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Sample GSM632208 Query DataSets for GSM632208
Status Public on Dec 01, 2011
Title NRG1_grown_at 30C
Sample type SRA
 
Source name NRG1_grown_at 30℃
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
ecotype: transgene Bri1-Xa21 plant
cultivation temperature: 30℃
age: 4-week-old
tissue: seedlings
Treatment protocol Total RNA was isolated from 4-week-old 22ºC or 30ºC-grown plants.
Growth protocol Arabidopsis Col-0 and NRG1 transgenic plants were grow at 22°C or 30°C for 4 weeks.
Extracted molecule total RNA
Extraction protocol Small RNAs were prepared from Arabidopsis seedings, 16-28 nt size fractionation was separated from total RNA and ligated to a 5' and a 3' adaptor sequentially, and then RT-PCR amplified. PCR products were provided for sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer
 
Description Solexa gene sequencing
Data processing The 18-30nt tags from Solexa sequencing will go through the primary analysis first, which includes getting rid of the 5' adaptor, low quality tags and summarise the length distribution of the clean tags.
 
Submission date Dec 01, 2010
Last update date May 15, 2019
Contact name Li Qun
E-mail(s) qli@sibs.ac.cn
Phone +86 21 54924122
Organization name Institute of plant physiology & ecology, SIBS, CAS
Department National Key Laboratory of Plant Molecular Genetics
Street address 300 Fenglin Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL9062
Series (1)
GSE25738 Examination of smallRNA in wildtype and transgenic Arabidopsis grown under different temperature
Relations
SRA SRX032395
BioSample SAMN00139223

Data table header descriptions
SEQUENCE 18-30nt tag
COUNT cleaned tag count

Data table
SEQUENCE COUNT
TGACAGAAGAGAGTGAGCAC 251548
TTGACAGAAGATAGAGAGCAC 182220
TGAAGCTGCCAGCATGATCTA 130864
TCCCAAATGTAGACAAAGCA 97188
TTGACAGAAGAGAGTGAGCAC 80656
TCGGACCAGGCTTCATTCCCC 74490
GGGGATGTAGCTCAGATGGTA 68970
GGGGATGTAGCTCAGATGGT 63706
TAAAACGACTCTCGGCAACGG 56804
GCGTCTGTAGTCCAACGGTTA 41570
GCGTCTGTAGTCCAACGGT 35459
TATTCTGGTGTCCTAGGCGTA 35350
GGGGATGTAGCTCAGATGG 34430
GGGGATGTAGCTCAGATGGTAG 32962
AACGACTCTCGGCAACGGATAT 32068
CACGTCTGCCTGGGTGTCACA 31304
GCGTCTGTAGTCCAACGGTT 30729
AACGACTCTCGGCAACGGATATC 30550
GGGGATGTAGCTCAGATGGTAGA 30295
TCGCTTGGTGCAGGTCGGGAA 29906

Total number of rows: 1867032

Table truncated, full table size 47282 Kbytes.




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

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