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Sample GSM272412 Query DataSets for GSM272412
Status Public on Mar 13, 2008
Title ATL-1 - mAdbID:91501
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-1
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: 780;; 680
ScanPower: 100;; 100
LaserPower: 1.18;; 2.6
Temperature: 35.69
Description mAdb experiment ID: 91501
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 -0.647 0.639 1 1 1 800 396 0 31 1403 327 24 18 0 -0.647
1728380_1 -1.356 0.391 1 1 2 170 192 0 27 503 128 24 17 0 -1.356
1729712_1 -3.562 0.085 1 1 3 9 21 0 34 141 94 24 17 0 -3.562
1730972_1 -2.825 0.141 1 1 4 10 30 0 39 101 44 23 18 0 -2.825
1732304_1 -5.183 0.028 1 1 5 1 3 0 31 63 49 23 17 0 -5.183
1733564_1 -4.436 0.046 1 1 6 6 19 0 28 166 79 23 17 0 -4.436
1734896_1 -2.816 0.142 1 1 7 4 21 0 28 56 32 25 18 0 -2.816
1736156_1 0.262 1.199 1 1 8 475 332 0 34 460 99 24 22 0 0.262
1737488_1 0.192 1.142 1 1 9 1190 605 0 21 1170 390 23 16 0 0.192
1738748_1 -5.744 0.019 1 1 10 2 8 0 14 142 79 24 17 0 -5.744
1740080_1 -1.767 0.294 1 1 11 67 120 0 24 275 156 24 18 0 -1.767
1741340_1 -5.031 0.031 1 1 12 1 6 0 32 61 44 25 17 0 -5.031
1742672_1 -1.390 0.381 1 1 13 35 60 0 30 125 65 24 17 0 -1.390
1743932_1 -0.390 0.763 1 1 14 348 301 0 30 525 168 23 17 0 -0.390
1745264_1 -3.143 0.113 1 1 15 29 80 0 34 306 129 24 17 0 -3.143
1746524_1 -1.113 0.462 1 1 16 134 146 0 34 343 122 24 17 0 -1.113
1747856_1 -1.288 0.410 1 1 17 16 45 0 21 68 36 25 18 0 -1.288
1749116_1 -0.064 0.956 1 1 18 450 328 0 37 544 139 26 42 0 -0.064
1750448_1 0.168 1.124 1 1 19 43320 29154 0 67 42490 28454 43 44 0 0.168
1751708_1 0.305 1.236 1 1 20 568 390 0 59 535 174 29 25 0 0.305

Total number of rows: 35024

Table truncated, full table size 2232 Kbytes.




Supplementary file Size Download File type/resource
GSM272412.gpr.gz 2.7 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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