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Sample GSM152309 Query DataSets for GSM152309
Status Public on Dec 15, 2007
Title CA2 - Cloned TIL - mAdbID:64356
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 CA2 - Cloned TIL
Organism Homo sapiens
Characteristics Cell type: tumor infiltrating lymphocyte clone
Disease state: metastatic melanoma
Individual: CA2
genotype/variation: Non-responder
Treatment protocol Treatment type: Adoptive Cell Transfer
Treatment dose: 1.1-13.7 x 10e10 cells
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy Columns
Other: All RNA was isolated from respective TIL samples using Qiashredder homogenization columns followed by RNeasy columns (Qiagen) according to manufactures directions. RNA yield was determined using a Nanodrop photospectrometer.
Label cy5
Label protocol Ambion Message Amp - Cy5
Label method: amino allyl conjugation
Other: Approximately 0.5 Ÿ 1.0 ug of total RNA was then linearly amplified for one round using Amino Allyl Message Amp kits as recommended by the manufacturer (Ambion). All TIL antisense RNA (aRNA) were conjugated with Cyanine 5 while equivalently amplified control aRNA was conjugated with Cyanine 3.
 
 
Hybridization protocol NCI Oligo Microarray Hybridization
Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42øC 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). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100øC 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 42øC just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42øC 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. (Refer to "NCI Microarray Manual")
Scan protocol Creator: GenePix Pro 5.1.0.11
Scanner: GenePix 4000B [94874]
ScanPower: 100;; 100
LaserPower: 3.37;; 3.53
Temperature: 30.02
Description mAdb experiment ID: 64356
Data processing mAdb Standard Data Processing Protocol
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.
 
Submission date Dec 21, 2006
Last update date Jan 05, 2007
Contact name Keith Kerstann
E-mail(s) kwkerstann@expressiontherapeutics.com
Phone 301 451-6957
Organization name National Institutes of Health
Department Surgery Branch
Lab National Cancer Institute
Street address
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL1528
Series (1)
GSE6592 Gene Expression of Human Lymphocytes Used For ACT of Metastatic Melanoma

Data table header descriptions
ID_REF NCI mAdb well id plus replicate number
VALUE log ratio (log2 of PRE_VALUE 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
1173588_1 0.616 1.533 1 1 1 372 53 53 23 334 62 147 67 0 0.616
1174364_1 -1.521 0.348 1 1 2 8897 1013 55 36 22955 2830 149 49 0 -1.521
1175152_1 0.259 1.197 1 1 3 738 176 56 23 663 279 151 61 0 0.259
1175940_1 -0.207 0.866 1 1 4 1826 282 57 31 1995 283 160 63 0 -0.207
1176716_1 0.373 1.295 1 1 5 6090 1444 56 21 4342 918 154 41 0 0.373
1177504_1 -0.028 0.981 1 1 6 3219 612 57 21 3046 433 150 36 0 -0.028
1178580_1 -0.024 0.984 1 1 7 8163 1581 56 24 7556 1013 150 50 0 -0.024
1179356_1 -0.336 0.792 1 1 8 189 168 55 21 300 173 148 47 0 -0.336
1180144_1 0.634 1.552 1 1 9 1655 178 56 19 1081 129 155 51 0 0.634
1180932_1 -0.279 0.824 1 1 10 410 86 57 38 543 102 158 77 0 -0.279
1181708_1 0.088 1.063 1 1 11 756 113 57 40 740 146 149 65 0 0.088
1182496_1 -0.111 0.926 1 1 12 325 537 56 22 420 342 159 49 0 -0.111
1183572_1 -1.465 0.362 1 1 13 10466 2611 57 115 25980 4621 157 362 0 -1.465
1184348_1 -0.173 0.887 1 1 14 826 151 55 16 929 143 148 39 0 -0.173
1185136_1 -1.104 0.465 1 1 15 113 90 55 19 264 70 152 173 0 -1.104
1185924_1 0.281 1.215 1 1 16 1499 6555 54 19 1218 3978 149 118 0 0.281
1186700_1 -0.082 0.945 1 1 17 1912 669 56 38 1914 390 149 96 0 -0.082
1187488_1 0.946 1.926 1 1 18 1237 3472 56 39 702 415 151 97 0 0.946
1188564_1 1.172 2.253 1 1 19 5174 1545 56 55 2188 642 147 63 0 1.172
1189340_1 -0.150 0.901 1 1 20 370 115 55 20 465 171 151 60 0 -0.150

Total number of rows: 21794

Table truncated, full table size 1473 Kbytes.




Supplementary file Size Download File type/resource
GSM152309.gpr.gz 2.3 Mb (ftp)(http) GPR

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