|
| Status |
Public on Jan 23, 2018 |
| Title |
261O |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
strain: asexual BCN-10 clonal line
tissue: whole animal
treatment: gfp(RNAi) 4 weeks
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with TRIzol® (Invitrogen) following the manufacturer's instructions. Quantification of RNA was assessed with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific) and quality check was performed by capillary electrophoresis in an Agilent 2100 Bioanalyzer (Agilent Technologies)prior to library preparation.
cDNA libraries were prepared using the Illumina® TruSeq Stranded mRNA Library Prep Kit and sequenced as paired-end reads in an Illlumina® HiSeq 2000 sequencer. Quality check of the reads was performed with the FastQC suite.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Transcript abundances were calculated with kallisto v0.43.0.
Genome_build: S. mediterranea dd_Smed_v6 transcriptome assembly
Supplementary_files_format_and_content: Tab-separated values file containing TPM expression values.
|
| |
|
| Submission date |
Feb 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gustavo Rodriguez-Esteban |
| E-mail(s) |
gustavo.rodriguez@cnag.crg.eu
|
| Organization name |
Centro Nacional de Análisis Genómico
|
| Department |
Development
|
| Lab |
Single Cell Genomics
|
| Street address |
C. Baldiri Reixac, 4; Barcelona Science Park
|
| City |
Barcelona |
| State/province |
Catalonia |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL15553 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN06350912 |
| SRA |
SRX2579213 |
