|
| Status |
Public on Jul 08, 2010 |
| Title |
Chlamydomonas-ars11-Sulfur-Replete |
| Sample type |
SRA |
| |
|
| Source name |
Chlamydomonas cultured cells
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: ars11
medium: TAP
|
| Treatment protocol |
To impose S deprivation, cells in mid-logarithmic growth phase were washed twice with liquid TAP medium without S (TAP-S), and equal numbers of cells were resuspended in TAP or TAP-S.
|
| Growth protocol |
Cells were cultured under continuous light of ~60 μmol photon m-2s-1 at 23ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell aliquots were collected for RNA isolation just prior to and 1, 6 and 24 h after being transferred to TAP and TAP-S medium. Total RNA from cells after 0 and 6 h of being transferred to -S medium were submitted to Illumina for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Illumina's RNA-Seq whole transcriptome analysis
|
| 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 35-mers 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) 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.
Reference sequence: Chlamydomonas V3.1 unmasked assembly (JGI's Chlre3_1.fasta.gz, md5: c14cb6c004b90983e3a82404b1902173) with a total of 1266 scaffolds. Global genomic coordinates in the accompanying processed files refer to the first base of scaffold_1 when the reference sequence is sorted as in Chlre3_1.fasta.gz.
Processed files: k-hits files. Format (tab delimited). Headers: Global genomic position - length of the alignment - number of unique hits
|
| |
|
| Submission date |
Sep 04, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Arthur Grossman |
| E-mail(s) |
arthurg@stanford.edu
|
| Phone |
650-325-1521
|
| Fax |
650-325-685
|
| URL |
http://carnegiedpb.stanford.edu/grossman-lab
|
| Organization name |
Carnegie Institute for Science
|
| Department |
Plant Biology
|
| Street address |
260 Panama Street
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL9152 |
| Series (1) |
| GSE17970 |
RNA-seq analysis of the transcriptome from Sulfur Deprivation Chlamydomonas cells |
|
| Relations |
| SRA |
SRX019020 |
| BioSample |
SAMN00011124 |
