title: AB2886_H3K79ME1361912_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: WA305-34819 H3K4me3;target name: H3K4me3;host: Mouse;antigen: ART(me3-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA305-34819;short description: A protein G purified mouse monoclonal antibody to H3K3me3 (cat #305-34819) obtained from Waco. Used for ChIP.;


title: AB1791_H3_N2_L3 Hyb1 extraction1_array1

status: Public on Jul 07 2010

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: C. elegans  AB1791 H3 rabbit polyclonal antibody;target name: Histone H3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 100 to the C-terminus of Human Histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB1791;short description: An affinity purified rabbit polyclonal antibody to H3 obtained from Abcam (H3-AB1791);used for ChIP.;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v2. Array scanning and raw data extraction were performed according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software v2.5 according to the NimbleScan User?s Guide.

data_processing:
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180

label: Cy3 dye

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AB1791 H3 rabbit polyclonal antibody (target is Histone H3);Strain N2 extraction1_array1 channel_1

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
Worm_LM-PCR_Amplification_for_ChIP-chip_vIL1. 1/3 of ChIP and 10ng of input are blunted (T4 polymerase), ligated (concentrated T4 ligase) to annealed linkers and amplified by PCR using longer oligonucleotide as a primer. Generally two rounds of amplification are used to get the amount needed for microarray. Amplified DNA is tested by q-PCR and DNA gel is run to ensure small size and lack of degradation.

tag: strain

tag: developmental stage

value: L3 Larva

tag: genotype

value: wild type

tag: sex

value: mixed Male and Hermaphrodite population

label: Cy5 dye

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AB1791 H3 rabbit polyclonal antibody (target is Histone H3);Strain N2 extraction1_array1 channel_2


title: AB3594_H3K79ME2346021_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: AB3594 H3K79me2:346021;target name: H3K79me2;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 di methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab3594;reference: http://www.abcam.com/Histone-H3-di-methyl-K79-antibody-ChIP-Grade-ab3594.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide di-methylated at K79.;

data_processing:
ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS180

label_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

growth_protocol: Worm_embryo_growth_and_harvest_vSS4. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.

value: Early Embryo


title: AB8895_H3K4ME1733246_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab8895 H3K4me1:733246;target name: H3K4me1;host: Rabbit;antigen: Peptide including dimethyl-lysine 9 of histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8895;short description: A rabbit affinity purified antibody to H3K4me1 from Abcam (ab8895 lot #733246). Used for ChIP.;
channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.


title: AR0144_H3144_N2_L3_LM Hyb1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: C. elegans  AR0144 H3 rabbit serum;target name: histone H3;host: Rabbit;antigen: C-terminal peptide of histone H3;clonal: Polyclonal;purified: Crude;company: Lake Placid Bio;catalog: AR-0144;short description: Rabbit serum to Histone H3 (lot# 144) obtained from LP Bio. Used for ChIP;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0144 H3 rabbit serum (target is histone H3);Strain N2 extraction1_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0144 H3 rabbit serum (target is histone H3);Strain N2 extraction1_array1 channel_2


title: HK00008_H3K9ME26D11_N2_L3 Hyb2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HK00008 H3K9me2:6D11;target name: H3K9me2;host: Mouse;antigen: ARTKQTAR(me2-K)STGGKAPRKQC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00008;short description: A protein G purified mouse monoclonal antibody to H3K9me2 (clone 6D11) obtained from Hiroshi Kimura. Used for ChIP.;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00008 H3K9me2:6D11 (target is H3K9me2);Strain N2 extraction2_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00008 H3K9me2:6D11 (target is H3K9me2);Strain N2 extraction2_array1 channel_2


title: AB1791_H3_N2_L3 Hyb2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: C. elegans  AB1791 H3 rabbit polyclonal antibody;target name: Histone H3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 100 to the C-terminus of Human Histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB1791;short description: An affinity purified rabbit polyclonal antibody to H3 obtained from Abcam (H3-AB1791);used for ChIP.;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AB1791 H3 rabbit polyclonal antibody (target is Histone H3);Strain N2 extraction2_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AB1791 H3 rabbit polyclonal antibody (target is Histone H3);Strain N2 extraction2_array1 channel_2


title: AR0144_H3144_N2_L3 Hyb2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: C. elegans  AR0144 H3 rabbit serum;target name: histone H3;host: Rabbit;antigen: C-terminal peptide of histone H3;clonal: Polyclonal;purified: Crude;company: Lake Placid Bio;catalog: AR-0144;short description: Rabbit serum to Histone H3 (lot# 144) obtained from LP Bio. Used for ChIP;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0144 H3 rabbit serum (target is histone H3);Strain N2 extraction2_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0144 H3 rabbit serum (target is histone H3);Strain N2 extraction2_array1 channel_2


title: AR0144_H3144_N2_L3 Hyb1 extraction1_array1


title: WA30834809_H3K4ME2_N2_L3 Hyb1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: WA308-34809 H3K4me2;target name: H3K4me2;host: Mouse;antigen: ART(me2-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA308-34809;short description: A protein G purified mouse monoclonal antibody to H3K4me2 (cat #308-34809) obtained from Waco. Used for ChIP.;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody WA308-34809 H3K4me2 (target is H3K4me2);Strain N2 extraction1_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody WA308-34809 H3K4me2 (target is H3K4me2);Strain N2 extraction1_array1 channel_2


