|
Status |
Public on Nov 22, 2017 |
Title |
12F_ctrol-h-5 |
Sample type |
SRA |
|
|
Source name |
whole planarian tissue
|
Organism |
Schmidtea mediterranea |
Characteristics |
strain: CIW4 tissue: individual intact planarian RNAi: unc-22 RNAi feedings: 12F
|
Treatment protocol |
Animals fed in-vitro transcribed dsRNA in liver 10 times in 7 weeks (2x per week for 6 feedings, 1x per week for 4 feedings) or 12 times in 9 weeks (2x per week for 6 feedings, 1x per week for 6 feedings)
|
Growth protocol |
Standard planarian culture conditions
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA extracted from wounds in tail fragments with TriZOL reagent with 5 wounds per replicate. Extracted RNA was quantified by NanoDrop and Agilent Bioanalyzer Kapa Stranded mRNA-Seq Kit Illumina Platform (KapaBiosystems)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
12F_ctrol_nkx_10F_ctrol_myoD_readcounts.txt res_12F_ctrol_v_nkx1-1.txt
|
Data processing |
Basecalling was performed by Illumina CASAVA Sequenced reads were quality trimmed using cutadapt v1.8 with parameteres -m 20 -q 30,30 and mapped to the ddv4 transcriptome using Bowtie v1.1.1 with parameter --best Raw read counts were generated with Samtools idxstats and transcripts from different isoforms were summed (sum of counts for dd_v4_Smed_XXX_Y_Z for all Z) Differential expression was determined with DESeq Genome_build: Dresden S. mediterranea Transcriptome Assembly (ddv4, Lui et al, Nature 2013) https://idisk.mpi-cbg.de/~brandl/planaria/dd_Smed_v4.nuc.fasta.zip Supplementary_files_format_and_content: Tab-separated text files
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|
|
Submission date |
May 17, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Peter W Reddien |
Organization name |
Whitehead Institute for Biomedical Research
|
Street address |
9 Cambridge Center
|
City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02142 |
Country |
USA |
|
|
Platform ID |
GPL15553 |
Series (2) |
GSE99025 |
Gene expression profiling of intact individual planarians during homeostatic tissue turnover after inhibition of myoD or nkx1-1 |
GSE99067 |
Orthogonal muscle fibres have different instructive roles in planarian regeneration |
|
Relations |
BioSample |
SAMN07138344 |
SRA |
SRX2831822 |