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Sample GSM518445 Query DataSets for GSM518445
Status Public on Mar 24, 2010
Title Col-dcl2,3,4/Col-dcl2,3,4 rep2
Sample type SRA
 
Source name root total RNA
Organism Arabidopsis thaliana
Characteristics ecotype: Col-dcl2,3,4
sample time: five weeks after grafting
Growth protocol standard growth conditions (10hr light, 20 C)
Extracted molecule total RNA
Extraction protocol Total nucleic acid (TNA) extracts were prepared from pooled shoot and root samples derived from 3-4 individual grafts according to White and Kaper, 1989. To clone small RNAs, sRNAfractions were enriched from 12.5-25 µg of TNA using MirVana columns (Ambion) according to the manufacturer’s instruction. SRNAs were cloned by the Illumina sRNAcloning kit.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
 
Description Grafted plants are described using “shoot/root” notation
Data processing Small RNA adapters were removed using an exact match to the sequence of the appropriate adapter. Reads were aligned to the Arabidopsis thaliana genome (TAIR v8) using SSAHA v3.1.
 
Submission date Mar 05, 2010
Last update date May 15, 2019
Contact name Krys Kelly
Organization name University of Cambridge
Department Plant Sciences
Lab Baulcombe Group
Street address Downing Street
City Cambridge
ZIP/Postal code CB2 3EA
Country United Kingdom
 
Platform ID GPL9302
Series (1)
GSE20663 small RNAs sequences from grafted Arabidopsis thaliana and Nicotiana benthamiana tissues
Relations
SRA SRX017568
BioSample SAMN00009778

Data table header descriptions
SEQUENCE
COUNT Raw counts for genome matching reads

Data table
SEQUENCE COUNT
AAAAAAAAAAAAAAA 84
AAAAAAAAAAAAAAAA 49
AAAAAAAAAAAAAAAAA 37
AAAAAAAAAAAAAAAAAA 13
AAAAAAAAAAAAAAAAAAA 7
AAAAAAAAAAAAAAAAAAAA 7
AAAAAAAAAAAAAAAAAAAAA 8
AAAAAAAAAAAAAAAAAAAAAA 4
AAAAAAAAAAAAAAAAAAAAAAA 2
AAAAAAAAAAAAAAAAAAAAAAAA 2
AAAAAAAAAAAAAAAAAAAAAAAAA 2
AAAAAAAAAAAAAAAAAAAAAAAAAA 3
AAAAAAAAAAAAAAAAAAAAAAAAAAA 1
AAAAAAAAAAAAAAAAAAAAAAAAAAT 1
AAAAAAAAAAAAAAAATCAAA 1
AAAAAAAAAAAAAAACACA 1
AAAAAAAAAAAAAAAT 1
AAAAAAAAAAAAACAAAA 2
AAAAAAAAAAAAAGA 1
AAAAAAAAAAAACAAAAA 1

Total number of rows: 280465

Table truncated, full table size 7057 Kbytes.




Supplementary data files not provided
SRA Run SelectorHelp
Processed data included within Sample table
Raw data are available in SRA

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