|
| Status |
Public on Oct 14, 2015 |
| Title |
Amoeboid_2 |
| Sample type |
SRA |
| |
|
| Source name |
Amoeboid cells
|
| Organism |
Creolimax fragrantissima |
| Characteristics |
cell stage: Amoeba stage
time after filtering for 5um: 0 hr
|
| Growth protocol |
Marine Broth liquid medium, 12ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A culture grown for 3 days was filtered with a 5 um mesh, isolating amoeboid cells. mRNA from Amoebas was extracted immediately. Multinucleate stage was obtained after culturing amoebas for 24 hr. RNA was harvested using Trizol reagent. TruSeq Stranded mRNA Sample Prep kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to Creolimax genome using Tophat 2. tophat2 -i 30 -g 1 --library-type=fr-firststrand -r 5 -G
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a Cufflinks2. cuffdiff --max-bundle-frags 10000000 --library-type=fr-firststrand -N -u -b
Genome_build: Creolimax1
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all Samples. A FASTA file with the assembled sequences is available on the series record.
|
| |
|
| Submission date |
May 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Alex de Mendoza |
| E-mail(s) |
alexmendozasoler@gmail.com
|
| Organization name |
Queen Mary University of London
|
| Department |
School of Biological and Behavioural Sciences
|
| Lab |
de Mendoza Lab
|
| Street address |
Mile End Road. Fogg Building 5.14
|
| City |
London |
| ZIP/Postal code |
E1 4NS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20162 |
| Series (1) |
| GSE68616 |
Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals |
|
| Relations |
| BioSample |
SAMN03610052 |
| SRA |
SRX1019900 |