title: WA30834809_H3K4ME2_N2_L3 Hyb2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: WA308-34809 H3K4me2;target name: H3K4me2;host: Mouse;antigen: ART(me2-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA308-34809;short description: A protein G purified mouse monoclonal antibody to H3K4me2 (cat #308-34809) obtained from Waco. Used for ChIP.;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody WA308-34809 H3K4me2 (target is H3K4me2);Strain N2 extraction2_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody WA308-34809 H3K4me2 (target is H3K4me2);Strain N2 extraction2_array1 channel_2


title: HK00008_H3K9ME26D11_N2_L3 Hyb1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: HK00008 H3K9me2:6D11;target name: H3K9me2;host: Mouse;antigen: ARTKQTAR(me2-K)STGGKAPRKQC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00008;short description: A protein G purified mouse monoclonal antibody to H3K9me2 (clone 6D11) obtained from Hiroshi Kimura. Used for ChIP.;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00008 H3K9me2:6D11 (target is H3K9me2);Strain N2 extraction1_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00008 H3K9me2:6D11 (target is H3K9me2);Strain N2 extraction1_array1 channel_2


title: HK00001_H3K36ME313C9_N2_L3 Hyb2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura. Used for ChIP.;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00001 H3K36me3:13C9 (target is H3K36me3);Strain N2 extraction2_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00001 H3K36me3:13C9 (target is H3K36me3);Strain N2 extraction2_array1 channel_2


title: HK00013_H3K27ME31E7_N2_L3 Hyb2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HK00013 H3K27me3:1E7:JL:1;target name: H3K27me3;host: Mouse;antigen: KQLATKAAR(me3-K)SAPATGGVKC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00013;short description: A protein G purified mouse monocloonal antibody agsinst H3K27me3.  Used for ChIP;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00013 H3K27me3:1E7:JL:1 (target is H3K27me3);Strain N2 extraction2_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00013 H3K27me3:1E7:JL:1 (target is H3K27me3);Strain N2 extraction2_array1 channel_2


title: HK00001_H3K36ME313C9_N2_L3 Hyb1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura. Used for ChIP.;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00001 H3K36me3:13C9 (target is H3K36me3);Strain N2 extraction1_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00001 H3K36me3:13C9 (target is H3K36me3);Strain N2 extraction1_array1 channel_2


title: AR0144_H3144_N2_L3_LM Hyb2 extraction2_array1


title: AR0144_H3144_N2_L3_LM Hyb3 extraction3_array1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0144 H3 rabbit serum (target is histone H3);Strain N2 extraction3_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0144 H3 rabbit serum (target is histone H3);Strain N2 extraction3_array1 channel_2


title: HK00013_H3K27ME31E7_N2_L3 Hyb1 extraction1_array1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00013 H3K27me3:1E7:JL:1 (target is H3K27me3);Strain N2 extraction1_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00013 H3K27me3:1E7:JL:1 (target is H3K27me3);Strain N2 extraction1_array1 channel_2


title: HK00012_H3K36ME22C3_N2_L3 Hyb1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HK00012 H3K36me2:2C3;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me2-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00012;short description: A protein G purified mouse monoclonal antibody to H3K36me2 (clone 2C3) obtained from Hiroshi Kimura. Used for ChIP.;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00012 H3K36me2:2C3 (target is H3K36me3);Strain N2 extraction1_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00012 H3K36me2:2C3 (target is H3K36me3);Strain N2 extraction1_array1 channel_2


title: HK00012_H3K36ME22C3_N2_L3 Hyb2 extraction2_array1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00012 H3K36me2:2C3 (target is H3K36me3);Strain N2 extraction2_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody HK00012 H3K36me2:2C3 (target is H3K36me3);Strain N2 extraction2_array1 channel_2


title: SS00050_IGG_N2_EEMB_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: C. elegans  SS00050 IGG rabbit polyclonal antibody;target name: na;host: Rabbit;antigen: na;clonal: Polyclonal;purified: Crude;company: Other;catalog: SS00050 IGG;short description: Rabbit pre-immune serum;

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

growth_protocol: Worm_embryo_growth_and_harvest_vSS3. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85 % formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vPK1. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored in -20°C for future applications.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.


title: HK00009_H3K9ME32F3_N2_L3 Hyb1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: HK00009 H3K9me3:2F3;target name: H3K9me3;host: Mouse;antigen: ARTKQTAR(me3-K)STGGKAPRKQC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00009;short description: A protein G purified mouse monoclonal antibody to H3K9me3 (clone 2F3) obtained from Hiroshi Kimura. Used for ChIP.;

source_name: Strain N2;temperature 20;Antibody HK00009 H3K9me3:2F3 (target is H3K9me3);Developmental Stage L3 Larva extraction1_array1 channel_1

source_name: Strain N2;temperature 20;Antibody HK00009 H3K9me3:2F3 (target is H3K9me3);Developmental Stage L3 Larva extraction1_array1 channel_2


