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Sample GSM801990 Query DataSets for GSM801990
Status Public on Mar 23, 2012
Title NormalRIT_NO5-1_TB_SAPgrid
Sample type RNA
 
Channel 1
Source name NormalRIT_1_r, Normal Non-SSc Patient
Organism Homo sapiens
Characteristics biopsy: skin
Biomaterial provider Robert Lafyatis, Boston University
Treatment protocol 3 - 6 mm punch biopsy stored in RNA later
Extracted molecule total RNA
Extraction protocol Total RNA extract using Qiagen Rneasy Tissuekit
Label Cy3
Label protocol Agilent Low RNA Input Linear Amplification protocol: 100 ng of total RNA from each biopsy was converted to Cy3-CTP (Perkin Elmer) labeled cRNA, and Universal Human Reference (UHR) RNA (Stratagene) was converted to Cy5-CTP (Perkin Elmer) using a low input linear amplification kit (Agilent Technologies) as per manufacturers protocols. Labeled cRNA targets were then purified using RNeasy columns (Qiagen).
 
Channel 2
Source name Universal Human Reference
Organism Homo sapiens
Characteristics reference: Stratagene's Universal Human Reference (RNA pool from 10 different human cell lines; http://www.ncbi.nlm.nih.gov/pubmed/15113400)
Biomaterial provider Stratagene
Treatment protocol none
Extracted molecule total RNA
Extraction protocol Total RNA isolated by stratagene
Label Cy5
Label protocol Agilent Low RNA Input Linear Amplification protocol: 100 ng of total RNA from each biopsy was converted to Cy3-CTP (Perkin Elmer) labeled cRNA, and Universal Human Reference (UHR) RNA (Stratagene) was converted to Cy5-CTP (Perkin Elmer) using a low input linear amplification kit (Agilent Technologies) as per manufacturers protocols. Labeled cRNA targets were then purified using RNeasy columns (Qiagen).
 
 
Hybridization protocol Agilent Gene Expression Hybridization kit was used for hybridization. Cy3- and Cy5-labeled cRNA was hybridized to Agilent Whole Human genome oligo-array. Hybridization was carried out for 17 hours at 65oC with rotation.
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysis software.
Description NormalRIT_1_r, Normal Non-SSc Patient
Data processing Data for both channels were lowess-normalized and then log(2) ratio was taken. As for lowess program, we download from BASE.
 
Submission date Sep 26, 2011
Last update date Jun 13, 2017
Contact name Tammara Wood
E-mail(s) [email protected]
Organization name Dartmouth Medical School
Department Biomedical Data Science
Lab Whitfield Lab
Street address WTRB 674
City Lebanon
State/province NH
ZIP/Postal code 03756
Country USA
 
Platform ID GPL4133
Series (2)
GSE32413 Stable gene expression of serial skin biopsies defines patient subsets in diffuse cutaneous systemic sclerosis
GSE76809 Multi-tissue functional genomic study of systemic sclerosis
Relations
Reanalyzed by GSE56308

Data table header descriptions
ID_REF Spot Reference ID
VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN)
SPOT spot number on array
CH1_MEAN
CH1_SD standard deviation of channel 1 intensity
CH1_BKD_MEDIAN channel 1 background median intensity
CH1_BKD_SD standard deviation of channel 1 background median intensity
CH2_MEAN channel 2 mean intensity
CH2_SD standard deviation of channel 2 intensity
CH2_BKD_MEDIAN channel 2 background median intensity
CH2_BKD_SD standard deviation of channel 2 background median intensity
TOT_BPIX number of background pixels
TOT_SPIX number of spot pixels
CH2BN_MEDIAN channel 2 normalized background median intensity
CH2IN_MEAN channel 2 normalized mean intensity
CH1DL_MEAN channel 1 Lowess_normalized mean intensity
CH2DL_MEAN channel 2 Lowess_normalized mean intensity
LOG_RAT2N_MEAN log2_ratio of channel 2 normalized over channel 1 (global normalization)
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots

Data table
ID_REF VALUE SPOT CH1_MEAN CH1_SD CH1_BKD_MEDIAN CH1_BKD_SD CH2_MEAN CH2_SD CH2_BKD_MEDIAN CH2_BKD_SD TOT_BPIX TOT_SPIX CH2BN_MEDIAN CH2IN_MEAN CH1DL_MEAN CH2DL_MEAN LOG_RAT2N_MEAN CORR FLAG
1 -2.387 45220 13888 7632 36 1767 2710 1329 32 171 377 80 32 2765 13928 2663 -2.344 .98 0
2 .362 44688 39 10 34 7 34 7 31 4 311 80 31 34 3 4 -.737 .13 0
3 0 44156 40 9 34 7 31 5 31 5 338 80 31 31 0 0 0 .07 0
4 -1.068 43624 39 10 34 6 32 4 31 5 326 80 31 32 3 1 -2.322 .04 0
5 0 43092 42 10 34 7 31 5 31 5 338 80 31 31 0 0 0 .03 0
6 -.272 42560 38 9 35 7 33 5 32 5 326 80 32 33 1 1 -1.586 .13 0
7 0 42028 40 9 35 44 31 6 32 11 326 80 32 31 0 0 0 .08 0
8 -.72 41496 39 7 35 7 32 4 31 5 338 80 31 32 2 1 -2 -1 0
9 0 40964 40 8 34 8 31 5 31 5 327 80 31 31 0 0 0 .07 0
10 -1.116 40432 43 18 34 6 33 6 31 5 338 80 31 33 6 2 -2.171 .27 0
11 -1.351 39900 40 9 34 6 32 5 31 5 290 80 31 32 3 1 -2.582 .46 0
12 2.463 39368 63 23 34 12 201 111 32 30 318 80 32 205 29 164 2.577 .82 0
13 -1.214 38836 50 13 35 8 35 7 31 6 278 52 31 35 11 5 -1.905 .32 0
14 -.818 38304 268 147 35 39 178 84 31 14 314 80 31 181 245 139 -.635 .88 0
15 .138 37772 45 12 35 56 39 8 32 14 340 80 32 39 7 8 -.515 .85 0
16 1.885 37240 588 441 36 151 2246 1599 32 421 352 80 32 2291 575 2124 2.033 .97 0
17 -.144 36708 73 30 35 21 64 24 31 15 339 80 31 65 37 33 -.16 .7 0
18 .402 36176 56 20 35 30 56 19 32 28 304 80 32 57 19 25 .251 .9 0
19 -.853 35644 8729 6094 37 1588 4884 3127 33 582 339 80 33 4983 8727 4831 -.813 .97 0
20 -.831 35112 48 12 36 39 35 6 31 40 339 80 31 35 9 5 -1.586 .9 0

Total number of rows: 45220

Table truncated, full table size 3237 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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