|
| 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
|
| |
|
| 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 |
