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Sample GSM171029 Query DataSets for GSM171029
Status Public on Mar 01, 2007
Title H2A.Z HeLa RenLab ENCODE PCR tiling array replicate 2 ENC1429
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from HeLa cells using H2A.Z antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from HeLa cells using H2A.Z antibody
Extracted molecule genomic DNA
Extraction protocol NimbleGen
Label Cy5
Label protocol Cy3 input Cy5 ChIP sample
 
Channel 2
Source name Input DNA from HeLa cells
Organism Homo sapiens
Characteristics Input DNA from HeLa cells
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 Feb 26, 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 -0.074 1.31 1.232e-01 3299.00 2515.85 3563 3775 1764 264 335 306 4554 4807 1696 1082 1105 355 0 -0.074
2 -0.038 1.34 9.993e-02 2898.00 2155.72 3176 3344 1366 278 348 313 4050 4193 1398 1075 1108 348 0 -0.038
3 -0.234 1.17 2.443e-01 6747.00 5750.51 7014 7141 3365 267 345 347 9006 9210 3888 1070 1098 354 0 -0.234
4 -0.264 1.15 2.636e-01 4266.00 3712.90 4522 4629 1538 256 332 320 6182 6083 1776 1058 1093 352 0 -0.264
5 -0.266 1.15 2.655e-01 4167.00 3630.30 4421 4670 1711 254 329 310 6054 6098 1608 1044 1062 346 0 -0.266
6 -0.184 1.22 1.825e-01 8070.00 6641.06 8330 8308 2621 260 340 323 10231 10158 1884 1066 1084 344 0 -0.184
7 -0.399 1.05 4.174e-01 4373.00 4178.10 4621 4822 1942 248 326 311 6847 6921 1541 1081 1097 351 0 -0.399
8 -0.497 0.98 5.404e-01 2674.00 2734.68 2928 3128 1278 254 332 316 4848 4895 1178 1074 1086 348 0 -0.497
9 -0.476 0.99 5.140e-01 3441.00 3467.26 3702 3813 1290 261 341 323 5868 5940 1315 1083 1104 348 0 -0.476
10 -0.266 1.15 2.637e-01 4056.00 3533.20 4325 4425 1508 269 350 334 5932 5996 1490 1056 1091 361 0 -0.266
11 -0.164 1.23 1.753e-01 5233.00 4249.84 5481 5540 2112 248 331 325 6948 6726 2219 1083 1099 353 0 -0.164
12 0.467 1.91 2.877e-03 10771.00 5646.89 11029 10563 3291 258 335 312 8883 8630 2889 1090 1106 357 0 0.467
13 -0.212 1.19 2.068e-01 6106.00 5125.90 6369 6320 1801 263 384 612 8156 8116 1473 1082 1128 552 0 -0.212
14 -0.108 1.28 1.244e-01 16235.00 12674.89 16517 16148 3501 282 362 403 18600 17859 4389 1108 1124 374 0 -0.108
15 -0.003 1.38 7.288e-02 5856.00 4253.46 6121 6266 2140 265 333 314 6986 6793 1350 1116 1123 358 0 -0.003
16 -0.361 1.07 3.678e-01 7378.00 6864.24 7649 7499 2555 271 353 340 10588 10518 1794 1115 1116 360 0 -0.361
17 0.817 2.43 1.264e-04 13460.00 5537.47 13744 13232 3049 284 360 336 8742 8789 1305 1100 1118 351 0 0.817
18 -0.394 1.05 4.092e-01 7170.00 6825.83 7445 7357 2395 275 349 322 10552 10493 2162 1132 1143 355 0 -0.394
19 -0.273 1.14 2.759e-01 5566.00 4873.01 5832 5809 2485 266 345 332 7882 7540 2535 1157 1187 375 0 -0.273
20 0.439 1.87 2.825e-03 30806.00 16470.40 31083 30315 6169 277 379 395 23877 23456 3753 1147 1179 371 0 0.439

Total number of rows: 25246

Table truncated, full table size 2697 Kbytes.




Supplementary file Size Download File type/resource
GSM171029.gpr.gz 2.4 Mb (ftp)(http) GPR

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