|
Status |
Public on Jul 08, 2010 |
Title |
SUZ12_siGFP_foreskin_1of2 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
siGFP foreskin fibroblasts, SUZ12 input
|
Organism |
Homo sapiens |
Characteristics |
cell line: ATCC CRL-2091 cell type: foreskin fibroblasts treatment: siGFP sample type: input antibody: none
|
Treatment protocol |
Human foreskin fibroblasts (ATCC CRL-2091) were transfected with siGFP or siHOTAIR for 72 hrs. The cells were harvested for ChIP.
|
Growth protocol |
DMEM.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP was performed on 4x10^6 fibroblast cells with rabbit anti-SUZ12 (ab12073, #7333337, Abcam) and rabbit anti-LSD1 (ab17721, #703277, Abcam) antibodies using the Farnham ChIP protocol. ChIP DNA and input DNA were reverse-crossed at 65C overnight, QIAquick column-purified, and amplified using the Sigma WGA2 kit for 1 round of amplification.
|
Label |
Cy3
|
Label protocol |
Input DNA was labeled with Cy3 and ChIP DNA was labeled with Cy5 using the Standard NimbleGen ChIP labeling protocol (1 ug of amplified ChIP DNA, direct incorporation of Cy-labeled primers with Klenow extension).
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|
|
Channel 2 |
Source name |
siGFP foreskin fibroblasts, SUZ12 ChIP
|
Organism |
Homo sapiens |
Characteristics |
cell line: ATCC CRL-2091 cell type: foreskin fibroblasts treatment: siGFP sample type: ChIP antibody: anti-SUZ12 antibody vendor: Abcam antibody catalog #: ab12073 antibody lot #: 7333337
|
Treatment protocol |
Human foreskin fibroblasts (ATCC CRL-2091) were transfected with siGFP or siHOTAIR for 72 hrs. The cells were harvested for ChIP.
|
Growth protocol |
DMEM.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP was performed on 4x10^6 fibroblast cells with rabbit anti-SUZ12 (ab12073, #7333337, Abcam) and rabbit anti-LSD1 (ab17721, #703277, Abcam) antibodies using the Farnham ChIP protocol. ChIP DNA and input DNA were reverse-crossed at 65C overnight, QIAquick column-purified, and amplified using the Sigma WGA2 kit for 1 round of amplification.
|
Label |
Cy5
|
Label protocol |
Input DNA was labeled with Cy3 and ChIP DNA was labeled with Cy5 using the 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. Hybridization was performed in the NimbleGen MAUI 12 bay machine.
|
Scan protocol |
Arrays were scanned with Axon scanner at 5 um resolution according to standard NimbleGen protocols.
|
Description |
SUZ12 ChIP vs. input in siGFP foreskin fibroblasts.
|
Data processing |
Arrays were processed using NimbleGen's standard protocol for Nimblescan 2.4 ChIP data extraction. Log2 ChIP/input ratios were created from the two raw pair files.
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|
|
Submission date |
Jun 14, 2010 |
Last update date |
Jul 11, 2010 |
Contact name |
Miao-Chih Tsai |
E-mail(s) |
miaochih@gmail.com
|
Organization name |
Stanford University
|
Street address |
269 Campus Drive, CCSR 2140
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL6325 |
Series (2) |
GSE22344 |
ChIP-chip of siGFP- or siHOTAIR-treated foreskin fibroblasts with anti-LSD1 or anti-SUZ12 antibodies on human HG18 Nimblegen promoter arrays |
GSE22345 |
Long noncoding RNA as modular scaffold of histone modification complexes |
|