|
| Status |
Public on Apr 03, 2012 |
| Title |
Chlamydomonas reinhardtii sor1 mutant |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas cultured cells
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
genotype: sor1 mutant
strain: 4A+
medium: TAP
sequencing cycles / read length: 36
library type: single-end
|
| Treatment protocol |
Cells of cultures grown in 12 h light dark cycles for several days were adjusted to 2×106 cells ml-1 at the beginning of the dark cycle and the cells were collected 6 h after the lights came on from three independent biological replicates.
|
| Growth protocol |
The strains were grown mixotrophically in a Tris-acetate phosphate (TAP) medium at 25°C and 100 μmol photons m-2 s-1 photosynthetically active radiation (PAR) in a 12 h day night cycle.
|
| 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 |
non-genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| 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. Additional normalization was performed to estimate gene expression levels.
|
| |
|
| Submission date |
Nov 08, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Beat B Fischer |
| E-mail(s) |
beat.fischer@eawag.ch
|
| Phone |
+41 44 8235492
|
| Organization name |
Eawag
|
| Department |
Department of Environmental Toxicology
|
| Street address |
Ueberlandstr. 133
|
| City |
Dübendorf |
| ZIP/Postal code |
8600 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9100 |
| Series (1) |
| GSE33548 |
SINGLET OXYGEN RESISTANT 1 links reactive electrophile signaling to singlet oxygen acclimation in Chlamydomonas reinhardtii |
|
| Relations |
| SRA |
SRX105292 |
| BioSample |
SAMN00752518 |
