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Sample GSM272416 Query DataSets for GSM272416
Status Public on Mar 13, 2008
Title Normal-2 - mAdbID:91659
Sample type RNA
 
Channel 1
Source name Universal Human Reference RNA - Cy3
Organism Homo sapiens
Characteristics Other: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.
Biomaterial provider Stratagene (La Jolla, CA)
Extracted molecule total RNA
Extraction protocol Strategene UHR RNA Extraction
Other: not available
Label cy3
Label protocol Cy3 Sample Labeling Protocol - generic
Other: Labeled using amino allyl conjugation method.
 
Channel 2
Source name Normal-2
Organism Homo sapiens
Characteristics Tissue: blood
Cell type: monocytes
Disease state: Normal
Extracted molecule total RNA
Extraction protocol Sample Extraction Protocol
Other: Total RNA was prepared using RNAeasy kit (Qiagen, Valencia, CA).
Label cy5
Label protocol Invitrogen cDNA Labeling Kit - cy5
Other: Labeled sample with Cy5 using a NHS-ester coupling reaction following the manufacturer's cDNA Labeling Kit protocol (Invitrogen).
 
 
Hybridization protocol Hybridization Protocol
Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 40 ul of 2X F-hyb buffer and 20ul water to samples. Load 80 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry.
Scan protocol Creator: GenePix Pro 3.0.6.89
Scanner: GenePix 4000A [47890]
PMTVolts: 710;; 650
ScanPower: 100;; 100
LaserPower: 1.11;; 2.46
Temperature: 33.62
Description mAdb experiment ID: 91659
Data processing mAdb Data Processing Protocol (v. 2)
Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.
 
Submission date Mar 11, 2008
Last update date Mar 13, 2008
Contact name Thomas Wadlmann
E-mail(s) tawald@mail.nih.gov
Organization name NCI/NIH
Department Metabolism Branch
Street address 10 Center Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL3779
Series (1)
GSE10789 Induction of the IL-9 gene by HTLV-I Tax stimulates the spontaneous proliferation of primary adult T-cell leukemia cells

Data table header descriptions
ID_REF NCI mAdb well id plus replicate number
VALUE log ratio(CY5/CY3) with flagged values removed
PRE_VALUE Calibrated Ratio (CY5 channel/CY3 channel)
Slide_block Array block location
Slide_column Array column location
Slide_row Array row location
CY5_mean Red Channel Sample mean Signal (Background Subtracted)
CY5_SD Red Channel Sample Standard Deviation
CY5_BKD_median Red Channel Sample median Background Level
CY5_BKD_SD Red Channel Sample Background Standard Deviation
CY3_mean Green Channel Sample mean Signal (Background Subtracted)
CY3_SD Green Channel Sample Standard Deviation
CY3_BKD_median Green Channel Sample median Background Level
CY3_BKD_SD Green Channel Sample Background Standard Deviation
Flag Quality flag 0->good, -50->Not found, -100->Bad
UNF_VALUE log ratio (log2 of PRE_VALUE)

Data table
ID_REF VALUE PRE_VALUE Slide_block Slide_column Slide_row CY5_mean CY5_SD CY5_BKD_median CY5_BKD_SD CY3_mean CY3_SD CY3_BKD_median CY3_BKD_SD Flag UNF_VALUE
1727120_1 -0.390 0.763 1 1 1 801 245 264 72 2329 559 55 12 0 -0.390
1728380_1 -3.521 0.087 1 1 2 300 108 277 76 909 159 56 55 0 -3.521
1729712_1 0.021 1 1 3 213 117 264 74 207 129 54 30 -50 -5.565
1730972_1 0.028 1 1 4 220 105 268 70 168 88 54 12 -50 -5.141
1732304_1 0.053 1 1 5 165 102 250 69 117 53 56 12 -50 -4.239
1733564_1 -6.302 0.013 1 1 6 183 97 251 93 316 127 61 91 0 -6.302
1734896_1 0.057 1 1 7 194 114 246 78 113 53 56 46 -50 -4.141
1736156_1 0.348 1.273 1 1 8 626 186 246 78 1020 181 55 12 0 0.348
1737488_1 0.259 1.196 1 1 9 917 279 244 89 1874 360 56 75 0 0.259
1738748_1 0.026 1 1 10 193 103 252 86 180 113 55 47 -50 -5.274
1740080_1 -7.131 0.007 1 1 11 216 96 253 74 509 110 56 13 0 -7.131
1741340_1 0.069 1 1 12 167 107 234 72 103 49 56 12 -50 -3.862
1742672_1 0.026 1 1 13 215 103 234 68 179 110 57 13 -50 -5.239
1743932_1 -5.157 0.028 1 1 14 241 130 235 72 750 172 58 13 0 -5.157
1745264_1 -7.066 0.007 1 1 15 169 100 238 79 489 149 56 38 0 -7.066
1746524_1 -3.403 0.095 1 1 16 243 102 232 72 435 134 59 42 0 -3.403
1747856_1 0.049 1 1 17 187 103 228 73 126 64 60 31 -50 -4.352
1749116_1 0.224 1.168 1 1 18 508 182 239 74 821 126 77 50 0 0.224
1750448_1 1.641 3.118 1 1 19 44540 27291 245 77 45993 27162 92 53 0 1.641
1751708_1 -0.008 0.995 1 1 20 405 151 236 77 622 146 73 52 0 -0.008

Total number of rows: 35024

Table truncated, full table size 2295 Kbytes.




Supplementary file Size Download File type/resource
GSM272416.gpr.gz 2.9 Mb (ftp)(http) GPR
Processed data included within Sample table
Raw data provided as supplementary file
Raw data included within Sample table

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