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| Status |
Public on Aug 21, 2008 |
| Title |
Illumina G1 |
| Sample type |
SRA |
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| Source name |
developing grains
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| Organism |
Oryza sativa |
| Characteristics |
source: 1-5 days after fertilization grains, cv Nipponbare
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| Treatment protocol |
No treatment was applied to the biological material before sample collection
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| Growth protocol |
Rice plants that were used for sample collection were grown in a controlled glasshouse at 25±3oC with 16 hours of lights
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from approximately 1.5g of shoots and roots of 7 day-old seedlings, and 1-5 and 6-10 DAF de-husked rice grains. Tissues were ground into fine power in the presence of liquid nitrogen and processed using RNA extraction buffer (0.1M NaCl, 2% SDS, 50mM Tris/HCl, 10mM EDTA and 20mM beta-mercaptoethanol) and an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1). The aqueous fraction was subsequently extracted two times using an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1) and chloroform. Total RNA was then precipitated using LiCl (2M final concentration) overnight at -20oC. Low molecular weight (LMW) RNA was precipitated from the supernatant with an equal volume of isoproponol in the presence of 0.1% SDS at -20oC for 2 days. The precipitated LMW RNA was resuspended in DEPC-treated H2O. Approximately 150µg of LMW RNA was then mixed with a trace amount of 5'- 32P-labeled RNA markers (18 and 25nt) and size fractionated on a 15% polyacrylamide and 8M urea gel. The gel fragment spanning the 18-25nt RNA markers was excised. The excised gel was crushed into fine pieces and RNA eluted overnight in 0.3M NaCl at 4oC with gentle shaking.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Total RNA was provided to the Illumina Inc.
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| Data processing |
Custom Perl scripts were used for trimming, sorting, collating and other transformations of the data. Sequences less than 18bp in length were removed. Sequences were compared to known Oryza Sativa micro RNAs from miRBase 9.0. BLAST was used to match the small RNAs to the Oryza Sativa genome (TIGR Rice Annotation Release 5.0), using a word size of 7, e-value cut-off of 1000 and no query sequence filtering. Coordinates of perfect matches, or those with a single mismatch if no perfect matches, were retained. Annotation was added to all recorded genome matches, but here only annotation for those with a single hit to the genome are shown. Read numbers were scaled to tags per million from the total number of reads for each sample (46879, 55391, 21697, 11866, 3428861, 3412945 total reads for Samples GSM278532-GSM278535, GSM278571-GSM278572, respectively).
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| Submission date |
Apr 01, 2008 |
| Last update date |
Jul 14, 2013 |
| Contact name |
Andrew Spriggs |
| E-mail(s) |
andrew.spriggs@csiro.au
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| Phone |
612-6246-5193
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| Organization name |
CSIRO Plant Industry
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| Department |
Bioinformatics Group
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| Street address |
GPO Box 1600
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| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
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| Platform ID |
GPL9147 |
| Series (1) |
| GSE11014 |
A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains |
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| Relations |
| BioSample |
SAMN02250932 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM278571.txt.gz |
131.0 Mb |
(ftp)(http) |
TXT |
| GSM278571_tpm.txt.gz |
21.8 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Raw data provided as supplementary file |
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