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Sample GSM802046 Query DataSets for GSM802046
Status Public on Mar 23, 2012
Title NONRIT_SD0703A_TB_SAPgrid
Sample type RNA
 
Channel 1
Source name dSSc_6_FA_r, Non Rituximab Patient tissue
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 dSSc_6_FA_r, Non Rituximab Patient tissue
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 -3.287 45220 8757 7363 40 3103 1258 991 32 362 377 80 30 1198 10213 1046 -2.9 .96 0
2 -1.281 44688 45 16 37 11 32 4 31 3 311 80 29 30 4 1 -3 .11 0
3 0 44156 45 12 38 10 30 4 30 4 338 80 28 28 0 0 0 .05 0
4 0 43624 45 14 37 10 31 3 31 4 326 80 29 29 0 0 0 .15 0
5 -.29 43092 42 14 38 14 31 4 30 4 338 80 28 29 2 1 -2 .04 0
6 -1.087 42560 46 12 39 11 31 3 30 4 326 80 28 29 3 1 -2.806 .19 0
7 0 42028 48 18 40 58 31 4 31 8 326 80 29 29 0 0 0 .16 0
8 -1.087 41496 45 16 38 10 31 4 30 3 338 80 28 29 3 1 -2.806 .06 0
9 -.29 40964 42 10 38 10 32 3 31 4 327 80 29 30 2 1 -2 .17 0
10 0 40432 46 12 37 10 31 3 31 4 338 80 29 29 0 0 0 -1 0
11 .392 39900 43 12 38 11 32 4 30 4 290 80 28 30 2 3 -1.322 .66 0
12 2.061 39368 59 23 38 16 123 74 31 21 318 80 29 117 21 89 2.067 .65 0
13 -1.451 38836 48 16 39 10 32 4 31 5 278 52 29 30 4 1 -3.171 .23 0
14 -.957 38304 195 109 37 40 131 64 31 14 314 80 29 124 175 90 -.735 .89 0
15 .342 37772 44 14 37 42 33 6 30 11 340 80 28 31 4 5 -1.221 .83 0
16 2.021 37240 313 253 40 90 1508 1250 31 322 352 80 29 1436 315 1279 2.366 .95 0
17 -1.965 36708 95 52 39 42 44 13 31 13 339 80 29 41 53 13 -2.224 .58 0
18 -.238 36176 58 21 39 23 42 10 31 42 304 80 29 40 15 13 -.788 .78 0
19 -.501 35644 4341 2496 39 410 4220 2346 31 363 342 80 29 4019 5049 3568 -.109 .96 0
20 -1.493 35112 54 22 39 18 33 5 31 24 339 80 29 31 9 3 -2.911 .6 0

Total number of rows: 45220

Table truncated, full table size 3172 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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