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Sample GSM1415383 Query DataSets for GSM1415383
Status Public on Oct 21, 2014
Title 010-1
Sample type RNA
 
Source name TBI
Organism Homo sapiens
Characteristics source type: blood
dose: 150
treatment: none
time: 6
subject number: 10
condition/tp dx: ALL
gender: Male
Treatment protocol For the Ex Vivo samples, healthy consented adult donor was randomly assigned to a radiation group and labeled with the target dose of 0 cGy, 150 cGy, 300 cGy, or 600 cGy. In addition to the radiation exposures, the samples were also treated with either no treatment, GCSF, or LPS at time points 6 hours and 24 hours. Radiation expire times from the Cs137 irradiator were calculated to achieve target doses specific for tubes filled with blood and inserted in the roaring test tube holder. The dose rate was 480 cGy/min for the duration of the study. The healthy donors were enrolled to participate in this study following a protocol to collect PB samples that was previously approved by the Duke University Institutional Review Board.
For the TBI samples, adult patients, ages 21 to 66, were evaluated at the Duke University Adult Bone Marrow Transplantation Program enrolled in a Duke IRB-approved protocol to collect PB prior to and post TBI conditioning. With approval from the Duke University Institutional Review Board (IRB), between 5-12 mL of peripheral blood was collected from consented patients prior to and 6 hours following TBI with 150-200 cGy as part of their pre-transplantation conditioning. All patients receiving non-myeloablative conditioning were treated with 200 cGy of TBI from a linear accelerator at a dose rate of 20 cGy/min. All patients who underwent TBI-based myeloablative allogeneic or autologous stem-cell transplantation received radiation fractionated at 150 cGy per fraction at 20 cGy/min. All patients had PB collected (50 ml) prior to and 6 hours following exposure to either 200 cGy or 150 cGy radiation treatment. The dose exposure for TBI patients used in this study were 0 cGy, 150 cGy, 450 cGy and 1050 cGy at 0, 6, 30 and 78 hours post irradiation. Total RNA was extracted and assayed on the Affymetrix platform.
Extracted molecule total RNA
Extraction protocol Blood was collected in PAXgene fluid and total RNA was extracted using the RNeasy Protect Animal Blood Kit or Human Blood kit. RNA was beta globin reduced using Ambion Human GLOBINclear kit for the human studies. RNA was purified using the Qiagen RNEasy Mini Kit. All total RNA samples were assessed for quality using a NanoDrop ND8000 Spectrophotometer for absorbance ratios, and the Agilent Bioanalyzer 2100 for RIN scores.
Label biotin
Label protocol 500 ng of total RNA was amplified according to the MessageAmp Premier protocol (Ambion). Affymetrix GeneChip analysis was performed according to the manufacturer’s instructions,
 
Hybridization protocol Targets were hybridized to the Human U133A 2.0 GeneChip (Affymetrix, Santa Clara, CA). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hu133 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Data processing We are most interested in parsimonious models for estimating radiation exposure from gene expression. In order to obtain short gene lists, we utilized a two-step model building procedure. First, we selected genes with absolute correlation to dose greater than 0.3. Second, those genes were fed into an elastic net regression model to build the predictor. Elastic net is a penalized regression technique which automatically drops out unimportant variables. In order to control for overfitting, we utilized leave-one-out cross-validation. Graphs show results on held out (out-of-bag) samples. Cross-validation was carried out on both steps of the model building.
 
Submission date Jun 18, 2014
Last update date Oct 21, 2014
Contact name Holly K Dressman
E-mail(s) holly.dressman@duke.edu
Organization name Duke
Department IGSP
Lab Duke Microarray Facility
Street address 101 Science Drive
City Durham
State/province NC
ZIP/Postal code 27713
Country USA
 
Platform ID GPL571
Series (1)
GSE58613 A translatable predictor of human radiation injury

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 7.377441227
1053_at 6.980422003
117_at 10.68095322
121_at 8.149983194
1255_g_at 3.887974698
1294_at 9.020852967
1316_at 6.3375238
1320_at 4.6463049
1405_i_at 11.67545662
1431_at 4.092988976
1438_at 5.516105639
1487_at 8.335475124
1494_f_at 5.388056396
1598_g_at 7.958612695
160020_at 7.565210812
1729_at 9.739223003
177_at 5.082839074
1773_at 6.295275425
179_at 8.948258397
1861_at 6.40810803

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM1415383_2452_6730_31992_010-1_HG-U133A+2.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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