|
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 |
|