|
| Status |
Public on Apr 27, 2011 |
| Title |
N2_mixed_replica1 [ChIP03] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
LIN-54 ChIP DNA
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2 (Bristol)
antibody: LIN-54 antibody; non-commercial antibody raised in guinea pig, see Harrison et al. PNAS 2006
developmental stage: mixed staged worm culture
|
| Treatment protocol |
Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with anti-LIN-54 antibody.
|
| Growth protocol |
mixed stage wild-type worms were cultured in S-basal at 20oC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as described (Mukhopadhyay et al., Nat. Protocol., 2008). Briefly, mixed stage wild-type worms were cultured in S-basal at 20oC. Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with anti-LIN-54 antibody or pre-bleed antibody control. ChIP samples including the input were subjected to two rounds of linear amplification, using the genomePlex complete whole genome amplification kit (Sigma), and minimum difference between original precipitates and amplified precipitate confirmed by qPCR.
|
| Label |
Cy5
|
| Label protocol |
For each experiment, a control sample as well as an experimental sample were prepared with a concentration of ~250 ng/ul. At least 4 ug of each of these samples was then sent to Nimblegen where the samples were labeled with respectively Cy-3 and Cy-5 dyes using standard Nimblegen protocols.
|
| |
|
| Channel 2 |
| Source name |
input DNA from pre-bleed antibody control.
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2 (Bristol)
developmental stage: mixed staged worm culture
|
| Treatment protocol |
Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with pre-bleed antibody control.
|
| Growth protocol |
mixed stage wild-type worms were cultured in S-basal at 20oC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as described (Mukhopadhyay et al., Nat. Protocol., 2008). Briefly, mixed stage wild-type worms were cultured in S-basal at 20oC. Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with anti-LIN-54 antibody or pre-bleed antibody control. ChIP samples including the input were subjected to two rounds of linear amplification, using the genomePlex complete whole genome amplification kit (Sigma), and minimum difference between original precipitates and amplified precipitate confirmed by qPCR.
|
| Label |
Cy3
|
| Label protocol |
For each experiment, a control sample as well as an experimental sample were prepared with a concentration of ~250 ng/ul. At least 4 ug of each of these samples was then sent to Nimblegen where the samples were labeled with respectively Cy-3 and Cy-5 dyes using standard Nimblegen protocols.
|
| |
|
| |
| Hybridization protocol |
Samples were then hybridized on the Nimblegen C. elegans ChIP-chip 385K Whole-Genome Tiling - 3 Array Set (GPL7482, GPL7483, GPL7484) using standard Nimblegen protocols.
|
| Scan protocol |
Arrays were scanned on Nimblegen's 2-μm, high-resolution MS 200 Microarray Scanner. Data was extracted from the images at Roche NimbleGen, according to the protocol described NimbleScan v2.5 Software User's Guide, Version 2.5, October 2008.
|
| Description |
LIN-54 ChIP-chip on wild type worms (biological replica 1)
|
| Data processing |
Raw ChIP-chip data were retrieved from Nimblegen and analyzed using MA2C (Song et al., Genome Biol, 2007). MA2C analysis was performed with the following settings: # MA2C Score Method (median), Band Width (300), p-value cut off (-6), and other parameters were set as default. WS180 was used to annotate gene names. MA2C-defined LIN-54 ChIP peaks are listed in the file 'GSE28852_MA2C_processed_LIN-54_ChIP_peaks.txt'.
|
| |
|
| Submission date |
Apr 26, 2011 |
| Last update date |
Apr 27, 2011 |
| Contact name |
Kirsten Hagstrom |
| E-mail(s) |
kirsten.hagstrom@umassmed.edu
|
| Phone |
508-856-6843
|
| Fax |
508-856-8774
|
| Organization name |
University of Massachusetts, Medical School
|
| Department |
Molecular Medicine
|
| Lab |
Hagstrom Lab
|
| Street address |
377 Plantation street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL7484 |
| Series (2) |
| GSE28852 |
Chromosome-biased binding and gene reguation by the C. elegans DRM complex [ChIP-chip] |
| GSE28853 |
Chromosome-biased binding and gene regulation by the C. elegans DRM complex |
|
