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Series GSE60486 Query DataSets for GSE60486
Status Public on Sep 18, 2014
Title Consensus Preprocessing of GEO and ArrayExpress Normal and Diseased Lung Tissue Microarray Data
Sample organism Homo sapiens
Experiment type Expression profiling by array
Third-party reanalysis
Summary The Affymetrix oligonucleotide microarrays measure gene expression by quantifying intensity of fluorescently labeled gene fragments that bind to sets of 25-mer oligonucleotide probes on the chip with specific sequences tailored to be complementary to the target genes. Each gene is associated with a "probe set" containing several pairs (usually 11) of "perfect match" (perfectly complementary to target sequence) and "mismatch" (different base at position 13 of 25) probes. The raw measurements of each probe set consist of a set of intensities from the probes, which require in silico preprocessing by (1) correcting for background variability, (2) normalizing intensities across samples, and (3) summarizing intensities across the probe set into a single expression value. The output of the summarization step corresponds to the background-adjusted value for the mRNA of interest. We preprocess using GCRMA, which corrects for background variability by accounting for optical noise, probe affinity, and mismatch probe adjustment; normalizes intensities by quantile normalization; and summarizes intensities using a median polish method. To minimize preprocessing batch effects, it is desirable to preprocess all samples in the dataset together. However, preprocessing across multple platforms requires a consolidation of probes with identical sequences, precluding global preprocessing on datasets with multiple platforms using the standard preprocessing pipelines. To address this problem, we have developed and applied a custom preprocessing pipeline to combine the raw .CEL files from multiple platforms that share the same probe sets.
 
Overall design We preprocessed as a single dataset gene expression data collected from 26 publicly available GEO and ArrayExpress studies by applying a custom preprocessing pipeline based on GCRMA. The assembled dataset contains 1489 microarray samples of human tissue that measure gene expression of normal lung (NORM) and 5 different lung diseases (lung adenocarcinoma (ADC), lung squamous cell carcinoma (SCC), large cell lung carcinoma (LCLC), asthma (AST), and chronic obstructive pulmonary disease (COPD)) in preparation for subsequent disease classification analysis. The studies included are: GSE994, GSE10072, GSE10245, GSE10445, GSE10799, GSE12345, GSE12667, GSE14814, GSE1643, GSE1650, GSE17475, GSE18842, GSE18965, GSE19188, GSE2109, GSE3141, GSE4302, GSE5058, GSE6253, GSE7368, GSE7670, GSE8545, GSE8581, E-TABM-15, E-MEXP-231, and E-MTAB-47. These studies collected the microarray data using 2 platforms: Affymetrix U133-A (GPL96) and Affymetrix U133-Plus-2 (GPL570).

The following are included in this reanalysis:

79_1 ArrayExpress study E-TABM-15 sample 1, ADC lung surgical resection GPL96
47_1 ArrayExpress study E-TABM-15 sample 2, ADC lung surgical resection GPL96
41_1 ArrayExpress study E-TABM-15 sample 3, ADC lung surgical resection GPL96
61_1 ArrayExpress study E-TABM-15 sample 4, ADC lung surgical resection GPL96
92_1 ArrayExpress study E-TABM-15 sample 5, ADC lung surgical resection GPL96
60_1 ArrayExpress study E-TABM-15 sample 6, ADC lung surgical resection GPL96
86_1 ArrayExpress study E-TABM-15 sample 7, ADC lung surgical resection GPL96
53_1 ArrayExpress study E-TABM-15 sample 8, ADC lung surgical resection GPL96
40_1 ArrayExpress study E-TABM-15 sample 9, ADC lung surgical resection GPL96
33_1 ArrayExpress study E-TABM-15 sample 10, ADC lung surgical resection GPL96
71_1 ArrayExpress study E-TABM-15 sample 11, ADC lung surgical resection GPL96
23_1 ArrayExpress study E-TABM-15 sample 12, ADC lung surgical resection GPL96
78_1 ArrayExpress study E-TABM-15 sample 13, ADC lung surgical resection GPL96
89_1 ArrayExpress study E-TABM-15 sample 14, ADC lung surgical resection GPL96
38_1 ArrayExpress study E-TABM-15 sample 15, ADC lung surgical resection GPL96
84_1 ArrayExpress study E-TABM-15 sample 16, ADC lung surgical resection GPL96
54_1 ArrayExpress study E-TABM-15 sample 17, ADC lung surgical resection GPL96
87_1 ArrayExpress study E-TABM-15 sample 18, ADC lung surgical resection GPL96
59_1 ArrayExpress study E-TABM-15 sample 19, ADC lung surgical resection GPL96
28_1 ArrayExpress study E-TABM-15 sample 20, ADC lung surgical resection GPL96
32_1 ArrayExpress study E-TABM-15 sample 21, ADC lung surgical resection GPL96
67_1 ArrayExpress study E-TABM-15 sample 22, ADC lung surgical resection GPL96
48_1 ArrayExpress study E-TABM-15 sample 23, ADC lung surgical resection GPL96
40_2 ArrayExpress study E-TABM-15 sample 24, NORM lung surgical resection GPL96
33_2 ArrayExpress study E-TABM-15 sample 25, NORM lung surgical resection GPL96
54_2 ArrayExpress study E-TABM-15 sample 26, NORM lung surgical resection GPL96
48_2 ArrayExpress study E-TABM-15 sample 27, NORM lung surgical resection GPL96
84_2 ArrayExpress study E-TABM-15 sample 28, NORM lung surgical resection GPL96
89_2 ArrayExpress study E-TABM-15 sample 29, NORM lung surgical resection GPL96
28_2 ArrayExpress study E-TABM-15 sample 30, NORM lung surgical resection GPL96
41_2 ArrayExpress study E-TABM-15 sample 31, NORM lung surgical resection GPL96
92_2 ArrayExpress study E-TABM-15 sample 32, NORM lung surgical resection GPL96
78_2 ArrayExpress study E-TABM-15 sample 33, NORM lung surgical resection GPL96
87_2 ArrayExpress study E-TABM-15 sample 34, NORM lung surgical resection GPL96
38_2 ArrayExpress study E-TABM-15 sample 35, NORM lung surgical resection GPL96
23_2 ArrayExpress study E-TABM-15 sample 36, NORM lung surgical resection GPL96
61_2 ArrayExpress study E-TABM-15 sample 37, NORM lung surgical resection GPL96
32_2 ArrayExpress study E-TABM-15 sample 38, NORM lung surgical resection GPL96
47_2 ArrayExpress study E-TABM-15 sample 39, NORM lung surgical resection GPL96
79_2 ArrayExpress study E-TABM-15 sample 40, NORM lung surgical resection GPL96
86_2 ArrayExpress study E-TABM-15 sample 41, NORM lung surgical resection GPL96
DL06 ArrayExpress study E-MEXP-231 sample 1, ADC lung surgical resection GPL96
DL01 ArrayExpress study E-MEXP-231 sample 2, ADC lung surgical resection GPL96
DL05 ArrayExpress study E-MEXP-231 sample 3, ADC lung surgical resection GPL96
DL14 ArrayExpress study E-MEXP-231 sample 4, ADC lung surgical resection GPL96
DL39 ArrayExpress study E-MEXP-231 sample 5, ADC lung surgical resection GPL96
DL34 ArrayExpress study E-MEXP-231 sample 6, ADC lung surgical resection GPL96
DL88 ArrayExpress study E-MEXP-231 sample 7, ADC lung surgical resection GPL96
DL09 ArrayExpress study E-MEXP-231 sample 8, ADC lung surgical resection GPL96
DL59 ArrayExpress study E-MEXP-231 sample 9, ADC lung surgical resection GPL96
DL65 ArrayExpress study E-MEXP-231 sample 10, ADC lung surgical resection GPL96
DL31 ArrayExpress study E-MEXP-231 sample 11, ADC lung surgical resection GPL96
DL45 ArrayExpress study E-MEXP-231 sample 12, ADC lung surgical resection GPL96
DL63 ArrayExpress study E-MEXP-231 sample 13, ADC lung surgical resection GPL96
DL36 ArrayExpress study E-MEXP-231 sample 14, ADC lung surgical resection GPL96
DL13 ArrayExpress study E-MEXP-231 sample 15, ADC lung surgical resection GPL96
T42-1 ArrayExpress study E-MEXP-231 sample 16, ADC lung surgical resection GPL96
DL68 ArrayExpress study E-MEXP-231 sample 17, ADC lung surgical resection GPL96
DL50 ArrayExpress study E-MEXP-231 sample 18, ADC lung surgical resection GPL96
DL46 ArrayExpress study E-MEXP-231 sample 19, ADC lung surgical resection GPL96
DL30 ArrayExpress study E-MEXP-231 sample 20, ADC lung surgical resection GPL96
DL40 ArrayExpress study E-MEXP-231 sample 21, ADC lung surgical resection GPL96
DL51 ArrayExpress study E-MEXP-231 sample 22, ADC lung surgical resection GPL96
DL08 ArrayExpress study E-MEXP-231 sample 23, ADC lung surgical resection GPL96
DL35 ArrayExpress study E-MEXP-231 sample 24, ADC lung surgical resection GPL96
DL58 ArrayExpress study E-MEXP-231 sample 25, ADC lung surgical resection GPL96
DL61 ArrayExpress study E-MEXP-231 sample 26, ADC lung surgical resection GPL96
DL33 ArrayExpress study E-MEXP-231 sample 27, ADC lung surgical resection GPL96
DL16 ArrayExpress study E-MEXP-231 sample 28, ADC lung surgical resection GPL96
DL37 ArrayExpress study E-MEXP-231 sample 29, ADC lung surgical resection GPL96
DL12 ArrayExpress study E-MEXP-231 sample 30, ADC lung surgical resection GPL96
DL67 ArrayExpress study E-MEXP-231 sample 31, ADC lung surgical resection GPL96
DL91 ArrayExpress study E-MEXP-231 sample 32, ADC lung surgical resection GPL96
DL54 ArrayExpress study E-MEXP-231 sample 33, ADC lung surgical resection GPL96
DL47 ArrayExpress study E-MEXP-231 sample 34, ADC lung surgical resection GPL96
DL57 ArrayExpress study E-MEXP-231 sample 35, ADC lung surgical resection GPL96
DL03 ArrayExpress study E-MEXP-231 sample 36, ADC lung surgical resection GPL96
DL41 ArrayExpress study E-MEXP-231 sample 37, ADC lung surgical resection GPL96
DL15 ArrayExpress study E-MEXP-231 sample 38, ADC lung surgical resection GPL96
DL66 ArrayExpress study E-MEXP-231 sample 39, ADC lung surgical resection GPL96
DL11 ArrayExpress study E-MEXP-231 sample 40, ADC lung surgical resection GPL96
DL44 ArrayExpress study E-MEXP-231 sample 41, ADC lung surgical resection GPL96
DL38 ArrayExpress study E-MEXP-231 sample 42, ADC lung surgical resection GPL96
DL56 ArrayExpress study E-MEXP-231 sample 43, ADC lung surgical resection GPL96
DL60 ArrayExpress study E-MEXP-231 sample 44, ADC lung surgical resection GPL96
DL48 ArrayExpress study E-MEXP-231 sample 45, ADC lung surgical resection GPL96
DL89 ArrayExpress study E-MEXP-231 sample 46, ADC lung surgical resection GPL96
DL42 ArrayExpress study E-MEXP-231 sample 47, ADC lung surgical resection GPL96
DL32 ArrayExpress study E-MEXP-231 sample 48, ADC lung surgical resection GPL96
DL55 ArrayExpress study E-MEXP-231 sample 49, ADC lung surgical resection GPL96
DL15N ArrayExpress study E-MEXP-231 sample 50, NORM lung surgical resection GPL96
DL50N ArrayExpress study E-MEXP-231 sample 51, NORM lung surgical resection GPL96
DL4_1N ArrayExpress study E-MEXP-231 sample 52, NORM lung surgical resection GPL96
DL4_17N ArrayExpress study E-MEXP-231 sample 53, NORM lung surgical resection GPL96
DL4_7N ArrayExpress study E-MEXP-231 sample 54, NORM lung surgical resection GPL96
DL4_11N ArrayExpress study E-MEXP-231 sample 55, NORM lung surgical resection GPL96
DL86N ArrayExpress study E-MEXP-231 sample 56, NORM lung surgical resection GPL96
DL79N ArrayExpress study E-MEXP-231 sample 57, NORM lung surgical resection GPL96
DL67N ArrayExpress study E-MEXP-231 sample 58, NORM lung surgical resection GPL96
Biopsy_07 ArrayExpress study E-MTAB-47 sample 1, NORM lung surgical resection GPL570
Biopsy_11 ArrayExpress study E-MTAB-47 sample 2, NORM lung surgical resection GPL570
Biopsy_06 ArrayExpress study E-MTAB-47 sample 3, NORM lung surgical resection GPL570
Biopsy_13 ArrayExpress study E-MTAB-47 sample 4, NORM lung surgical resection GPL570
Biopsy_10 ArrayExpress study E-MTAB-47 sample 5, NORM lung surgical resection GPL570
Biopsy_01 ArrayExpress study E-MTAB-47 sample 6, NORM lung surgical resection GPL570
Biopsy_22 ArrayExpress study E-MTAB-47 sample 7, NORM lung surgical resection GPL570
Biopsy_04 ArrayExpress study E-MTAB-47 sample 8, NORM lung surgical resection GPL570
Biopsy_20 ArrayExpress study E-MTAB-47 sample 9, NORM lung surgical resection GPL570
Biopsy_14 ArrayExpress study E-MTAB-47 sample 10, NORM lung surgical resection GPL570
Biopsy_02 ArrayExpress study E-MTAB-47 sample 11, NORM lung surgical resection GPL570
Biopsy_08 ArrayExpress study E-MTAB-47 sample 12, NORM lung surgical resection GPL570

We preprocess using the MATLAB implementation of GCRMA. To minimize preprocessing batch effects, it is desirable to preprocess all samples in the entire dataset together. Preprocessing requires microarray platform-specific chip specifications indicating the locations of each probe on the chip, precluding global preprocessing on meta-analyses that use multiple platforms. To address this problem, we developed and applied a preprocessing pipeline to combine the raw .CEL files from multiple platforms that share the same probe sets. Importantly, our pipeline maps the locations of probes containing identical sequences from the different platforms to enable grouping of these probes and subsequent processing. These "consensus datasets" are then preprocessed normally by applying the GCRMA algorithm. The output of this consensus preprocessing contains only the 22,227 probes that exist on both microarray platforms that we use; probes that only appear on one of the platforms are excluded from preprocessing. We also include "presence/marginal/absence" calls based on the MAS5 protocol, in which the measured values on the "perfect match" (perfectly complementary to target) probes are compared to the values on the "mismatch" (basepair mismatch at position 13 of 25) probes with Wilcoxon signed rank test. "Present" calls are made when the p-value of difference is less than 0.04; "marginal" calls are made when the p-value lies between 0.04 and 0.06, and "absent" calls are made when the p-value is greater than 0.06.
GCRMA signal
 
Contributor(s) Ma S, Sung J, Magis AT, Wang Y, Geman D, Price ND
Citation(s) 25330348
Submission date Aug 18, 2014
Last update date Dec 18, 2014
Contact name Shuyi Ma
E-mail(s) shuyima1@uw.edu
Organization name University of Washington
Department Department of Pediatrics
Lab Shuyi Ma Lab
Street address 307 Westlake Avenue North
City Seattle
State/province Washington
ZIP/Postal code 98109
Country USA
 
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Reanalysis of GSM370964
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Reanalysis of GSM370966
Reanalysis of GSM370968
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Reanalysis of GSM370950
Reanalysis of GSM370955
Reanalysis of GSM370967
Reanalysis of GSM370972
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Reanalysis of GSM370980
Reanalysis of GSM27794
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Reanalysis of GSM27800
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Reanalysis of GSM28358
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Reanalysis of GSM435876
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Reanalysis of GSM467037
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Reanalysis of GSM475790
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Reanalysis of GSM475811
Reanalysis of GSM475656
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Reanalysis of GSM475727
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Reanalysis of GSM475769
Reanalysis of GSM475774
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Reanalysis of GSM475802
Reanalysis of GSM475805
Reanalysis of GSM475664
Reanalysis of GSM475668
Reanalysis of GSM475674
Reanalysis of GSM475694
Reanalysis of GSM475713
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Reanalysis of GSM475728
Reanalysis of GSM475730
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Reanalysis of GSM475735
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Reanalysis of GSM475672
Reanalysis of GSM475676
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Reanalysis of GSM475687
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Reanalysis of GSM475692
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Reanalysis of GSM475761
Reanalysis of GSM475765
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Reanalysis of GSM475779
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Reanalysis of GSM475792
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Reanalysis of GSM475799
Reanalysis of GSM475803
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Reanalysis of GSM475810
Reanalysis of GSM102447
Reanalysis of GSM102505
Reanalysis of GSM102512
Reanalysis of GSM102548
Reanalysis of GSM102555
Reanalysis of GSM117632
Reanalysis of GSM117671
Reanalysis of GSM117731
Reanalysis of GSM117756
Reanalysis of GSM117770
Reanalysis of GSM117772
Reanalysis of GSM137910
Reanalysis of GSM137912
Reanalysis of GSM137916
Reanalysis of GSM137931
Reanalysis of GSM137945
Reanalysis of GSM138001
Reanalysis of GSM138002
Reanalysis of GSM152592
Reanalysis of GSM152594
Reanalysis of GSM152681
Reanalysis of GSM179786
Reanalysis of GSM179827
Reanalysis of GSM179918
Reanalysis of GSM179951
Reanalysis of GSM203643
Reanalysis of GSM203787
Reanalysis of GSM277695
Reanalysis of GSM301693
Reanalysis of GSM325836
Reanalysis of GSM353885
Reanalysis of GSM353897
Reanalysis of GSM353908
Reanalysis of GSM38058
Reanalysis of GSM38060
Reanalysis of GSM38104
Reanalysis of GSM46824
Reanalysis of GSM46843
Reanalysis of GSM46860
Reanalysis of GSM46903
Reanalysis of GSM46904
Reanalysis of GSM46941
Reanalysis of GSM46961
Reanalysis of GSM46975
Reanalysis of GSM53170
Reanalysis of GSM76488
Reanalysis of GSM76574
Reanalysis of GSM76585
Reanalysis of GSM76587
Reanalysis of GSM76590
Reanalysis of GSM76595
Reanalysis of GSM76621
Reanalysis of GSM88953
Reanalysis of GSM88962
Reanalysis of GSM88981
Reanalysis of GSM88983
Reanalysis of GSM88997
Reanalysis of GSM89046
Reanalysis of GSM89060
Reanalysis of GSM89072
Reanalysis of GSM102449
Reanalysis of GSM102451
Reanalysis of GSM102455
Reanalysis of GSM102507
Reanalysis of GSM102553
Reanalysis of GSM102556
Reanalysis of GSM117610
Reanalysis of GSM117629
Reanalysis of GSM117763
Reanalysis of GSM138003
Reanalysis of GSM152624
Reanalysis of GSM152670
Reanalysis of GSM152757
Reanalysis of GSM179801
Reanalysis of GSM203641
Reanalysis of GSM203699
Reanalysis of GSM203732
Reanalysis of GSM231874
Reanalysis of GSM231885
Reanalysis of GSM231897
Reanalysis of GSM231899
Reanalysis of GSM231907
Reanalysis of GSM231950
Reanalysis of GSM277678
Reanalysis of GSM277696
Reanalysis of GSM301680
Reanalysis of GSM353933
Reanalysis of GSM38100
Reanalysis of GSM38103
Reanalysis of GSM46817
Reanalysis of GSM46833
Reanalysis of GSM46850
Reanalysis of GSM46868
Reanalysis of GSM46884
Reanalysis of GSM46936
Reanalysis of GSM46973
Reanalysis of GSM46976
Reanalysis of GSM53167
Reanalysis of GSM88949
Reanalysis of GSM179881
Reanalysis of GSM203779
Reanalysis of GSM231895
Reanalysis of GSM231896
Reanalysis of GSM46909
Reanalysis of GSM46913
Reanalysis of GSM88959
Reanalysis of GSM70127
Reanalysis of GSM70129
Reanalysis of GSM70130
Reanalysis of GSM70131
Reanalysis of GSM70136
Reanalysis of GSM70138
Reanalysis of GSM70140
Reanalysis of GSM70144
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Reanalysis of GSM70159
Reanalysis of GSM70161
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Reanalysis of GSM70164
Reanalysis of GSM70169
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Reanalysis of GSM70179
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Reanalysis of GSM70190
Reanalysis of GSM70193
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Reanalysis of GSM70199
Reanalysis of GSM70201
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Reanalysis of GSM70214
Reanalysis of GSM70218
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Reanalysis of GSM70125
Reanalysis of GSM70126
Reanalysis of GSM70128
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Reanalysis of GSM70133
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Reanalysis of GSM70137
Reanalysis of GSM70139
Reanalysis of GSM70141
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Reanalysis of GSM70143
Reanalysis of GSM70146
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Reanalysis of GSM70149
Reanalysis of GSM70152
Reanalysis of GSM70157
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Reanalysis of GSM70160
Reanalysis of GSM70162
Reanalysis of GSM70165
Reanalysis of GSM70166
Reanalysis of GSM70167
Reanalysis of GSM70168
Reanalysis of GSM70176
Reanalysis of GSM70178
Reanalysis of GSM70180
Reanalysis of GSM70182
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Reanalysis of GSM70186
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Reanalysis of GSM70191
Reanalysis of GSM70192
Reanalysis of GSM70198
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Reanalysis of GSM70210
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Reanalysis of GSM98141
Reanalysis of GSM98144
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Reanalysis of GSM98148
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Reanalysis of GSM98166
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Reanalysis of GSM98187
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Reanalysis of GSM98197
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Reanalysis of GSM98204
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Reanalysis of GSM98210
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Reanalysis of GSM98216
Reanalysis of GSM98220
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Reanalysis of GSM98226
Reanalysis of GSM98227
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Reanalysis of GSM98205
Reanalysis of GSM98231
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Reanalysis of GSM98237
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Reanalysis of GSM98207
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Reanalysis of GSM98213
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Reanalysis of GSM98221
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Reanalysis of GSM98254
Reanalysis of GSM98258
Reanalysis of GSM98203
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Reanalysis of GSM98196
Reanalysis of GSM98189
Reanalysis of GSM98185
Reanalysis of GSM98178
Reanalysis of GSM98176
Reanalysis of GSM98170
Reanalysis of GSM98165
Reanalysis of GSM98157
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Reanalysis of GSM98143
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Reanalysis of GSM98160
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Reanalysis of GSM98164
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Reanalysis of GSM101107
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Reanalysis of GSM101095
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Reanalysis of GSM114100
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Reanalysis of GSM185841
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Reanalysis of GSM185862
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Reanalysis of GSM252879
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Reanalysis of GSM252885
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Reanalysis of GSM252867
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Reanalysis of GSM252841
Reanalysis of GSM254163
Reanalysis of GSM254169
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Reanalysis of GSM254173
Reanalysis of GSM254174
Reanalysis of GSM254175
Reanalysis of GSM254176
Reanalysis of GSM210005
Reanalysis of GSM210009
Reanalysis of GSM210014
Reanalysis of GSM210015
Reanalysis of GSM210087
Reanalysis of GSM210192
Reanalysis of GSM210196
Reanalysis of GSM210979
Reanalysis of GSM211008
Reanalysis of GSM212067
Reanalysis of GSM212068
Reanalysis of GSM212070
Reanalysis of GSM212787
Reanalysis of GSM212789
Reanalysis of GSM212790
Reanalysis of GSM212811
Reanalysis of GSM212853
Reanalysis of GSM213035
Reanalysis of GSM213036
Reanalysis of GSM210004
Reanalysis of GSM210006
Reanalysis of GSM210008
Reanalysis of GSM210011
Reanalysis of GSM210071
Reanalysis of GSM210194
Reanalysis of GSM210992
Reanalysis of GSM210993
Reanalysis of GSM211007
Reanalysis of GSM211009
Reanalysis of GSM212074
Reanalysis of GSM212788
Reanalysis of GSM212810
Reanalysis of GSM212848
Reanalysis of GSM212852
Reanalysis of GSM213020
BioProject PRJNA258392

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE60486_normalized.txt.gz 53.7 Mb (ftp)(http) TXT
Processed data are available on Series record

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