|
| Status |
Public on Mar 09, 2014 |
| Title |
Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 2h + acetate |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 2h after acetate boost
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain/background: sta6 (CC-4348)
treatment: 48 h minus nitrogen, then acetate boost
time point: 2h after acetate boost
|
| Treatment protocol |
Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints.
|
| Growth protocol |
Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012.
For quantitative transcriptomes, RNAs were sequenced at LANL.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
UGTWs6nA2HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA
|
| Data processing |
Illumina's proprietary software was used for basecalling.
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length.
Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html)
Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs.
|
| |
|
| Submission date |
Feb 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabeeha Merchant |
| E-mail(s) |
merchant@chem.ucla.edu
|
| Phone |
310-825-8300
|
| Organization name |
University of California Los Angeles
|
| Department |
Department of Chemistry and Biochemistry
|
| Street address |
607 Charles E. Young Drive East
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095-1569 |
| Country |
USA |
| |
|
| Platform ID |
GPL15922 |
| Series (1) |
| GSE55253 |
The Path to Triacylglyceride Obesity in the sta6 Strain of Chlamydomonas reinhardtii |
|
| Relations |
| BioSample |
SAMN02649440 |
| SRA |
SRX474562 |
