|
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.
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|
|
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)
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|
|
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 |