title: AB2886_H3K79ME1361912_N2_EEMB_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: WA305-34819 H3K4me3;target name: H3K4me3;host: Mouse;antigen: ART(me3-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA305-34819;short description: A protein G purified mouse monoclonal antibody to H3K3me3 (cat #305-34819) obtained from Waco. Used for ChIP.;


title: HK00009_H3K9ME32F3_N2_L3 Hyb2 extraction2_array1

source_name: Strain N2;temperature 20;Antibody HK00009 H3K9me3:2F3 (target is H3K9me3);Developmental Stage L3 Larva extraction2_array1 channel_1

source_name: Strain N2;temperature 20;Antibody HK00009 H3K9me3:2F3 (target is H3K9me3);Developmental Stage L3 Larva extraction2_array1 channel_2


title: SS00050_IGG_N2_EEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: C. elegans  SS00050 IGG rabbit polyclonal antibody;target name: na;host: Rabbit;antigen: na;clonal: Polyclonal;purified: Crude;company: Other;catalog: SS00050 IGG;short description: Rabbit pre-immune serum;
channel ch2 is input DNA;

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS2. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo purification kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.


title: SDQ0790_MRG1_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ0790 MRG1;target name: MRG1;host: Rabbit;antigen: YKFERPQYNDLVKKRAMEKGIDITNPTALQDSGFRPSQEYGIVHFLRMLAKLPDYLKLTQWNDHVINRIMIGVHDLIVFLNKNHGKYYRGSSDYQGASND;clonal: Polyclonal;purified: Crude;company: SDI;catalog: SDQ0790;short description: Crude rabbit serum to MRG-1 raised against AA220-319 obtained from SDI (MRG1-Q0790);

growth_protocol: Worm_embryo_growth_and_harvest_vSS2. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at ?80°C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS1. Protein A or G-coupled Dynal magnetic beads from 20 ul of slurry were washed 3 times in 1ml of 5mg/ml IgG-Free BSA in PBS (wash buffer). Beads were resuspended in 100ul of the wash buffer and rotated with 5ug of the appropriate antibody overnight at 4 oC. Beads were further washed 2 times in the wash buffer and resuspended in 30ul of the wash buffer. Before beginning IP, 5% of starting material of protein (3-6mg) was saved as "input" at -20 oC. The antibody-conjugated Dynal beads were mixed with 3-6mg of protein and nutated for 2hrs at 4 oC. After washing the beads, captured proteins were eluted by incubating beads in 300 ul of TE with 1% SDS and 250mM NaCl for 2 times 15 minutes at 65 oC. Samples were treated with proteinase K and reverse-crosslinked at 65 oC overnight. DNA was purified using Zymo DNA purification column and eluted in in 43ul dH2O. RNA was digest for 1 hour at 37 oC with RNase One (Promega). For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn:  http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.


title: SDQ0791_MES4_N2_EEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ0791 MES4;target name: MES4;host: Rabbit;antigen: GTASKKSEISPSKPSTSSASSTSFVQQASWPISQNKKNLKKNSNQPVADTGSTLSTSTELNFHEKPQELLSPVSSRSRAASSSTPRAQKSKSRRDDVESE;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ0791;short description: An affinity purified rabbit polyclonal antibody raised against AA 729-828 to MES-4 obtained from SDI (MES4-Q0791); used for ChIP;
channel ch2 is input DNA;


title: JL00001_DPY27_YPT41_MXEMB_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: JL00001 DPY27;target name: DPY-27;host: Mouse;antigen: 1-409;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: JL00001 DPY27;reference: PMID: 17293863;short description: *  recombinant proteins were cloned and expressed with Novagen's Pet30-EkLIC system
* rabbit polyclonal antibodies were produced at Covance Immunology Services
* DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.;

growth_protocol: Worm_embryo_growth_and_harvest_vSE1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature. Embryos were then washed once with 100 mM Tris, twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_v1. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 7 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

value: Mixed Embryo


title: JL00001_DPY27_YPT41_MXEMB_1 extraction1_array1


title: NA_N2_EEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: No Antibody Control;target name: Not Applicable;host: None-Control;antigen: NONE;clonal: None-Control;purified: None-Control;company: None-Control;catalog: Not Applicable;reference: Not Applicable;short description: Specific Antibodies were omitted from this immunoprecipitation reaction (as a negative control).;
channel ch2 is input DNA;

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS1. Protein A or G-coupled Dynal magnetic beads from 20 ul of slurry were washed 3 times in 1ml of 5mg/ml IgG-Free BSA in PBS (wash buffer). Beads were resuspended in 100?l of the wash buffer and rotated with 5?g of the appropriate antibody overnight at 4°C. Beads were further washed 2 times in the wash buffer and resuspended in 30?l of the wash buffer. Before beginning IP, 5% of starting material of protein (3-6mg) was saved as "input" at -20°C. The antibody-conjugated Dynal beads were mixed with 3-6mg of protein and nutated for 2hrs at 4°C. After washing the beads, captured proteins were eluted by incubating beads in 300 ?l of TE with 1% SDS and 250mM NaCl for 2 times 15 minutes at 65°C. Samples were treated with proteinase K and reverse-crosslinked at 65°C overnight. DNA was purified using Zymo DNA purification column and eluted in in 43?l dH2O. RNA was digest for 1 hour at 37°C with RNase One (Promega). For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn:  http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.


