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Sample GSM490208 Query DataSets for GSM490208
Status Public on Jun 14, 2010
Title GL2_EXP_1_(294548)
Sample type mixed
Channel 1
Source name INTACT-derived amplified nuclear cDNA.
Organism Arabidopsis thaliana
Characteristics tissue: root epidermis non-hair cell nuclei
cell line: GL2p:NTF/ACT2p:BirA
Extracted molecule nuclear RNA
Extraction protocol RNA isolation was done with Qiagen RNeasy micro kit. cDNA preparation ond amplification were done with the Sigma WTA2 kit. Detailed protocol is located on the Series record.
Label Cy3
Label protocol Standard NimbleGen protocol using 5 hour labeling reaction rather than 2 hour reaction.
Channel 2
Source name Fragmented genomic DNA.
Organism Arabidopsis thaliana
Characteristics tissue: total root
Extracted molecule genomic DNA
Extraction protocol DNA isolation was done with the Qiagen DNeasy Plant Kit and was not amplified.
Label Cy5
Label protocol Standard NimbleGen protocol using 5 hour labeling reaction rather than 2 hour reaction.
Hybridization protocol Standard NimbleGen protocol.
Scan protocol Standard NimbleGen protocol.
Description Expression profiling of nuclear RNA from INTACT-purified Arabidopsis non-hair cell nuclei.
Data processing Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy3/Cy5 were computed. Then the log ratios for up to 100 exonic probes starting from the 3' ends of TAIR8 genes were averaged to give a single expression value for each gene in the supplementary file GL2_EXP_1.dat . The supplementary files GL2_EXP_1.gff and GL2_EXP_1.bedgraph contain the bi-weight mean adjusted log base 2 ratios.
Submission date Dec 24, 2009
Last update date Apr 18, 2012
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platform ID GPL7143
Series (1)
GSE19654 INTACT method for gene expression and chromatin profiling of individual cell types within a tissue

Data table header descriptions
VALUE Standard deviate of log base 2 (Cy3/Cy5)

Data table
CHR1V01212004FS000000001 -2.322
CHR1V01212004FS000000061 -0.535
CHR1V01212004FS000000121 0.185
CHR1V01212004FS000000181 -0.341
CHR1V01212004FS000000241 0.15
CHR1V01212004FS000000301 -0.398
CHR1V01212004FS000000361 0.87
CHR1V01212004FS000000421 0.322
CHR1V01212004FS000000481 -1.152
CHR1V01212004FS000000541 -0.483
CHR1V01212004FS000000601 -0.466
CHR1V01212004FS000000661 -0.301
CHR1V01212004FS000000721 1.127
CHR1V01212004FS000000781 -0.112
CHR1V01212004FS000000841 0.367
CHR1V01212004FS000000901 0.253
CHR1V01212004FS000000961 1.195
CHR1V01212004FS000001021 0.967
CHR1V01212004FS000001081 1.207
CHR1V01212004FS000001141 1.578

Total number of rows: 1982954

Table truncated, full table size 60811 Kbytes.

Supplementary file Size Download File type/resource
GSM490208_GL2_EXP_1.bedgraph.gz 15.7 Mb (ftp)(http) BEDGRAPH
GSM490208_GL2_EXP_1.dat.gz 202.3 Kb (ftp)(http) DAT
GSM490208_GL2_EXP_1.gff.gz 22.0 Mb (ftp)(http) GFF
GSM490208_GL2_EXP_1_532.pair.gz 32.6 Mb (ftp)(http) PAIR
GSM490208_GL2_EXP_1_635.pair.gz 33.0 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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