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Sample GSM272417 Query DataSets for GSM272417
Status Public on Mar 13, 2008
Title ATL-3 - mAdbID:91660
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 ATL-3
Organism Homo sapiens
Characteristics Tissue: blood
Cell type: monocytes
Disease state: smodering ATL
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: 760;; 650
ScanPower: 100;; 100
LaserPower: 1.11;; 2.48
Temperature: 33.18
Description mAdb experiment ID: 91660
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 -0.747 0.596 1 1 1 637 260 78 71 1573 340 58 142 0 -0.747
1728380_1 -0.906 0.534 1 1 2 278 180 79 54 661 235 59 35 0 -0.906
1729712_1 -1.332 0.397 1 1 3 130 64 84 49 246 68 59 17 0 -1.332
1730972_1 -0.845 0.557 1 1 4 131 83 81 46 201 47 56 12 0 -0.845
1732304_1 -0.631 0.646 1 1 5 109 69 77 47 136 29 56 12 0 -0.631
1733564_1 -1.183 0.440 1 1 6 138 85 81 54 269 73 60 14 0 -1.183
1734896_1 0.404 1 1 7 100 57 87 70 113 47 61 29 -50 -1.309
1736156_1 -0.696 0.617 1 1 8 316 155 87 54 658 158 59 16 0 -0.696
1737488_1 0.439 1.355 1 1 9 1066 428 93 72 1218 273 59 45 0 0.439
1738748_1 -0.721 0.607 1 1 10 154 86 89 57 230 65 57 13 0 -0.721
1740080_1 -0.410 0.753 1 1 11 260 178 87 49 429 99 58 13 0 -0.410
1741340_1 -4.995 0.031 1 1 12 84 55 82 55 160 46 57 12 0 -4.995
1742672_1 -0.290 0.818 1 1 13 162 116 84 61 214 68 60 26 0 -0.290
1743932_1 -0.853 0.554 1 1 14 271 149 82 51 609 122 58 16 0 -0.853
1745264_1 -1.296 0.407 1 1 15 158 93 76 49 383 105 58 15 0 -1.296
1746524_1 -0.404 0.756 1 1 16 201 102 83 53 313 125 61 23 0 -0.404
1747856_1 0.442 1.359 1 1 17 162 79 77 57 167 40 66 25 0 0.442
1749116_1 0.908 1.877 1 1 18 696 317 102 74 598 188 87 63 0 0.908
1750448_1 0.669 1.590 1 1 19 46745 26609 114 97 47465 26359 110 81 0 0.669
1751708_1 -0.138 0.909 1 1 20 353 157 89 118 557 136 88 85 0 -0.138

Total number of rows: 35024

Table truncated, full table size 2275 Kbytes.




Supplementary file Size Download File type/resource
GSM272417.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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