title: NA_N2_EEMB_2 extraction2_array1


title: AB8898_H3K9ME3339901_N2_EEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: AB8898 H3K9ME3:339901;target name: H3K9me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of human histone H3 tri methylated at K9.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB8898;short description: An affinity purified rabbit polyclonal antibody to H3K9me3 (lot# 339901) obtained from Abcam. Used for ChIP.;
channel ch2 is input DNA;


title: JL00001_DPY27_11DH_MXEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JL00001 DPY27;target name: DPY-27;host: Mouse;antigen: 1-409;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: JL00001 DPY27;reference: PMID: 17293863;short description: *  recombinant proteins were cloned and expressed with Novagen's Pet30-EkLIC system
* rabbit polyclonal antibodies were produced at Covance Immunology Services
* DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.;
channel ch2 is input DNA;


title: JL00001_DPY27_11DH_MXEMB_1 extraction1_array1


title: AB9049_H3K36ME2608457_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: AB9049 H3K36me2:608457;target name: H3K36me2;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of Human Histone H3.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB9049;short description: An affinity purified rabbit polyclonal antibody to H3K36me2 (lot# 608457) obtained from Abcam. Used for ChIP.;


title: ABAB817_8WG16_N2_EEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ABAB817 8WG16;target name: RNA polII CTD domain unphosophorylated;host: Mouse;antigen: Native RNA Polymerase II purified from wheat germ;clonal: Monoclonal;purified: Size;company: Covance;catalog: Covance (MMS126R);short description: A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP.;
channel ch2 is input DNA;


title: AB1791_H3609253_N2_EEMB_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: C. elegans  AB1791 H3 rabbit polyclonal antibody;target name: Histone H3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 100 to the C-terminus of Human Histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB1791;short description: An affinity purified rabbit polyclonal antibody to H3 obtained from Abcam (H3-AB1791);used for ChIP.;
channel ch2 is input DNA;


title: JL00012_DPY28_N2_MXemb_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: JL00012 DPY28;target name: DPY-28;host: Rabbit;antigen: 1481-1499 CKSAVADDDSDSDEFMLDD;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Kirsten Hagstrom;short description: Antibody was donated by Kirsten Hagstrom.;

growth_protocol: Worm_embryo_growth_and_harvest_v3. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.


title: AR0144_H3144_N2_EEMB_3 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: C. elegans  AR0144 H3 rabbit serum;target name: histone H3;host: Rabbit;antigen: C-terminal peptide of histone H3;clonal: Polyclonal;purified: Crude;company: Lake Placid Bio;catalog: AR-0144;short description: Rabbit serum to Histone H3 (lot# 144) obtained from LP Bio. Used for ChIP;
channel ch2 is input DNA;


title: JL00001_DPY27_N2_L4_3 extraction4_array1

growth_protocol: Worm_L4_growth_and_harvest_vSE1.doc. Worms were grown in standard S-basal media liquid culture. The culture was synchronized by starving hatched embryos at L1 stage and grown at 20C in liquid culture until they reach L4 stage. Worms were collected over 34 uM Nitex membrane, and washed with M9 Buffer + protease inhibitors (Calbiochem). Worms were resuspended in 1 pellet volume of M9, frozen as ?popcorn? in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_germlineless_adult_soma_extract_v2.2. Frozen worms were ground to a powder using mortar and pestle. Worm powder was diluted in M9 + 1% formaldehyde+1mM PMSF and fixed 5 or 10 minutes. Fixing was quenched by the addition of 125 mM glycine for 5 minutes. Cells were collected by centrifuging 5 minutes at 4000 g at 4C. Samples were washed and resuspended in FA Buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and 10 mgs were used per ChIP.
Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

value: L4 Larva


title: JL00001_DPY27_N2_L4_2B extraction3_array1


title: JL00001_DPY27_N2_L4_2A extraction2_array1


title: AR0144_H3144_N2_EEMB_2 extraction2_array1

growth_protocol: Worm_embryo_growth_and_harvest_vSS6. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Embryos were then washed once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.


title: AR0144_H3144_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: C. elegans  AR0144 H3 rabbit serum;target name: histone H3;host: Rabbit;antigen: C-terminal peptide of histone H3;clonal: Polyclonal;purified: Crude;company: Lake Placid Bio;catalog: AR-0144;short description: Rabbit serum to Histone H3 (lot# 144) obtained from LP Bio. Used for ChIP;


title: WA30534819_H3K4ME3_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: WA305-34819 H3K4me3;target name: H3K4me3;host: Mouse;antigen: ART(me3-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA305-34819;short description: A protein G purified mouse monoclonal antibody to H3K3me3 (cat #305-34819) obtained from Waco. Used for ChIP.;
channel ch2 is input DNA;


title: WA30534819_H3K4ME3_N2_EEMB_1 extraction1_array1


title: HK00009_H3K9ME32F3_N2_EEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HK00009 H3K9me3:2F3;target name: H3K9me3;host: Mouse;antigen: ARTKQTAR(me3-K)STGGKAPRKQC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00009;short description: A protein G purified mouse monoclonal antibody to H3K9me3 (clone 2F3) obtained from Hiroshi Kimura. Used for ChIP.;
channel ch2 is input DNA;


title: JL00001_DPY27_N2_MXEMB_1_A extraction1_array1

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol:
Worm_embryo_extraction_v3. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_vKI1. ChIP or input DNA was incubated with T4-DNA polymerase followed by T4-polynucleotide kinase to ensure 5?-phospho and 3?-hydroxyl blunt ends. The DNA fragments were ligated to the double-strand DNA linker with 5?-phosphate and then amplified by using primer corresponding to the linker sequences.


