|
| Status |
Public on Jan 04, 2020 |
| Title |
Replicate1_T8 |
| Sample type |
SRA |
| |
|
| Source name |
Capsaspora adherent cells_7h15 after release
|
| Organism |
Capsaspora owczarzaki |
| Characteristics |
cell type: Filopodial
strain: ATCC 30864
treatment: Released from cell cycle overnight arrest using Hydroxyurea 10mM
time point: 7h15 after release
|
| Treatment protocol |
Cultures at 30-50% confluency were treated with Hydroxyurea to a final concentration of 10mM, and left incubating for 14 hours overnight. Cells were released from Hydroxyurea by washing prior to elution in fresh medium; samples were collected by scraping and washing two hours after release, and from there on every 45 minutes until thirteen hours.
|
| Growth protocol |
Cells were incubated at 23 degrees Celsius in ATCC medium 1034 (modified PYNFH medium).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Time point samples were washed in 1xPBS, poured in Trizol, and frozen at -80oC. Total RNA was purified using Zymo RNA miniprep kit (Zymo Research, Irvine, CA, USA, #R2050).
mRNA libraries were prepared using the TruSeq Stranded mRNA Sample Prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
t8_23779_GATCAG_L007
processed data file: R1_table_tpms.txt
|
| Data processing |
Transcriptome mapping for every independent time point using kallisto v0.43.1 with standard parameters (-q read1 read2) onto a set of the largest isoforms of the Capsaspora transcriptome.
Genome_build: Capsaspora genome v3 (Iñaki Ruiz-Trillo lab)
https://figshare.com/articles/Genome_-_Capsaspora_owczarzaki_v3_/4123158/2
Supplementary_files_format_and_content: Resulting transcript-per-million lists from kallisto of every sample bound together in columns of a single matrix using bash and awk
|
| |
|
| Submission date |
Nov 28, 2019 |
| Last update date |
Jan 04, 2020 |
| Contact name |
Alberto Perez-Posada |
| E-mail(s) |
alberto.perez@upf.edu
|
| Organization name |
Institut de Biologia Evolutiva
|
| Lab |
Multicellgenome Lab
|
| Street address |
Passeig Marítim de la Barceloneta, 37-49
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL27855 |
| Series (1) |
| GSE141156 |
Gradual evolution of cell cycle regulation by cyclin-dependant kinases during the transition to animal multicellularity |
|
| Relations |
| BioSample |
SAMN13423100 |
| SRA |
SRX7237413 |
