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Sample GSM529552 Query DataSets for GSM529552
Status Public on Apr 01, 2010
Title FB-bCat-prom1-replicate1
Sample type genomic
 
Channel 1
Source name b-Catenin ChIP DNA from human fetal brain tissue
Organism Homo sapiens
Characteristics tissue: Brain
gender: Female
chip antibody: Anti-b-Catenin (Upstate cell signaling solutions, Catalog #06-734, Lot# 32480)
Extracted molecule genomic DNA
Extraction protocol Fetal brain tissue was chopped on a cold clean suface into small pieces and added to 10mls of Dulbecco's Eagle Medium. Formaldehyde was added at a final of 1%. Sample was rotated at room temperature for 15 minutes. Crosslinking stopped with glycine at a final concentration of 0.125M and rotated at room temperature for 5 minutes. Samples were centrifuged at 1,200rpm for 5 minutes and washes twice with cold 1X PBS. Tissues was disaggegrated with a dounce homogenizer and lysed with three different lysis buffers. Lysis buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100; fresh protease inhibitor cocktail mix 1:100) on ice for 10 minutes and centrifuged. Lysis buffer 2 (1mM EDTA, 0.5mM EGTA, 10mM Tris-HCl pH8, 200mM NaCl; fresh protease inhibitor cocktail mix 1:100) on ice for 10 minutes, rotated for 5 minutes, and centrifuged. Lysis buffer 3 (1mM EDTA, 0.5mM EGTA, 10mM Tris-HCl; fresh protease inhibitor cocktail mix 1:100) vortexed and pipetted sample. Crosslinked sample was sheared at average size of 500bp for 9 1/2 minutes, 30 second pulse on and 15 second pulse off at a 40% amplitude using a Sonicator. Lysate was centrifuged.
Label Cy5
Label protocol Label protocol according Nimblegen manufacturer protocol.
 
Channel 2
Source name Input DNA from human fetal brain tissue
Organism Homo sapiens
Characteristics tissue: Brain
Extracted molecule genomic DNA
Extraction protocol Fetal brain tissue was chopped on a cold clean suface into small pieces and added to 10mls of Dulbecco's Eagle Medium. Formaldehyde was added at a final of 1%. Sample was rotated at room temperature for 15 minutes. Crosslinking stopped with glycine at a final concentration of 0.125M and rotated at room temperature for 5 minutes. Samples were centrifuged at 1,200rpm for 5 minutes and washes twice with cold 1X PBS. Tissues was disaggegrated with a dounce homogenizer and lysed with three different lysis buffers. Lysis buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100; fresh protease inhibitor cocktail mix 1:100) on ice for 10 minutes and centrifuged. Lysis buffer 2 (1mM EDTA, 0.5mM EGTA, 10mM Tris-HCl pH8, 200mM NaCl; fresh protease inhibitor cocktail mix 1:100) on ice for 10 minutes, rotated for 5 minutes, and centrifuged. Lysis buffer 3 (1mM EDTA, 0.5mM EGTA, 10mM Tris-HCl; fresh protease inhibitor cocktail mix 1:100) vortexed and pipetted sample. Crosslinked sample was sheared at average size of 500bp for 9 1/2 minutes, 30 second pulse on and 15 second pulse off at a 40% amplitude using a Sonicator. Lysate was centrifuged.
Label Cy3
Label protocol Label protocol according Nimblegen manufacturer protocol.
 
 
Hybridization protocol Hybridize protocol according to Nimblegen manufacturer protocol.
Scan protocol Arrays were scanned on the Agilent Scanner according to manufacturer protocol.
Data processing Nimblescan 2.4 software was used for peak finding ('peaks_mapToFeatures.txt' supplementary files) and data processing was based on standard protocols. Values represent scaled log2 ratio, which is the ratio of the input signals for the experimental (IP) and control (input) samples co-hybridized to the array. The log2 ratio is computed and scaled to center the ratio data around zero. Centering is performed by subtracting the bi-weight mean for the log-ratio values for all features on the array from each log-ratio value.
 
Submission date Mar 31, 2010
Last update date Mar 31, 2010
Contact name Herb Lachman
E-mail(s) herb.lachman@einstein.yu.edu
Organization name Albert Einstein College of Medicine
Department Psychiatry
Lab Behavioral Genetics
Street address 1300 Morris Park Ave., F103
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
 
Platform ID GPL6325
Series (1)
GSE21151 ChIP-chip from fetal brain tissue with b-Catenin

Supplementary file Size Download File type/resource
GSM529552_221365_532.pair.gz 6.9 Mb (ftp)(http) PAIR
GSM529552_221365_635.pair.gz 6.9 Mb (ftp)(http) PAIR
GSM529552_221365_635_ratio_peaks.txt.gz 78.8 Kb (ftp)(http) TXT
Processed data provided as supplementary file

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