title: HK00009_H3K9ME32F3_N2_EEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: HK00009 H3K9me3:2F3;target name: H3K9me3;host: Mouse;antigen: ARTKQTAR(me3-K)STGGKAPRKQC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00009;short description: A protein G purified mouse monoclonal antibody to H3K9me3 (clone 2F3) obtained from Hiroshi Kimura. Used for ChIP.;


title: JL00002_SDC3_N2_MXEMB_1_B extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: JL00002 SDC3;target name: SDC-3;host: Rabbit;antigen: 1067-1340;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: JL00002 SDC3;reference: PMID: 17293863;

growth_protocol: Worm_embryo_growth_and_harvest_v1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C.

extract_protocol:
Worm_embryo_extraction_v1. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 7 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit.
Worm_Whole_Genome_Amplification_for_ChIP-chip_v2. Samples were amplified using a modified Whole Genome Amplification Kit protocol (Sigma).


title: HK00001_H3K36ME313C9_N2_EEMB_4 extraction3_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura. Used for ChIP.;


title: HK00001_H3K36ME313C9_N2_EEMB_1 extraction1_array1


title: HK00001_H3K36ME313C9_N2_EEMB_3 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura. Used for ChIP.;
channel ch2 is input DNA;


title: SDQ0791_MES4_N2_EEMB_3 extraction3_array3

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ0791 MES4;target name: MES4;host: Rabbit;antigen: GTASKKSEISPSKPSTSSASSTSFVQQASWPISQNKKNLKKNSNQPVADTGSTLSTSTELNFHEKPQELLSPVSSRSRAASSSTPRAQKSKSRRDDVESE;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ0791;short description: An affinity purified rabbit polyclonal antibody raised against AA 729-828 to MES-4 obtained from SDI (MES4-Q0791); used for ChIP;

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.


title: JL00005_SDC2_N2_MXemb_3 extraction3_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: JL0005 SDC2;target name: SDC-2;host: Rabbit;antigen: 1-455;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: Jason Lieb;short description: Recombinant protein was cloned and expressed with Novagen's Pet30-EkLIC system. Rabbit polyclonal antibodies were produced at Covance Immunology Services. DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.;

extract_protocol:
Worm_embryo_extraction_vSE1. Embryos were resuspended in FA buffer and dounced 30 times (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.


title: AB1791_H3609253_N2_EEMB_2 extraction2_array1


title: UP07442_H3K9ME3_N2_L3 Hyb2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: C. elegans  UP07442 H3K9ME3 rabbit polyclonal antibody;target name: Trimethylated Lys-9 on histone H3;host: Rabbit;antigen: synthetic 2X-branched peptide containing the sequence AR[me3K]ST in which me3K corresponds to trimethyl-lysine at residue 9 of human Histone H3;clonal: Polyclonal;purified: Protein A/G;company: Upstate;catalog: UP07442;short description: A protein A purified rabbit polyclonal antibody to H3K9me3 obtained from Upstate (H3K9me3-07442);used for ChIP.;

data_processing:
ChIP-chip normalization standard MA2C:JL:1 protocol. ChIP-chip_normalization_standard_MA2C_v1. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means the INPUT or IP values for any probes who have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS180    Processed data are obtained using following parameters: win_size is 500
ChIP-chip normalization standard MA2C:JL:1 protocol. ChIP-chip_normalization_standard_MA2C_v1. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means the INPUT or IP values for any probes who have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS180    Processed data are obtained using following parameters: win_size is 500

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  UP07442 H3K9ME3 rabbit polyclonal antibody (target is Trimethylated Lys-9 on histone H3);Strain N2 extraction2_array1 channel_1

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vPK1. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored in -20°C for future applications.
Worm_LM-PCR_Amplification_for_ChIP-chip_vPK1. 1/3 of ChIP and 10ng of input are blunted (T4 polymerase), ligated (concentrated T4 ligase) to annealed linkers and amplified by PCR using longer oligonucleotide as a primer. Generally two rounds of amplification are used to get the amount needed for microarray. Amplified DNA is tested by q-PCR and DNA gel is run to ensure small size and lack of degradation.

