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Sample GSM753454 Query DataSets for GSM753454
Status Public on Oct 15, 2011
Title IRF8 ChIP_LY1_promoter1
Sample type genomic
 
Channel 1
Source name IRF8 ChIP DNA from LY1
Organism Homo sapiens
Characteristics genotype/variation: IRF8 positive
antibody: anti-mouse IRF8 (Santa Cruz Biotechnology)
Treatment protocol no special treatment
Growth protocol RPMI medium supplemented with 200 U/ml penicillin G and 10% FCS
Extracted molecule genomic DNA
Extraction protocol cell lines were cross-linked with formaldehyde and the chromatin extracts were sonicated (Misonix Sonicater 3000). Following immunoprecipitation with anti-mouse IRF8 antibody (Santa Cruz Biotechnology), DNAs were purified from ChIP samples and input control samples. Purified DNAs were blunt ended, ligated with linkers and amplified by PCR.
Label Cy5
Label protocol Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension
 
Channel 2
Source name Input control DNA from LY1
Organism Homo sapiens
Characteristics genotype/variation: IRF8 positive
antibody: none (input)
Treatment protocol no special treatment
Growth protocol RPMI medium supplemented with 200 U/ml penicillin G and 10% FCS
Extracted molecule genomic DNA
Extraction protocol cell lines were cross-linked with formaldehyde and the chromatin extracts were sonicated (Misonix Sonicater 3000). Following immunoprecipitation with anti-mouse IRF8 antibody (Santa Cruz Biotechnology), DNAs were purified from ChIP samples and input control samples. Purified DNAs were blunt ended, ligated with linkers and amplified by PCR.
Label Cy3
Label protocol Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension
 
 
Hybridization protocol Standard Nimblegen hybridization kits and protocols were used
Scan protocol Arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols
Description comaprison of ChIP DNA with input DNA
Data processing Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction
 
Submission date Jul 01, 2011
Last update date Apr 28, 2014
Contact name Dong-Mi Shin
E-mail(s) shindm@snu.ac.kr
Organization name seoul national university
Street address 1 gwanak-ro
City Seoul
ZIP/Postal code 151742
Country South Korea
 
Platform ID GPL6325
Series (2)
GSE30357 Chip-chip from human diffuse large B cell lymphoma cell lines with IRF8
GSE30359 Transcriptional network governed by IRF8 and/or PU.1 in germinal center B cells

Data table header descriptions
ID_REF
VALUE scaled log2 ratios (Cy5/Cy3) by Nimblegen standard protocol

Data table
ID_REF VALUE
CHR10P001020948 -0.09
CHR10P001021048 -0.08
CHR10P001026162 0.37
CHR10P001022248 0.04
CHR10P001023448 -0.03
CHR10P001023148 0.14
CHR10P001026962 -0.5
CHR10P001021248 0.9
CHR10P001021748 0.03
CHR10P001024348 0.2
CHR10P001026062 0.71
CHR10P001021648 -0.39
CHR10P001023548 0.38
CHR10P001023248 -0.04
CHR10P001027262 0.14
CHR10P001022548 -0.23
CHR10P001025462 -0.07
CHR10P001026762 -0.34
CHR10P001027562 0.68
CHR10P001021348 0.66

Total number of rows: 378943

Table truncated, full table size 7909 Kbytes.




Supplementary file Size Download File type/resource
GSM753454_LY1_promoter1_Cy3.txt.gz 7.0 Mb (ftp)(http) TXT
GSM753454_LY1_promoter1_Cy5.txt.gz 7.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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