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| Status |
Public on Sep 25, 2010 |
| Title |
Chlamy_N_454 |
| 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. Full-length cDNA pools were generated with the Clontech SMART cDNA library construction kit (Clontech, Mountain View, CA, USA). cDNA was synthesized using a modified cDNA synthesis primer (5’TAGAGACCGAGGCGGCCGACATGTTTTGTTTTTTTTTCTTTTTTTTTTVN3’). Full-length cDNAs were amplified by PCR and pooled to increase their concentration. An SfiI digest was performed, followed by size fractionation. Fractions with the highest intensity and size distribution were pooled and purified. The resulting cDNA pools were then submitted to the MSU-Research Technologies Service Facility (RTSF) for sequencing on a 454 GSFLX Titanium Sequencer (454 Life Sciences, Branford, CT, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX |
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| Description |
ESTs under N-deprived conditions.
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| Data processing |
For 454 data, default parameters were used to pass reads using 454 quality control tools. The filtered 454 sequencing reads were mapped to the C. reinhardtii v4.0 assembly from the Joint Genome Institute with GMAP (Wu and Watanabe, 2005). In GMAP, the maximum intron length was set at 980bp, which is at the 95 percentile of annotated C. reinhardtii intron lengths.
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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 |
GPL10980 |
| Series (2) |
| GSE24366 |
Global Changes following N-deprivation in Chlamydomonas: 454 sequencing |
| GSE24367 |
Global Changes following N-deprivation in Chlamydomonas |
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| Relations |
| SRA |
SRX027239 |
| BioSample |
SAMN00113620 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM600883_2.gmap_summary.txt.gz |
16.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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