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  UP07442 H3K9ME3 rabbit polyclonal antibody (target is Trimethylated Lys-9 on histone H3);Strain N2 extraction2_array1 channel_2


title: JL00002_SDC3_N2_MXEMB_1_A extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JL00002 SDC3;target name: SDC-3;host: Rabbit;antigen: 1067-1340;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: JL00002 SDC3;reference: PMID: 17293863;
channel ch2 is input DNA;

extract_protocol:
Worm_embryo_extraction_v1. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 7 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_v1. 2mg extract was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 uL IgG dynabeads (Dyna), captured using a magnetic holder, and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
Worm_Whole_Genome_Amplification_for_ChIP-chip_v2. Samples were amplified using a modified Whole Genome Amplification Kit protocol (Sigma).


title: JL00005_SDC2_N2_MXemb_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JL0005 SDC2;target name: SDC-2;host: Rabbit;antigen: 1-455;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: Jason Lieb;short description: Recombinant protein was cloned and expressed with Novagen's Pet30-EkLIC system. Rabbit polyclonal antibodies were produced at Covance Immunology Services. DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.;
channel ch2 is input DNA;


title: JL00005_SDC2_N2_MXemb_1 extraction1_array1


title: SDQ0790_MRG1_N2_EEMB_3 extraction3_array3

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ0790 MRG1;target name: MRG1;host: Rabbit;antigen: YKFERPQYNDLVKKRAMEKGIDITNPTALQDSGFRPSQEYGIVHFLRMLAKLPDYLKLTQWNDHVINRIMIGVHDLIVFLNKNHGKYYRGSSDYQGASND;clonal: Polyclonal;purified: Crude;company: SDI;catalog: SDQ0790;short description: Crude rabbit serum to MRG-1 raised against AA220-319 obtained from SDI (MRG1-Q0790);
channel ch2 is input DNA;


title: UP07442_H3K9ME3_N2_L3 Hyb3 extraction3_array1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  UP07442 H3K9ME3 rabbit polyclonal antibody (target is Trimethylated Lys-9 on histone H3);Strain N2 extraction3_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  UP07442 H3K9ME3 rabbit polyclonal antibody (target is Trimethylated Lys-9 on histone H3);Strain N2 extraction3_array1 channel_2


title: HK00012_H3K36ME22C3_N2_EEMB_1 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HK00012 H3K36me2:2C3;target name: H3K36me2;host: Mouse;antigen: KSAPATGGV(me2-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00012;short description: A protein G purified mouse monoclonal antibody to H3K36me2 (clone 2C3) obtained from Hiroshi Kimura. Used for ChIP.;


title: UP07442_H3K9ME3_N2_L3 Hyb1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: C. elegans  UP07442 H3K9ME3 rabbit polyclonal antibody;target name: Trimethylated Lys-9 on histone H3;host: Rabbit;antigen: synthetic 2X-branched peptide containing the sequence AR[me3K]ST in which me3K corresponds to trimethyl-lysine at residue 9 of human Histone H3;clonal: Polyclonal;purified: Protein A/G;company: Upstate;catalog: UP07442;short description: A protein A purified rabbit polyclonal antibody to H3K9me3 obtained from Upstate (H3K9me3-07442);used for ChIP.;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  UP07442 H3K9ME3 rabbit polyclonal antibody (target is Trimethylated Lys-9 on histone H3);Strain N2 extraction1_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  UP07442 H3K9ME3 rabbit polyclonal antibody (target is Trimethylated Lys-9 on histone H3);Strain N2 extraction1_array1 channel_2


title: JA00002_IGG_N2_L3 Hyb2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: C. elegans  JA00002 IGG rabbit polyclonal antibody;target name: na;host: Rabbit;antigen: na;clonal: Polyclonal;purified: Protein A/G;company: Other;catalog: JA00002 IGG;short description: A protein A purified rabbit polyclonal antibody preimmune from rabbit GB01257 (24/Sep/2001) was used for ChIP.;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  JA00002 IGG rabbit polyclonal antibody (target is na);Strain N2 extraction2_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  JA00002 IGG rabbit polyclonal antibody (target is na);Strain N2 extraction2_array1 channel_2


title: JL00001_DPY27_N2_L4_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: JL00001 DPY27;target name: DPY-27;host: Mouse;antigen: 1-409;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: JL00001 DPY27;reference: PMID: 17293863;short description: *  recombinant proteins were cloned and expressed with Novagen's Pet30-EkLIC system
* rabbit polyclonal antibodies were produced at Covance Immunology Services
* DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.;


title: ABAB817_8WG16_N2_EEMB_3_OID18184 extraction3_array3

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ABAB817 8WG16;target name: RNA polII CTD domain unphosophorylated;host: Mouse;antigen: Native RNA Polymerase II purified from wheat germ;clonal: Monoclonal;purified: Size;company: Covance;catalog: Covance (MMS126R);short description: A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP.;


title: JA00002_IGG_N2_L3 Hyb3 extraction3_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: C. elegans  JA00002 IGG rabbit polyclonal antibody;target name: na;host: Rabbit;antigen: na;clonal: Polyclonal;purified: Protein A/G;company: Other;catalog: JA00002 IGG;short description: A protein A purified rabbit polyclonal antibody preimmune from rabbit GB01257 (24/Sep/2001) was used for ChIP.;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  JA00002 IGG rabbit polyclonal antibody (target is na);Strain N2 extraction3_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  JA00002 IGG rabbit polyclonal antibody (target is na);Strain N2 extraction3_array1 channel_2


title: SDQ3148_SDC2_N2_MXemb_1 extraction3_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ3148 SDC2;target name: SDC-2;host: Rabbit;antigen: 1749-1848 (LIQNEKKLALSHKSHKNDENRRFRLNTVVKWYDAIICHCKEELTQAIVDAFPLNAITKNKETSHVAMENGDDEAMLSDTSDNQMSTTDYQMPKNICRNSE);clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDI;short description: Antibody was produced by Strategic Diagnostics Inc. SDI to indicated antigen.;

