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| Status |
Public on Sep 25, 2010 |
| Title |
Chlamy_N_RNA_seq_3 |
| Sample type |
SRA |
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| Source name |
Chlamydomonas culture, N-deprived
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| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
strain: dw15.1
genotype: cw15, nit2, mt+
condition: N-deprivation
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| 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.
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| Growth protocol |
The cells were grown in liquid cultures under continuous light (~80 µmole photons m-2 s-1).
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
RNA-seq under N-deprived conditions.
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| 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.
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| Submission date |
Sep 24, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Guangxi Wu |
| E-mail(s) |
wuguangx@msu.edu
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| Organization name |
Michigan State University
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| Street address |
S308 Plant Bio Bld
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| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
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| Platform ID |
GPL9100 |
| Series (2) |
| GSE24365 |
Global Changes following N-deprivation in Chlamydomonas: Illumina sequencing |
| GSE24367 |
Global Changes following N-deprivation in Chlamydomonas |
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| Relations |
| SRA |
SRX027246 |
| BioSample |
SAMN00113626 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM600881_435NLAAXX_7_N3_pf.fastq.hitsm.txt.gz |
772.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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