|
| Status |
Public on Jun 18, 2012 |
| Title |
SMEU37Fe20TP2 |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas reinhardtii 2137 - Fe replete (TAP)
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: 2137
medium: TAP
|
| Treatment protocol |
To generate Fe-deficient and Fe-limited cultures, cells in the pretransfer culture are grown under Fe-replete conditions to mid to late log phase (10e6-10e7 cells/ml) and diluted to 10e4 cells/ml into fresh Fe-deficient or Fe-limited medium. Two sequential transfers (from 10e6-10e7 cells/ml into fresh Fe-deficient medium) are performed to ensure that residual iron in the Fe-deficient or Fe-limited cultures is reduced.
|
| Growth protocol |
Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium or minimal media.
|
| 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 by whole transcriptome analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chlamydomonas reinhardtii 2137 - Fe replete - Replicate #2
|
| Data processing |
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 biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe20TP2_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe20TP2_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
|
| |
|
| Submission date |
Jan 24, 2012 |
| 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 |
GPL15083 |
| Series (1) |
| GSE35305 |
Systems and trans-system level analysis identifies conserved Fe-deficiency responses in the plant lineage |
|
| Relations |
| SRA |
SRX117660 |
| BioSample |
SAMN00778924 |
