|
| Status |
Public on Jan 10, 2013 |
| Title |
Chlamydomonas reinhardtii 2137 - Nitrogen deficiency second long time course - t=2h |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas cultured cells
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
group: 2nd long time course
treatment: Nitrogen deficiency
time: t=2h
strain: 2137
medium: TAP
sequencing cycles / read length: 100
library type: paired-end
mean/std insert size: 191.6/34.7
|
| Treatment protocol |
N-starved cells were grown to approximately 4x10^6 cells/mL, collected by centrifugation (2170 xg, room temperature, 5 min), washed and resuspended in the same medium to 2 x 10^6 cells/mL. For growth in reduced nitrogen, N-free TAP medium supplemented with NH4Cl to 7, 3.5, 1.75, 0.7 or 0.35 mM. Cultures were inoculated to 1x10^5 cells/mL and collected for RNA at 1 x 10^6 cells/mL, when the growth rates of all cultures were identical
|
| Growth protocol |
Chlamydomonas reinhardtii strains CC-3269/ 2137 (wild-type nit2 mt+) were cultured at 24°C (180 rpm, ~90 mmol/m2/s, cool white fluorescent bulbs at 4100K and warm white fluorescent bulbs at 3000K were used in the ratio of 2:1) in TAP medium, -N TAP or TAP suppemented with various amounts of NH4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced by whole transcriptome analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
non-genomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Illumina's RNA-Seq whole transcriptome analysis
|
| Data processing |
RNAs were sequenced at Illumina and Los Alamos National Laboratory on a GAIIx system for estimating transcript abundance in each of the three N-deficiency time course experiments. 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 where 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. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates.
Processed files correpond to the bowtie standard output format.
|
| |
|
| Submission date |
Dec 20, 2011 |
| 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 |
GPL9100 |
| Series (1) |
| GSE34585 |
Three acyltransferases and a nitrogen responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas |
|
| Relations |
| SRA |
SRX113675 |
| BioSample |
SAMN00769251 |
