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Sample GSM600880 Query DataSets for GSM600880
Status Public on Sep 25, 2010
Title Chlamy_N_RNA_seq_2
Sample type SRA
Source name Chlamydomonas culture, N-deprived
Organism Chlamydomonas reinhardtii
Characteristics strain: dw15.1
genotype: cw15, nit2, mt+
condition: N-deprivation
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-deprived 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
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
SRA SRX027245
BioSample SAMN00113625

Supplementary file Size Download File type/resource
GSM600880_435U5AAXX_8_N2_pf.fastq.hitsm.txt.gz 897.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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