|
| Status |
Public on Sep 04, 2023 |
| Title |
alx-3(RNAi) Intact rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole animal
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
tissue: Whole animal
genotype: Asexual CIW4
treatment: 9 RNAi feeds
time: Intact
|
| Treatment protocol |
In all homeostatic experiments and regeneration experiments, RNAi food was fed to 7-day starved worms every third day for a total of 9 feedings. Amputations were performed 4 days after the 9th feed and animals were allowed to regenerate for the specified amount of time.
|
| Growth protocol |
Asexual populations of Schmidtea mediterranea (strain CIW4) were maintained as previously described (Sánchez Alvarado, Newmark, Robb, & Juste, 2002). Planarians were kept at 18°C in milliQ water supplemented with 0.21g/L Instant Ocean, 0.1 mM KCl, 0.1 mM MgSO4, 0.12 mM NaHCO3. Animals were fed calf liver paste approximately once per week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reaagent and RNA quality was analyzed on a bioanalyzer
Samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapter sequences were removed using trimmomatic (v0.39)
Trimmed sequence reads were then aligned to a previously described planarian transcriptome (NCBI Bio Project PRJNA215411) with the program Salmon (v1.4.0)
R package DESeq2 (v 1.30.1) was used to analyze differences in gene expression between control(RNAi) and alx-3(RNAi) (adj. p <0.05)
Assembly: NCBI BioProject PRJNA215411 SmedASXL_transcripts_20130210.nt
Supplementary files format and content: Excel, normalized_reads.xlsx contains normalized abundance measurments (generated using DESeq2 output). deseq_results.xlsx contains significant diffential expression (analysis performed with DeSeq2)
|
| |
|
| Submission date |
Aug 23, 2023 |
| Last update date |
Sep 04, 2023 |
| Contact name |
Bret J Pearson |
| E-mail(s) |
pearsobr@ohsu.edu
|
| Organization name |
Oregon Health and Science University
|
| Department |
Pediatrics
|
| Lab |
Pearson
|
| Street address |
3181 SW Sam Jackson Park Rd., BRB Room 305
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL29967 |
| Series (1) |
| GSE241516 |
aristaless-like homeobox-3 is wound induced in muscle and stem cells and is required for planarian head regeneration |
|
| Relations |
| BioSample |
SAMN37120895 |
| SRA |
SRX21463501 |
