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Sample GSM334748 Query DataSets for GSM334748
Status Public on Aug 31, 2010
Title HealthyEpidermis_T4vsT1_rep1
Sample type RNA
 
Channel 1
Source name T1 cell fraction (basal keratinocytes) [reference from sample 1]
Organism Homo sapiens
Characteristics gender: Female
health state: healthy
Growth protocol Cells were not cultured (direct processing from ex vivo samples)
Extracted molecule total RNA
Extraction protocol Total RNA extraction with QIAGEN RNeasy mini or midi kits
Label Cy3 on AQQ002 slide, Cy5 on swap-array AQQ003
Label protocol Reverse transcription of 10-20µg of total RNA with Superscript II enzyme and oligo-dT12-18 primers (Invitrogen) in the presence of aminoallyl-dUTP (Sigma-Aldrich), purification with cleanup module of Labelstar Array kit (Qiagen), labelling with monofunctional NHS ester Cy3 or Cy5 dye (Amersham), purification, pooling of samples to compare and concentration under vacuum followed by addition of 50µl of hybridization buffer containing 2x SSC, 0.1% SDS and 0.1% salmon sperm DNA (Invitrogen)
 
Channel 2
Source name T4 cell fraction (granular keratinocytes) [test from sample 1]
Organism Homo sapiens
Characteristics gender: Female
health state: healthy
Growth protocol Cells were not cultured (direct processing from ex vivo samples)
Extracted molecule total RNA
Extraction protocol Total RNA extraction with QIAGEN RNeasy mini or midi kits
Label Cy5 on AQQ002 slide, Cy3 on swap-array AQQ003
Label protocol Reverse transcription of 10-20µg of total RNA with Superscript II enzyme and oligo-dT12-18 primers (Invitrogen) in the presence of aminoallyl-dUTP (Sigma-Aldrich), purification with cleanup module of Labelstar Array kit (Qiagen), labelling with monofunctional NHS ester Cy3 or Cy5 dye (Amersham), purification, pooling of samples to compare and concentration under vacuum followed by addition of 50µl of hybridization buffer containing 2x SSC, 0.1% SDS and 0.1% salmon sperm DNA (Invitrogen)
 
 
Hybridization protocol cDNA were deposited on previously re-hydrated and blocked microarrays under coverslip, and slides were placed into hybridization chamber for 16 hours at 50°C. After 4 washes (2x SSC + 0.1% SDS ; 1x/0.2x/0.05x SCC) and drying, slides were scanned.
Scan protocol Slides were scanned on a GenePix 4000A scanner and image intensity data were extracted with GenePix Pro 6.0 analysis software
Description test (T4) and reference (T1) are obtained from the same biological sample
AQQ002 and AQQ003
Data processing Median intensities of each spot, local background substraction, log transformation and lowess normalization using Bioplot software. Spots with signal intensity greater than average signal for all buffer spots plus 2 SD and detected by more than half of the samples (i.e. with 4 values at least) were analyzed, other were removed from analysis. Note that the array design includes for a very few genes (including negative controls and ACTB / GAPD housekeeping genes) multiple spot replicates; when several of the spot replicates were positive, corresponding ratios where merged, and by convention the ID mentioned in the Matrix corresponds to the ID of the first spot in the GPL1946 table registered in GEO. Note also that ID in .gpr raw data files do NOT correspond to ID in GPL1946 Table, but to the INTERNAL_ID.
 
Submission date Oct 17, 2008
Last update date Nov 26, 2009
Contact name Nicolas Mattiuzzo
E-mail(s) nicolas.mattiuzzo@gmail.com
Phone +33 56158433
Organization name Centre National de la Recherche Scientifique (CNRS, France)
Department UMR CNRS-UPS (Univ. Paul Sabatier) 5165
Lab Unité Différenciation Epidermique et Autoimmunité Rhumatoïde
Street address CHU Purpan, place du Dr Baylac, TSA40031
City Toulouse
ZIP/Postal code 31073
Country France
 
Platform ID GPL1946
Series (1)
GSE13263 Study of keratinocyte differentiation in normal human epidermis

Data table header descriptions
ID_REF
VALUE Lowess normalized log2 ratio (T4/T1)

Data table
ID_REF VALUE
1 -0.205959502
2 -0.150151221
3 1.249044972
4 0.102979754
5 0.195329328
6
7 -0.260106976
8 -0.454439793
9
10 0.085705689
11 -0.010297979
12 -0.030561764
14 -1.069328659
15 0.103976411
18
19
20 -0.208617156
25
27 -0.117596252
28 -0.401621073

Total number of rows: 11520

Table truncated, full table size 176 Kbytes.




Supplementary file Size Download File type/resource
GSM334748_AQQ002.gpr.gz 2.3 Mb (ftp)(http) GPR
GSM334748_AQQ003.gpr.gz 2.1 Mb (ftp)(http) GPR
Raw data provided as supplementary file
Processed data included within Sample table

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