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Sample GSM387520 Query DataSets for GSM387520
Status Public on Jul 31, 2009
Title Endogenous small RNAs from synthetic allopolyploid, F7 generation, wild type, flower (F7F)
Sample type SRA
 
Source name flower, F7
Organisms Arabidopsis thaliana; Arabidopsis arenosa
Characteristics genotype/variation: synthetic allopolyploid F7
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from leaves and flower buds using TRIZOL (Invitrogen) according to manufacturer’s instructions.
Small RNAs of 15-100-nt in size were purified in a 15% polyacrylamide gel and ligated to the 5’ and 3’ RNA adaptors, respectively. The resulting RNA bands ranged from 55- to 140-nt. The ligated RNAs from each sample were reverse-transcriptase transcribed, and the first-stranded cDNAs were amplified using the primer pair that contains 2 specific nucleotides (out of 4) as a “barcode”. A. arenosa and F1 leaf libraries were sequenced separately, and the remaining eight libraries were combined in two pools, and an aliquot of pooled DNA was cloned and sequenced to determine the quality and representation of inserts. After the quality control was done, the pooled DNA was subjected to high-through pyrosequencing, producing a total of ~1.5-million reads in eight runs.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model 454 GS
 
Description F7 generation of synthetic allopolyploid derived from A. thaliana and A. arenosa
5'adoptor sequence: GCCTCCCTCGCGCCATCAGgctgATCGTAGGCACCTGAAA
raw data file(s): EJSVVZQ01.sff, EJSVVZQ02.sff, EJSVYDC01.sff, EJSVYDC02.sff
Data processing The raw sequences were processed by identifying the barcodes, base call quality, and removing adaptor sequences. Each of the 10 libraries had a unique 4-nucleotide tag within the 5’-end adaptor sequences. After trimming adaptor sequences at both 5’ and 3’ ends, pyrosequenced cDNAs were aligned to full genomic sequences of A. thaliana. Sequences matching other cellular RNAs including pre-tRNAs, rRNAs, snoRNAs, and snRNAs were regarded as degradation products of other cellular RNAs and excluded for analysis. Also excluded were sequences matching genome sequences of mitochondria and chloroplasts. Remaining sequences 20-25-nt in length.
 
Submission date Mar 29, 2009
Last update date May 27, 2014
Contact name Misook Ha
E-mail(s) misook.ha@gmail.com
Phone 7732795900
Organization name National Heart Lung Blood Institute
Lab Laboratory of Epigenome Biology
Street address NIH
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL18731
Series (1)
GSE15443 Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids
Relations
BioSample SAMN02198678

Data table header descriptions
SEQUENCE
COUNT number of reads sequenced

Data table
SEQUENCE COUNT
AGTAGTAGAACGGCGACTATCAGA 1
ACAATTGGTCTCTGTGTCAATAG 1
GCACTTGAGCATACCACTCCATAC 1
GGGTGAACGACCTGTGTGTCCAT 2
TCGGAGTCTTTGGACGTGTTCA 1
TACAACTGGTACGATTAGGTACA 1
ACTTGATGAAGGGTTTGGATCCCA 1
CGGGCCCCACGGTGGGCGTCA 1
ACACCGCAGACAGGTTATCACAA 1
CGGTGATGTGAAAAACTCAAGTGA 1
AGCCCACTTAGCATCCATACCACA 1
CATGGGCCACGGTTATGGAG 1
TAGGAATAAACAATTGACAGTGCA 2
CGTATCCGGTAGGGCCCTCCA 1
TCAAGCCTGTTGTAAATCTCTCA 1
TTGGCAATTTGGTTGTGTTAT 3
CACTGAGATTCAGCCCTTTGT 1
GAGACACGCCAGTTCCTATTATGG 1
TGGCCCAGCCCACTTTGCCTCA 3
ACTAATTGCTCGTGCGGCTTGAC 1

Total number of rows: 49303

Table truncated, full table size 1256 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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