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Sample GSM387515 Query DataSets for GSM387515
Status Public on Jul 31, 2009
Title Endogenous small RNAs from Arabidopsis arenoa, wild type, leaf (AaL)
Sample type SRA
 
Source name leaf, A. arenosa
Organism Arabidopsis arenosa
Characteristics genotype/variation: progenitor species
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 progenitor species
5' adaptor sequence:
ATCGTAGGCACCTGAAA
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 GPL9414
Series (1)
GSE15443 Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids
Relations
BioSample SAMN02198673

Data table header descriptions
SEQUENCE
COUNT number of reads sequenced

Data table
SEQUENCE COUNT
TACGAGCGAATGGGCCATTGAA 1
TTGGCTCAGGCCTGTGCTGCCT 5
CGTCGTGGCTGGGACTGCTGT 1
CGAGGTCCTAAATAAAAACGAA 1
TAGGAATAAACAATTGACAGTGCA 26
CTGTATTGTCACCGGAGTGTCTA 1
TGACTGTAGCTGTAGATTACAAGT 1
CATAAAGAAGGACTGCCACAA 19
ACGCCTCATTAGAAGCCTTTGAAC 1
TGTGTTGAGTGATGTTTGAAGCCT 1
TAGGAAACGTTATACGCGGCTGG 2
CCTGTGGTGAAGACAATCAA 1
TATGTTTGGTGGTAGTCTGCC 1
ACATATCAAGAGGTTGTCCGTA 1
TACACGAGCAAGTGGCTTTAC 1
CAACAGGGTGTCTCATACAATA 1
CGCACGGATTTGTTATTGGGC 1
TGCGCTTGTCTGTGGTATTTGGTC 1
GGACACATAAAGAAGGACTGC 2
ATAAATCCTGGAGTTGGATGTATT 1

Total number of rows: 42545

Table truncated, full table size 1072 Kbytes.




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

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