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Sample GSM278534 Query DataSets for GSM278534
Status Public on Aug 21, 2008
Title 454 Roots
Sample type SRA
 
Source name roots
Organism Oryza sativa
Characteristics source: 7 days old seedlings, cv Nipponbare
Treatment protocol No treatment was applied to the biological material before sample collection
Growth protocol Rice plants that were used for sample collection were grown in a controlled glasshouse at 25±3oC with 16 hours of lights
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model 454 GS
 
Description Small RNAs were ligated to a 3' adaptor that has a blocked 3' terminus by introduction of a O-C3 linker, and a 5' RNA/DNA adaptor, respectively. Small RNAs were then reverse transcribed and further PCR amplified to get amplicons for sequencing.
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).
 
Submission date Apr 01, 2008
Last update date Jul 12, 2013
Contact name Andrew Spriggs
E-mail(s) andrew.spriggs@csiro.au
Phone 612-6246-5193
Organization name CSIRO Plant Industry
Department Bioinformatics Group
Street address GPO Box 1600
City Canberra
State/province ACT
ZIP/Postal code 2601
Country Australia
 
Platform ID GPL9388
Series (1)
GSE11014 A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
Relations
BioSample SAMN00708988

Supplementary file Size Download File type/resource
GSM278534.fna.gz 296.4 Kb (ftp)(http) FNA
GSM278534.qual.gz 716.8 Kb (ftp)(http) QUAL
GSM278534_tpm.txt.gz 784.4 Kb (ftp)(http) TXT
Processed data included within Sample table
Raw data provided as supplementary file

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