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Sample GSM96334 Query DataSets for GSM96334
Status Public on Nov 18, 2008
Title HaCaT_2hr vs 4hr_low dose UVB (Y24_L3L4)
Sample type RNA
 
Channel 1
Source name L4
Organism Homo sapiens
Characteristics HaCaT Cell line, Gender: male, Tissue: skin keratinocytes
Biomaterial provider kindly provided by Dr. P. Boukamp, DKFZ, Heidelberg, Germany through Dr. T.C., Lee, SINICA, Taipei, Taiwan
Treatment protocol Cells exposed to UVB 233 J/m2 , and then incubate for 4 hr
Growth protocol Cells were maintained at 37 oC and 5 % CO2 /95% air in DMEM (Gibico) supplemented with 2mM L-glutamine, 100 U/ml penicillin/ 100£gg/ml streptomycin(Gibico), and 10% fetal bovine serum(Hyclone).
Extracted molecule total RNA
Extraction protocol Total RNA was extracte by lying directly in the 100mm petri dish with 2 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer¡¦s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).
Label Cy5
Label protocol 3 DNA array 50 kit protocol (Genisphere)
 
Channel 2
Source name L3
Organism Homo sapiens
Characteristics HaCaT Cell line, Gender: male, Tissue: skin keratinocytes
Biomaterial provider kindly provided by Dr. P. Boukamp, DKFZ, Heidelberg, Germany through Dr. T.C., Lee, SINICA, Taipei, Taiwan
Treatment protocol Cells exposed to UVB 233 J/m2 , and then incubate for 2 hr
Growth protocol Cells were maintained at 37 oC and 5 % CO2 /95% air in DMEM (Gibico) supplemented with 2mM L-glutamine, 100 U/ml penicillin/ 100£gg/ml streptomycin(Gibico), and 10% fetal bovine serum(Hyclone).
Extracted molecule total RNA
Extraction protocol Total RNA was extracte by lying directly in the 100mm petri dish with 2 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer¡¦s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).
Label Cy3
Label protocol 3 DNA array 50 kit protocol (Genisphere)
 
 
Hybridization protocol 3 DNA array 50 kit protocol (Genisphere)
Scan protocol Barcode=12494745 PMTVolts=700 600 Scanner=GenePix 4000B [84942] LaserPower=3.04 3.66 Temperature=30.26 ScanPower=33 33
Description We applied loop design for our microarray experiments in order to reduce the systemic error.
Data processing Data processing will detailed description in http://140.114.106.30/publication/cho/
 
Submission date Feb 09, 2006
Last update date Nov 18, 2007
Contact name ChengWei Chang
E-mail(s) d924546@oz.nthu.edu.tw
Organization name nthu
Department bmes
Lab mbpl
Street address 101, Section 2 Kuang Fu Road
City Hsinchu
ZIP/Postal code 30013
Country Taiwan
 
Platform ID GPL2573
Series (1)
GSE4223 Studying Gene Expression Profiles of UV-Irradiated Human Keratinocytes by cDNA Microarray

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
SPOT SIZE diameter of spot (um)
CH1_SIG_MEAN mean of Cy5 (635nm) channel intensity
CH1_SIG_SD standard deviation of Cy5 (635nm) channel intensity
CH1_BKD_MEDIAN median of Cy5 (635nm) channel background
CH2_SIG_MEAN mean of Cy3 (532nm) channel intensity
CH2_SIG_SD standard deviation of Cy3 (532nm) channel intensity
CH2_BKD_MEDIAN median of Cy3 (532nm) channel background
FLAGS flag the bad spots, -100 indicate absence of spot, -50 bad spot, 0 no specific flag.
UNF_VALUE log ratio (Cy5/Cy3)

Data table
ID_REF VALUE SPOT SIZE CH1_SIG_MEAN CH1_SIG_SD CH1_BKD_MEDIAN CH2_SIG_MEAN CH2_SIG_SD CH2_BKD_MEDIAN FLAGS UNF_VALUE
1 120 39 22 33 99 42 78 -50 -3.907
2 -1.585 125 64 51 35 128 62 90 0 -1.585
3 120 43 25 34 99 42 81 -50 Null
4 -2.755 110 63 51 34 136 54 76 0 -2.755
5 120 58 52 40 131 61 92 -50 Null
6 120 21974 2314 174 17639 2625 175 -50 0.324
7 120 998 4178 40 888 3521 95 -50 0.222
8 120 52 42 35 108 88 86 -50 Null
9 -4.801 70 66 56 35 311 168 94 0 -4.801
10 -3.209 100 82 76 34 350 140 86 0 -3.209
11 -4.765 95 67 56 35 385 156 86 0 -4.765
12 120 44 29 35 115 47 81 -50 -4.858
13 Null 105 43 29 35 166 59 76 0 Null
14 -6.392 90 50 34 35 164 63 76 0 -6.392
15 Null 90 44 32 35 159 57 78 0 Null
16 -5.267 110 50 53 35 166 58 80 0 -5.267
17 -0.094 130 609 414 36 726 456 87 0 -0.094
18 -0.807 115 163 111 37 289 104 91 0 -0.807
19 -1.950 100 97 75 37 276 140 90 0 -1.950
20 -0.348 120 648 354 36 848 349 87 0 -0.348

Total number of rows: 32448

Table truncated, full table size 1469 Kbytes.




Supplementary file Size Download File type/resource
GSM96334.gpr.gz 2.2 Mb (ftp)(http) GPR

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