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Sample GSM257594 Query DataSets for GSM257594
Status Public on Jul 28, 2008
Title UNC_lieb_cwhittle_N2_embryo_HTZ-1_CHIP3_array2
Sample type genomic
 
Channel 1
Source name gDNA from HTZ-1 ChIP in N2 embryos, labeled with Cy5.
Organism Caenorhabditis elegans
Characteristics Strain: N2
Stage: Mixed Embryos
Fix: 2% Formaldehyde, 30 minutes
Treatment protocol Embryos were prepared by bleaching from gravid N2 adults grown in S-basal media liquid culture. Live embryos were cross-linked using 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 15 minutes. Embryos were then washed twice with M9 Buffer and once by ChIP buffer. Pellets were frozen at -80C.
Growth protocol Standard C. elegans growth in liquid culture for N2 wildtype.
Extracted molecule genomic DNA
Extraction protocol Extracts were prepared by resuspending embryo pellets in 1 volume ChIP Buffer (50mM HEPES-KOH pH 7.5, 300mM NaCl, 1mM EDTA pH 8.0, 1% TritonX-100, 0.1% sodium deoxycholate, 10% glycerol, protease inhibitors (Calbiochem)), followed by dounce homogenization (50X) and sonication (4X, 1s on, 0.5s off, at 20% amplitude on ice) using a Branson Sonifier. In a volume of 500uL, 2mg extract was used for each ChIP with 5% taken as Input directly into 400uL elution buffer (0.1M NaHCO3, 1% SDS). 2-6ug antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were pulled down with 10uL protein-A or protein G sepharose (Amersham) and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer with 500mM or 1M NaCl, LiCl solution (10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA), and TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were treated with 20ug RNAse for 30 minutes at 37C. IP samples were eluted twice with 200uL elution buffer. 16ul NaCl (200mM final) was added to each sample and crosslinks were reversed by incubation overnight at 65C. DNA was cleaned up using Zymo (Zymo Research) DNA purification columns.
Label Cy5
Label protocol Samples were amplified and labeled using LM-PCR as described in Ercan et al. (2007) Nat Genet. 2007 Mar;39(3):403-8.
 
Channel 2
Source name Input gDNA from ChIP in N2 embryos, labeled with Cy3
Organism Caenorhabditis elegans
Characteristics Strain: N2
Stage: Mixed Embryos
Fix: 2% Formaldehyde, 30 minutes
Treatment protocol Embryos were prepared by bleaching from gravid N2 adults grown in S-basal media liquid culture. Live embryos were cross-linked using 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 15 minutes. Embryos were then washed twice with M9 Buffer and once by ChIP buffer. Pellets were frozen at -80C.
Growth protocol Standard C. elegans growth in liquid culture for N2 wildtype.
Extracted molecule genomic DNA
Extraction protocol Extracts were prepared by resuspending embryo pellets in 1 volume ChIP Buffer (50mM HEPES-KOH pH 7.5, 300mM NaCl, 1mM EDTA pH 8.0, 1% TritonX-100, 0.1% sodium deoxycholate, 10% glycerol, protease inhibitors (Calbiochem)), followed by dounce homogenization (50X) and sonication (4X, 1s on, 0.5s off, at 20% amplitude on ice) using a Branson Sonifier. In a volume of 500uL, 2mg extract was used for each ChIP with 5% taken as Input directly into 400uL elution buffer (0.1M NaHCO3, 1% SDS). 2-6ug antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were pulled down with 10uL protein-A or protein G sepharose (Amersham) and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer with 500mM or 1M NaCl, LiCl solution (10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA), and TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were treated with 20ug RNAse for 30 minutes at 37C. IP samples were eluted twice with 200uL elution buffer. 16ul NaCl (200mM final) was added to each sample and crosslinks were reversed by incubation overnight at 65C. DNA was cleaned up using Zymo (Zymo Research) DNA purification columns.
Label Cy3
Label protocol Samples were amplified and labeled using LM-PCR as described in Ercan et al. (2007) Nat Genet. 2007 Mar;39(3):403-8. PMID: 17293863
 
 
Hybridization protocol Samples were hybridized by Nimblegen Systems, Inc. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697
Scan protocol Samples were scanned by Nimblegen Systems, Inc. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697
Description NA
Data processing Data was normalized by median centering log2 ratios (IP/input). Log ratios from each experiment were converted to z-scores.
 
Submission date Jan 17, 2008
Last update date Jul 28, 2008
Contact name Christina M Whittle
E-mail(s) cwhittle@email.unc.edu
Phone 9198433229
Organization name University of North Carolina-Chapel Hill
Department Biology
Lab Jason Lieb
Street address 406 Fordham Hall, CB#3280
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL4619
Series (2)
GSE10201 ChIP-chip analysis of HTZ-1 and RNA Polymerase II in wildtype (N2) embryos
GSE26186 Broad chromosomal domains of histone modification patterns in C. elegans

Data table header descriptions
ID_REF
VALUE z-score of the median centered log2(ChIP/Input)

Data table
ID_REF VALUE
CHRIVP6157385 3.15
CHRIVP6157471 2.35
CHRIVP6157557 1.01
CHRIVP6157643 2.17
CHRIVP6157729 1.41
CHRIVP6157815 0.55
CHRIVP6157901 -0.09
CHRIVP6157987 0.31
CHRIVP6158073 0.58
CHRIVP6158159 0.67
CHRIVP6158245 0.03
CHRIVP6158331 0.74
CHRIVP6158417 -3.08
CHRIVP6158503 0.25
CHRIVP6158589 -0.49
CHRIVP6158675 0.16
CHRIVP6158761 1.41
CHRIVP6158847 -0.09
CHRIVP6158933 0.37
CHRIVP6159019 -0.18

Total number of rows: 577211

Table truncated, full table size 10864 Kbytes.




Supplementary file Size Download File type/resource
GSM257594_532.pair.gz 9.9 Mb (ftp)(http) PAIR
GSM257594_635.pair.gz 9.9 Mb (ftp)(http) PAIR
Processed data included within Sample table

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