|
| Status |
Public on Oct 24, 2011 |
| Title |
Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 2 |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas cultured cells
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
genetic background: Chlamydomonas reinhardtii 2137
genotype: wt
treatment: copper deficient
medium: TAP
analysis: Illumina's Digital Gene Expression
sequencing cycles / read length: 17
library type: single-end
|
| Treatment protocol |
Inoculum cultures were maintained under copper-deficient conditions. The minimal medium cultures were under constant aeration. Cells were collected at a density of 3x106 cell ml-1 (steady-state).
|
| Growth protocol |
Cultures were grown in Tris-acetate-phosphate (TAP), or minimal medium (TP) at 24 C with shaking (180 rpm), and under continuous light (~90x10-6mol/m2/s)
|
| Extracted molecule |
polyA 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 either the NlaIII tag protocol or by whole transcriptome analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| 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 03, 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) |
| GSE25124 |
Systems analysis of Chlamydomonas Cu nutrition reveals connections between Cu and multiple O2-dependent metabolic steps |
|
| Relations |
| SRA |
SRX039454 |
| BioSample |
SAMN00199085 |
