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Sample GSM556174 Query DataSets for GSM556174
Status Public on Jul 08, 2010
Title LSD1_siGFP_foreskin_1of2
Sample type genomic
 
Channel 1
Source name siGFP foreskin fibroblasts, LSD1 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).
 
Channel 2
Source name siGFP foreskin fibroblasts, LSD1 ChIP
Organism Homo sapiens
Characteristics cell line: ATCC CRL-2091
cell type: foreskin fibroblasts
treatment: siGFP
sample type: ChIP
antibody: anti-LSD1
antibody vendor: Abcam
antibody catalog #: ab17721
antibody lot #: 703277
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 LSD1 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.
 
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

Data table header descriptions
ID_REF
VALUE Log2 ratio of ChIP/input

Data table
ID_REF VALUE
CHR10P001020948 0.38
CHR10P001021048 0.8
CHR10P001026162 -0.24
CHR10P001022248 -0.29
CHR10P001023448 1.14
CHR10P001023148 0.36
CHR10P001026962 -0.3
CHR10P001021248 -0.33
CHR10P001021748 -0.07
CHR10P001024348 0.33
CHR10P001026062 -0.71
CHR10P001021648 -0.34
CHR10P001023548 -0.18
CHR10P001023248 -0.06
CHR10P001027262 0.33
CHR10P001022548 0.28
CHR10P001025462 -0.22
CHR10P001026762 0.12
CHR10P001027562 -0.03
CHR10P001021348 -0.42

Total number of rows: 378943

Table truncated, full table size 7906 Kbytes.




Supplementary file Size Download File type/resource
GSM556174_179120_532.pair.gz 6.9 Mb (ftp)(http) PAIR
GSM556174_179120_635.pair.gz 6.9 Mb (ftp)(http) PAIR
GSM556174_179120_635_ratio.gff.gz 4.8 Mb (ftp)(http) GFF
Processed data included within Sample table
Processed data provided as supplementary file

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