strain/biotype: clonal line CIW4
tissue: anterior third of tail fragments
genotype: egr-2_RNAi
treatment: 2 days post-amputation
|
| 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.
|
| 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.
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
E2_4
|
| 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.
|
| |
|
| Submission date |
Mar 11, 2023 |
| Last update date |
Mar 15, 2023 |
| Contact name |
David J Forsthoefel |
| E-mail(s) |
david-forsthoefel@omrf.org
|
| Phone |
405-271-4047
|
| Organization name |
Oklahoma Medical Research Foundation
|
| Department |
Genes and Human Disease Research Program
|
| Lab |
S-314
|
| Street address |
825 NE 13th St
|
| City |
Oklahoma |
| State/province |
OK |
| ZIP/Postal code |
73104 |
| Country |
USA |
| |
|
| Platform ID |
GPL30113 |
| Series (1) |
| GSE227155 |
Identification of dysregulated transcripts in egr-2(RNAi) planarians |
|
| Relations |
| BioSample |
SAMN33725830 |
| SRA |
SRX19639404 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
