|
| Status |
Public on Feb 20, 2014 |
| Title |
C.reinhardtii _Fe_Long_2_hours |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas cultured cells
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: CC-4532 (2137)
treatment: iron deprivation
cultured in: TAP medium without Fe-EDTA for 2h
|
| Treatment protocol |
Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times.
|
| Growth protocol |
Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium.
|
| 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 at Illumina HiSeq 2000 platform (UCLA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SMEU37Fe2hTS
|
| 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 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.
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 files correpond to expression estimates per lane, in units of RPKMs.
|
| |
|
| Submission date |
Feb 25, 2013 |
| Last update date |
Apr 04, 2024 |
| 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) |
| GSE44611 |
Changes in membrane lipid composition during Iron depletion and starvation in Chlamydomonas reinhardtii |
|
| Relations |
| Reanalyzed by |
GSE263199 |
| SRA |
SRX245327 |
| BioSample |
SAMN01924675 |
