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Sample GSM802026 Query DataSets for GSM802026
Status Public on Mar 23, 2012
Title RIT12_BASE_SD0515A
Sample type RNA
 
Channel 1
Source name RIT12_BASE_FA, 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 RIT12_BASE_FA, 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 -1.879 45220 19973 4466 40 16 5865 836 34 7 482 80 45 7820 20677 5621 -1.358 .96 0
2 0 44688 58 12 44 13 32 4 34 5 104 12 45 42 0 0 0 .1 0
3 -.494 44156 61 21 41 15 35 8 32 3 68 12 42 46 9 6 -2.322 .1 0
4 -.908 43624 57 11 40 11 34 3 33 4 176 32 44 45 5 3 -4.083 .03 0
5 0 43092 60 13 44 10 34 4 34 5 97 12 45 45 0 0 0 -1 0
6 -.472 42560 61 15 39 10 36 4 32 4 176 32 42 48 11 7 -1.873 .04 0
7 0 42028 59 12 38 9 33 4 33 4 297 52 44 44 0 0 0 -1 0
8 -.138 41496 55 13 38 8 36 5 33 4 297 52 44 48 7 6 -2.089 .17 0
9 -.908 40964 55 12 38 7 34 5 33 4 290 52 44 45 5 3 -4.083 .03 0
10 -.545 40432 58 12 40 14 35 3 33 4 68 12 44 46 7 4 -3.171 .32 0
11 -.481 39900 52 11 38 8 34 5 33 4 395 80 44 45 4 3 -3.816 .03 0
12 1.407 39368 77 18 38 8 122 23 34 5 408 80 45 162 35 95 1.585 .78 0
13 -.24 38836 74 16 39 9 47 9 33 4 354 80 44 62 24 20 -.96 .55 0
14 -.655 38304 127 28 39 8 83 20 33 4 454 80 44 110 83 52 -.415 .83 0
15 .051 37772 65 18 38 8 44 8 33 4 302 52 44 58 16 17 -.946 .52 0
16 .789 37240 477 126 38 8 917 246 33 4 355 80 44 1222 473 818 1.424 .94 0
17 -.119 36708 71 20 37 7 48 9 33 4 373 80 44 64 23 21 -.766 .56 0
18 .212 36176 74 18 38 8 57 11 33 4 366 80 44 76 27 31 -.17 .69 0
19 -.203 35644 5106 1360 40 9 4897 1228 33 6 378 80 44 6529 5326 4626 .356 .96 0
20 -.456 35112 62 14 38 214 38 6 33 5 294 52 44 50 12 9 -2 .03 0

Total number of rows: 45220

Table truncated, full table size 3176 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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