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.


title: AR0169_H3K4ME3_N2_L3 Hyb3 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: C. elegans  AR0169 H3K4ME3 rabbit polyclonal antibody;target name: Trimethylated Lys-4 of histone H3;host: Rabbit;antigen: C-terminus of H3 trimethylated at Lys-4;clonal: Polyclonal;purified: Crude;company: Other;catalog: AR0169;short description: A rabbit polyclonal antiserum to H3K4me3 obtained from LP Bio (H3K4me3-AR0169);used for ChIP.;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0169 H3K4ME3 rabbit polyclonal antibody (target is Trimethylated Lys-4 of histone H3);Strain N2 extraction3_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0169 H3K4ME3 rabbit polyclonal antibody (target is Trimethylated Lys-4 of histone H3);Strain N2 extraction3_array1 channel_2


title: SDQ3146_SDC2_N2_MXemb_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ3146 SDC2;target name: SDC-2;host: Rabbit;antigen: 1749-1848 (LIQNEKKLALSHKSHKNDENRRFRLNTVVKWYDAIICHCKEELTQAIVDAFPLNAITKNKETSHVAMENGDDEAMLSDTSDNQMSTTDYQMPKNICRNSE);clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDI;short description: Antibody was produced by Strategic Diagnostics Inc. SDI to indicated antigen.;
channel ch2 is input DNA;


title: AR0169_H3K4ME3_N2_L3 Hyb2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: C. elegans  AR0169 H3K4ME3 rabbit polyclonal antibody;target name: Trimethylated Lys-4 of histone H3;host: Rabbit;antigen: C-terminus of H3 trimethylated at Lys-4;clonal: Polyclonal;purified: Crude;company: Other;catalog: AR0169;short description: A rabbit polyclonal antiserum to H3K4me3 obtained from LP Bio (H3K4me3-AR0169);used for ChIP.;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0169 H3K4ME3 rabbit polyclonal antibody (target is Trimethylated Lys-4 of histone H3);Strain N2 extraction2_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0169 H3K4ME3 rabbit polyclonal antibody (target is Trimethylated Lys-4 of histone H3);Strain N2 extraction2_array1 channel_2


title: JA00002_IGG_N2_L3 Hyb1 extraction1_array1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  JA00002 IGG rabbit polyclonal antibody (target is na);Strain N2 extraction1_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  JA00002 IGG rabbit polyclonal antibody (target is na);Strain N2 extraction1_array1 channel_2


title: AR0169_H3K4ME3_N2_L3 Hyb1 extraction1_array1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0169 H3K4ME3 rabbit polyclonal antibody (target is Trimethylated Lys-4 of histone H3);Strain N2 extraction1_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AR0169 H3K4ME3 rabbit polyclonal antibody (target is Trimethylated Lys-4 of histone H3);Strain N2 extraction1_array1 channel_2


title: JL00012_DPY28_N2_MXemb_2 extraction2_array2

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: JL00012 DPY28;target name: DPY-28;host: Rabbit;antigen: 1481-1499 CKSAVADDDSDSDEFMLDD;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Kirsten Hagstrom;short description: Antibody was donated by Kirsten Hagstrom.;


title: AB9050_H3K36ME3_N2_L3 Hyb3 extraction3_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: C. elegans  AB9050 H3K36ME3 rabbit polyclonal antibody;target name: trimethylated Lys-36 of histone H3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 tri methylated at K36.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB9050;short description: An affinity purified rabbit polyclonal antibody to H3K36me3 obtained from Abcam (H3K36me3-AB9050);used for ChIP.;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AB9050 H3K36ME3 rabbit polyclonal antibody (target is trimethylated Lys-36 of histone H3);Strain N2 extraction3_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AB9050 H3K36ME3 rabbit polyclonal antibody (target is trimethylated Lys-36 of histone H3);Strain N2 extraction3_array1 channel_2


title: JL00002_SDC3_YPT47_MXemb_2 extraction2_array1


title: HK00012_H3K36ME22C3_N2_EEMB_2 extraction2_array1

description: channel ch2 is ChIP DNA; Antibody information listed below: official name: HK00012 H3K36me2:2C3;target name: H3K36me2;host: Mouse;antigen: KSAPATGGV(me2-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00012;short description: A protein G purified mouse monoclonal antibody to H3K36me2 (clone 2C3) obtained from Hiroshi Kimura. Used for ChIP.;


title: AB9050_H3K36ME3_N2_L3 Hyb2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: C. elegans  AB9050 H3K36ME3 rabbit polyclonal antibody;target name: trimethylated Lys-36 of histone H3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 tri methylated at K36.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB9050;short description: An affinity purified rabbit polyclonal antibody to H3K36me3 obtained from Abcam (H3K36me3-AB9050);used for ChIP.;
channel ch2 is input DNA;

