NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM632209 Query DataSets for GSM632209
Status Public on Dec 01, 2011
Title NRG1_grown_from 30C to 22C
Sample type SRA
 
Source name NRG1_grown_from 30℃ to 22℃
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
ecotype: transgene Bri1-Xa21 plant
cultivation temperature: 30℃ to 22℃
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 SRX032396
BioSample SAMN00139224

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

Data table
SEQUENCE COUNT
TGAAGCTGCCAGCATGATCTA 208195
TCCCAAATGTAGACAAAGCA 162923
TTGACAGAAGATAGAGAGCAC 160626
TGACAGAAGAGAGTGAGCAC 150256
GGGGATGTAGCTCAGATGGTA 133467
AACGACTCTCGGCAACGGATAT 122370
TAAAACGACTCTCGGCAACGG 102367
GGGGATGTAGCTCAGATGGT 77367
GGGGATGTAGCTCAAATGGTA 63726
TCGGACCAGGCTTCATTCCCC 54685
AAAACGACTCTCGGCAACGG 54373
AACGACTCTCGGCAACGG 53651
AACGACTCTCGGCAACGGATATC 43888
AACGACTCTCGGCAACGGATA 42417
TTGACAGAAGAGAGTGAGCAC 41774
GGGGATGTAGCTCAGATGGTAG 40909
GCGTCTGTAGTCCAACGGT 40881
GCGTCTGTAGTCCAACGGTTA 40334
AACGACTCTCGGCAACGGATATCTCGG 40263
GGGGATGTAGCTCAGATGG 39235

Total number of rows: 2073832

Table truncated, full table size 52337 Kbytes.




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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap