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Sample GSM802063 Query DataSets for GSM802063
Status Public on Mar 23, 2012
Title RIT5_6MOS_SD0507B
Sample type RNA
 
Channel 1
Source name RIT5_6MOS_B, 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 RIT5_6MOS_B, 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 -.245 45220 28088 9127 38 14 24345 4175 37 15 481 80 44 28982 28422 23989 .045 .93 0
2 -.23 44688 50 10 38 9 37 5 34 7 380 80 40 44 6 5 -1.586 .28 0
3 -.609 44156 49 10 37 6 36 6 34 5 408 80 40 42 6 3 -2.582 .13 0
4 0 43624 48 9 37 7 35 6 35 6 257 52 41 41 0 0 0 .13 0
5 -.892 43092 49 10 39 9 35 5 34 5 145 32 40 41 4 2 -3.322 .03 0
6 .209 42560 48 9 37 7 38 7 34 6 437 80 40 45 6 7 -1.136 .23 0
7 .417 42028 50 9 38 9 40 10 34 6 211 32 40 47 7 9 -.778 .15 0
8 -.253 41496 52 9 42 11 36 8 34 6 104 12 40 42 4 4 -2.322 .09 0
9 .692 40964 53 8 41 9 43 8 35 6 68 12 41 51 7 12 -.264 .14 0
10 .246 40432 49 11 37 6 39 8 34 6 308 52 40 46 7 8 -1 .18 0
11 -1.409 39900 49 9 36 7 36 7 35 6 405 80 41 42 5 2 -3.699 .1 0
12 .582 39368 123 32 36 6 165 34 35 6 354 80 41 196 86 130 .833 .84 0
13 -.009 38836 82 24 36 7 70 17 34 6 356 80 40 83 40 40 -.097 .74 0
14 -.947 38304 139 37 36 6 83 20 34 5 392 80 40 98 98 51 -.829 .8 0
15 -.259 37772 78 18 36 6 60 15 34 6 270 52 40 71 36 30 -.438 .6 0
16 1.568 37240 302 94 37 6 939 215 34 6 398 80 40 1117 284 843 2.023 .91 0
17 .157 36708 68 18 36 7 60 13 35 6 370 80 41 71 26 29 -.092 .56 0
18 .158 36176 81 23 36 6 74 17 34 6 313 80 40 88 40 44 .094 .71 0
19 .102 35644 6325 2038 37 8 7356 1683 36 7 312 80 42 8757 6547 7029 .471 .93 0
20 -.073 35112 61 14 37 6 47 11 34 6 366 80 40 55 18 17 -.678 .44 0

Total number of rows: 45220

Table truncated, full table size 3169 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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