NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM600877 Query DataSets for GSM600877
Status Public on Sep 25, 2010
Title Chlamy_T_RNA_seq_2
Sample type SRA
 
Source name Chlamydomonas culture, N-replete
Organism Chlamydomonas reinhardtii
Characteristics strain: dw15.1
genotype: cw15, nit2, mt+
condition: N-repletion
Treatment protocol For N-replete growth, TAP medium (Harris, 2009a) with 10 mM NH4+ (TAP+N) was used. N-deprivation was defined as growth in TAP+N to 5x10^6 cells/mL, followed by transfer to TAP-N for 48 hours.
Growth protocol The cells were grown in liquid cultures under continuous light (~80 µmole photons m-2 s-1).
Extracted molecule total RNA
Extraction protocol To generate material for high-throughput sequencing, cells were grown in 100 TAP+N to 5x10^6 cells/mL. The cultures were split in half and cells were collected by centrifugation, with one pellet being resuspended in 50 mL TAP+N, and the other in 50 mL TAP-N. After 48 hours, the total RNA was harvested using a QIAGEN RNeasy Plant Mini kit (QIAGEN, Valencia, CA, USA). The RNA samples were treated with QIAGEN RNase-free DNase I during extraction. Total RNA was submitted directly to the MSU-RTSF for sequencing on an Illumina Genome Analyzer II (Illumina, Inc., San Diego, CA, USA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description RNA-seq under N-replete conditions.
Data processing Default parameters were used to pass reads using Illumina quality control tools. The Illumina reads were mapped with Bowtie (Langmead et al., 2009) to the C. reinhardtii v4.0 assembly from the Joint Genome Institute with GMAP (Wu and Watanabe, 2005) using parameters as follow: ≤ 2 mismatches, sum of Phred quality values at all mismatched positions ≤ 70, and excluding reads mapped to > 1 locations.
 
Submission date Sep 24, 2010
Last update date May 15, 2019
Contact name Guangxi Wu
E-mail(s) wuguangx@msu.edu
Organization name Michigan State University
Street address S308 Plant Bio Bld
City East Lansing
State/province MI
ZIP/Postal code 48824
Country USA
 
Platform ID GPL9100
Series (2)
GSE24365 Global Changes following N-deprivation in Chlamydomonas: Illumina sequencing
GSE24367 Global Changes following N-deprivation in Chlamydomonas
Relations
SRA SRX027242
BioSample SAMN00113622

Supplementary file Size Download File type/resource
GSM600877_435NLAAXX_2_T2_pf.fastq.hitsm.txt.gz 982.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap