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Sample GSM171035 Query DataSets for GSM171035
Status Public on Mar 01, 2007
Title TAFII p250 (6B3) GM06990 RenLab ENCODE PCR tiling array replicate 2 ENC1527
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from GM06990 cells using TAFII p250 (6B3) antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from GM06990 cells using TAFII p250 (6B3) antibody
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM06990
Extracted molecule genomic DNA
Extraction protocol NimbleGen
Label Cy5
Label protocol Cy3 input Cy5 ChIP sample
 
Channel 2
Source name Input DNA from GM06990 cells
Organism Homo sapiens
Characteristics Input DNA from GM06990 cells
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM06990
Extracted molecule genomic DNA
Extraction protocol NimbleGen
Label Cy3
Label protocol Cy3 input Cy5 ChIP sample
 
 
Hybridization protocol NimbleGen
Scan protocol NimbleGen
Description ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.
Data processing raw data
 
Submission date Feb 23, 2007
Last update date Aug 28, 2007
Contact name Bing Ren
E-mail(s) biren@ucsd.edu
Organization name Ludwig Institute for Cancer Research
Department Department of Cellular and Molecular Medicine
Lab Laboratory of Gene Regulation
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093-0653
Country USA
 
Platform ID GPL1454
Series (1)
GSE7118 Ludwig Institute/UCSD ENCODE project March 2007 Release

Data table header descriptions
ID_REF ID_REF
VALUE same as UNF_VALUE but with flagged values removed
STATISTICS statistics
PVAL p-value
F635_INT F635 intensity with background intensity subtracted (normalized)
F532_INT F532 intensity with background intensity subtracted (normalized)
F635_MEDIAN F635 mdian intensity
F635_MEAN F635 mean intensity
F635_SD F635 standard deviation
B635_MEDIAN B635 median intensity
B635_MEAN B635 mean intensity
B635_SD B635 standard deviation
F532_MEDIAN F532 median intensity
F532_MEAN F532 mean intensity
F532_SD F532standard deviation
B532_MEDIAN B532 median intensity
B532_MEAN B532 mean intensity
B532_SD B532 standard deviation
FLAG flag from GenePro, 0 is useful
UNF_VALUE log ratio (F635/F532)

Data table
ID_REF VALUE STATISTICS PVAL F635_INT F532_INT F635_MEDIAN F635_MEAN F635_SD B635_MEDIAN B635_MEAN B635_SD F532_MEDIAN F532_MEAN F532_SD B532_MEDIAN B532_MEAN B532_SD FLAG UNF_VALUE
1 -0.619 0.80 8.013e-01 517.00 649.55 580 592 241 63 76 64 966 967 287 172 173 57 0 -0.619
2 -0.788 0.71 8.970e-01 462.00 652.82 526 535 214 64 76 61 969 968 291 171 172 57 0 -0.788
3 -1.026 0.60 9.690e-01 1304.00 2172.79 1370 1363 445 66 78 62 2827 2706 751 171 176 63 0 -1.026
4 -1.040 0.59 9.719e-01 865.00 1455.34 930 947 355 65 74 57 1951 1922 405 172 173 56 0 -1.040
5 -0.862 0.67 9.316e-01 924.00 1374.35 987 971 303 63 73 59 1850 1856 438 170 172 57 0 -0.862
6 -0.534 0.84 7.464e-01 1793.00 2124.52 1855 1816 468 62 74 59 2769 2735 438 172 174 57 0 -0.534
7 -0.957 0.63 9.566e-01 1005.00 1596.05 1068 1083 400 63 72 58 2122 2056 469 171 173 57 0 -0.957
8 -1.195 0.53 9.864e-01 407.00 762.44 469 478 211 62 72 56 1103 1092 278 171 173 57 0 -1.195
9 -1.021 0.60 9.676e-01 685.00 1137.11 748 777 308 63 74 60 1559 1569 368 169 171 54 0 -1.021
10 -1.164 0.55 9.848e-01 474.00 868.79 536 546 205 62 72 58 1230 1218 286 168 172 56 0 -1.164
11 -1.027 0.60 9.669e-01 763.00 1272.10 825 825 344 62 72 59 1723 1652 511 168 171 58 0 -1.027
12 -0.739 0.73 8.811e-01 1945.00 2655.45 2005 1954 653 60 70 57 3416 3189 837 170 173 57 0 -0.739
13 -0.615 0.80 8.074e-01 853.00 1068.40 917 923 316 64 74 59 1481 1477 226 175 178 58 0 -0.615
14 -0.215 1.05 4.183e-01 5178.00 4915.77 5244 5215 870 66 78 65 6188 6253 694 179 180 57 0 -0.215
15 -0.840 0.68 9.261e-01 733.00 1073.30 797 791 254 64 74 57 1489 1471 237 177 179 58 0 -0.840
16 -0.850 0.68 9.295e-01 1091.00 1608.32 1155 1156 360 64 74 57 2140 2115 366 174 176 57 0 -0.850
17 -0.923 0.64 9.501e-01 569.00 882.70 634 650 232 65 75 58 1255 1250 191 176 177 58 0 -0.923
18 -0.731 0.74 8.810e-01 2247.00 3051.39 2310 2344 621 63 75 62 3909 4020 632 179 182 61 0 -0.731
19 1.22 4.386e-01 10.00 8.18 63 71 55 63 72 55 175 176 56 182 185 59 -50 0
20 -0.286 1.00 4.961e-01 7171.00 7153.18 7235 7072 1615 64 75 58 8928 8682 1489 184 186 59 0 -0.286

Total number of rows: 25246

Table truncated, full table size 2386 Kbytes.




Supplementary file Size Download File type/resource
GSM171035.gpr.gz 2.0 Mb (ftp)(http) GPR

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