|
| Status |
Public on Oct 24, 2011 |
| Title |
Chlamydomonas reinhardtii 2137 - TAP supplemented with a revised trace element recipe - 1 |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas cultured cells
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: 2137
medium: TAP
sequencing cycles / read length: 35
library type: single-end
|
| Treatment protocol |
Cells grown on TAP agar plates supplemented with Hutner's trace elements were grown to mid to late log phase (10e6-10e7 cells/ml) in TAP supplemented with a revised trace element recipe and diluted 1/100 into fresh medium.
|
| Growth protocol |
Cells were cultured under continuous light of ~50-90 μmol photon m-2s-1 at 23ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium supplemented with a revised trace element recipe.
|
| 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 |
| |
|
| Description |
Illumina's RNA-Seq whole transcriptome analysis
poly-A purification, random fragmentation
|
| Data processing |
Processed sequence files from the Solexa pipeline output were aligned against the v.3.1 assembly of the Chlamydomonas genome. The SOAP alignment program (Li et al., 2008) was used to map the short reads in two steps. In a first alignment round, the raw sequences were aligned to the genomic sequence with a tolerance of up to two mismatches and no indels. For those sequences that did not align to the genome a second round alignment was performed in which we recursively trim one base at a time (up to 21-mers or half of the read length) at either the 5’ or 3’ end of the reads until we found a (perfect) match to the genome.
Alignments from both rounds were tagged as either unique or not unique and combined. The most 5’ position of each alignment is recorded along with the length of the alignment. For differential expression analysis, per-base unique hits from both strands were pooled and summed across the genome to obtain gene counts.
|
| |
|
| Submission date |
Nov 26, 2010 |
| 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 |
GPL9152 |
| Series (1) |
| GSE25622 |
A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii |
|
| Relations |
| SRA |
SRX032428 |
| BioSample |
SAMN00139261 |
