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Sample GSM449829 Query DataSets for GSM449829
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

Supplementary file Size Download File type/resource
GSM449829_AGDGa1SP-1.hits.txt.gz 5.2 Mb (ftp)(http) TXT
GSM449829_AGDGa1SP-2.hits.txt.gz 5.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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