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Sample GSM252691 Query DataSets for GSM252691
Status Public on Oct 30, 2008
Title Section of Root from 270 mm to 340 mm harvested immediately rep2
Sample type RNA
 
Source name Section of Root from 270 mm to 340 mm harvested immediately
Organism Arabidopsis thaliana
Characteristics Genotype: Col-0
Root Early Differention Region
Biomaterial provider Arabidopsis Stock Center
Treatment protocol Seedlings at 4 dpg were transferred to a plate of 5% agar solid medium (1X MS salts, 0.5% sucrose) to ensure a hard support and the root tip was surgically excised under a dissecting microscope using a 30G sterile dental needle (ExelInt), with a cutting error of about 5 um. The plant was immediately returned to a standard 0.8% agar solid medium (1X MS salts, 0.5% sucrose) for recovery. For microarray analysis, 130 um of uncut tip or 70 um of regenerating stumps were manually excised with the 30G needle
Growth protocol Plants were grown for 4 days in long day (16hr light/8hr dark) 22 oC conditions in a Percival (Percival Scientific). Plants were grown on agar in 1x MS All plant lines are in the Col-0 background.
Extracted molecule total RNA
Extraction protocol Sets of 5 tissue samples were collected each in 2.5 ul of extraction buffer (XB) of the Pico Pure RNA Isolation Kit (Araturus), flash-frozen in liquid nitrogen and ground. At least 25 samples were pooled for each experimental replicate (4 replicates)
Label biotin
Label protocol Biotinylated cRNA from all isolated samples was prepared according to the standard two-cycle Affymetrix protocol from 50 ng total RNA
 
Hybridization protocol Following fragmentation, 8 ug of cRNA were hybridized for 16 hr at 45C on an Affymetrix ATH1 GeneChip Arabidopsis Whole Genome Array in the Affymetrix Hybridization oven 640 following standard Affymetrix protocol. GeneChips were washed and stained using the 'EukGE-WS2v4_450' protocol in the Affymetrix GeneChip Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner according to standard Affymetrix protocols.
Description Roots grown horizontally on square plates
Data processing The data was normlized using MAS5 with a target intensity of 250
 
Submission date Dec 20, 2007
Last update date Aug 28, 2018
Contact name Kenneth David Birnbaum
E-mail(s) ken.birnbaum@nyu.edu
Phone 212-998-8257
Organization name New York University
Department Biology
Lab Birnbaum
Street address 12 Waverly Place
City New York
State/province NY
ZIP/Postal code 10003
Country USA
 
Platform ID GPL198
Series (1)
GSE9996 Organ regeneration in plants is independent of stem cell niche activity
Relations
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
VALUE MAS5.0 signal

Data table
ID_REF VALUE
261585_at 10.1
261568_at 9.8
261584_at 161.8
261579_at 2596.4
261569_at 55.2
261576_at 3.9
261577_at 71.7
261583_at 4464.5
261578_at 7151.9
261580_at 30
261570_at 9.5
261575_at 45
261581_at 8.4
261571_at 6
261582_at 255.4
261572_at 135.6
261573_at 6.2
261574_at 8.5
261042_at 70.2
261043_at 437.8

Total number of rows: 22746

Table truncated, full table size 338 Kbytes.




Supplementary file Size Download File type/resource
GSM252691.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM252691.EXP.gz 275 b (ftp)(http) EXP
Processed data included within Sample table

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