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Sample GSM225140 Query DataSets for GSM225140
Status Public on Dec 01, 2008
Title YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 4 ENC842_hela_yy1_122204_660_600.gpr
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from HeLa Chromatin cells using YY1 antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from HeLa Chromatin cells using YY1 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 Chromatin cells
Organism Homo sapiens
Characteristics Input DNA from HeLa Chromatin 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 Aug 27, 2007
Last update date Aug 14, 2011
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)
GSE8887 Ludwig Institute/UCSD ENCODE project August 2007 Release

Data table header descriptions
ID_REF ID_REF
VALUE log ratio (F635/F532)
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

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
1 0.258 1.12 1.103e-01 1062.00 949.82 1118 1108 279 56 59 38 1070 1079 220 182 184 50 0
2 0.236 1.10 1.497e-01 893.00 810.77 952 936 317 59 62 41 936 942 298 178 180 49 0
3 0.108 1.01 4.673e-01 2223.00 2206.63 2282 2343 477 59 64 47 2237 2218 366 174 177 50 0
4 0.219 1.09 1.811e-01 996.00 915.59 1053 998 336 57 62 43 1033 996 289 177 181 50 0
5 0.218 1.09 1.815e-01 1141.00 1049.30 1198 1166 332 57 62 49 1163 1149 353 182 183 51 0
6 -0.040 0.91 8.533e-01 1140.00 1253.59 1195 1195 255 55 61 47 1355 1348 224 183 184 50 0
7 0.094 1.00 5.081e-01 1073.00 1074.97 1131 1144 261 58 62 40 1186 1183 236 181 184 51 0
8 0.184 1.06 2.564e-01 819.00 771.20 876 842 249 57 60 44 899 872 235 178 181 51 0
9 0.157 1.04 3.243e-01 854.00 819.33 910 923 229 56 59 38 943 935 189 177 180 51 0
10 0.160 1.04 3.147e-01 790.00 756.22 846 840 202 56 60 37 888 895 140 181 183 50 0
11 0.080 0.99 5.509e-01 1163.00 1176.58 1220 1239 299 57 60 40 1282 1271 275 182 184 49 0
12 0.186 1.06 2.500e-01 736.00 692.04 792 809 200 56 61 41 832 838 186 185 187 51 0
13 -0.067 0.89 8.962e-01 988.00 1107.06 1045 1072 198 57 60 38 1221 1216 187 186 185 50 0
14 0.089 0.99 5.252e-01 1874.00 1884.67 1931 1919 322 57 61 46 1947 1967 242 185 186 49 0
15 -0.163 0.84 9.754e-01 720.00 862.11 777 784 222 57 62 54 996 979 177 190 193 52 0
16 -0.121 0.86 9.511e-01 1281.00 1489.98 1339 1304 350 58 62 41 1583 1518 336 190 191 51 0
17 0.103 1.00 4.811e-01 970.00 965.87 1028 1022 197 58 61 41 1093 1086 154 190 193 52 0
18 0.052 0.97 6.343e-01 1763.00 1818.35 1822 1801 363 59 63 42 1889 1910 298 189 193 51 0
19 -0.082 0.88 9.153e-01 953.00 1079.25 1012 1008 215 59 65 47 1209 1193 193 200 203 52 0
20 0.102 1.00 4.840e-01 1782.00 1775.57 1841 1815 338 59 61 40 1861 1810 335 201 202 52 0

Total number of rows: 25246

Table truncated, full table size 2164 Kbytes.




Supplementary file Size Download File type/resource
GSM225140.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table

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