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AB9050 H3K36ME3 rabbit polyclonal antibody (target is trimethylated Lys-36 of histone H3);Strain N2 extraction2_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AB9050 H3K36ME3 rabbit polyclonal antibody (target is trimethylated Lys-36 of histone H3);Strain N2 extraction2_array1 channel_2


title: JL00001_DPY27_YPT47_MXemb_1 extraction1_array1


title: SDQ0791_MES4_N2_EEMB_2 extraction2_array2

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ0791 MES4;target name: MES4;host: Rabbit;antigen: GTASKKSEISPSKPSTSSASSTSFVQQASWPISQNKKNLKKNSNQPVADTGSTLSTSTELNFHEKPQELLSPVSSRSRAASSSTPRAQKSKSRRDDVESE;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ0791;short description: An affinity purified rabbit polyclonal antibody raised against AA 729-828 to MES-4 obtained from SDI (MES4-Q0791); used for ChIP;


title: JL00001_DPY27_YPT47_MXemb_3 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JL00001 DPY27;target name: DPY-27;host: Mouse;antigen: 1-409;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: JL00001 DPY27;reference: PMID: 17293863;short description: *  recombinant proteins were cloned and expressed with Novagen's Pet30-EkLIC system
* rabbit polyclonal antibodies were produced at Covance Immunology Services
* DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.;
channel ch2 is input DNA;


title: AB9050_H3K36ME3_N2_L3 Hyb1 extraction1_array1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AB9050 H3K36ME3 rabbit polyclonal antibody (target is trimethylated Lys-36 of histone H3);Strain N2 extraction1_array1 channel_1

source_name: Developmental Stage L3 Larva;temperature 20;Antibody C. elegans  AB9050 H3K36ME3 rabbit polyclonal antibody (target is trimethylated Lys-36 of histone H3);Strain N2 extraction1_array1 channel_2


title: UP07442_H3K9ME3_N2_EEMB_3_OID18184 extraction3_array2

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: C. elegans  UP07442 H3K9ME3 rabbit polyclonal antibody;target name: Trimethylated Lys-9 on histone H3;host: Rabbit;antigen: synthetic 2X-branched peptide containing the sequence AR[me3K]ST in which me3K corresponds to trimethyl-lysine at residue 9 of human Histone H3;clonal: Polyclonal;purified: Protein A/G;company: Upstate;catalog: UP07442;short description: A protein A purified rabbit polyclonal antibody to H3K9me3 obtained from Upstate (H3K9me3-07442);used for ChIP.;

extract_protocol:
Worm_embryo_extraction_vSS4. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then fixed for 10 min with formaldehyde. Nuclei were isolated and then sonicated 14 times in ice water bath followed by 1 minute pause at the highest setting. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS2. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo purification kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.


title: SDQ0790_MRG1_N2_EEMB_2 extraction2_array2

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ0790 MRG1;target name: MRG1;host: Rabbit;antigen: YKFERPQYNDLVKKRAMEKGIDITNPTALQDSGFRPSQEYGIVHFLRMLAKLPDYLKLTQWNDHVINRIMIGVHDLIVFLNKNHGKYYRGSSDYQGASND;clonal: Polyclonal;purified: Crude;company: SDI;catalog: SDQ0790;short description: Crude rabbit serum to MRG-1 raised against AA220-319 obtained from SDI (MRG1-Q0790);
channel ch2 is input DNA;


title: UP07442_H3K9ME3_N2_EEMB_2_OID18184 extraction2_array2

extract_protocol:
Worm_embryo_extraction_vSS5. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 14 times in ice water bath followed by 1 minute pause at the highest setting. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS2. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo purification kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.


title: UP07442_H3K9ME3_N2_EEMB_1 extraction1_array1


title: ABAB817_8WG16_N2_EEMB_2 extraction2_array2


title: Gene_Expression_replicates 1,2,3

status: Public on May 29 2009

type: mixed

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

country: USA

institute: University of Chicago

description:
test CEL files: expression_dscDNA_1.CEL expression_dscDNA_2.CEL expression_RNA.CEL
control CEL files: expression_gDNA_1.CEL expression_gDNA_2.CEL
Gene_Expression_replicates1,2,3

hyb_protocol: Affymetrix Hybridization Protocol - Hybridizations were performed at the Functional Genomics Facility (FGF) at the University of Chicago.

scan_protocol: Affymetrix Protocol - Scans were performed at the Functional Genomics Facility (FGF) at the University of Chicago.

data_processing:
.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files and peak finding
.bar and .bed are generated by MAT. .bar contains log2(IP/Input) fold changes for each probe. .bed files contains the peak calls at 1%fdr from MAT.

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

label_protocol: Affymetrix Labeling Protocol (TdT labeling)

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-12 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 pm and flies are allowed to lay eggs for 12 hours. 3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila embryos are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IP'd material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.

treatment_protocol: No treatment

tag: antibody

tag: test

value: RNA

value: gDNA


title: CTCF_KC_replicates 1,2,3

description:
test CEL files: CTCF_KC_1.CEL CTCF_KC_2.CEL KC NOE CTCF-N.CEL
control CEL files: CTCF_KC_Mock.CEL Input KC NOE cell.CEL
CTCF_KC_replicates 1,2,3

value: CTCF-C

value: Chromatin

value: INPUT


title: SDQ3146_SDC2_N2_MXemb_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ3146 SDC2;target name: SDC-2;host: Rabbit;antigen: 1749-1848 (LIQNEKKLALSHKSHKNDENRRFRLNTVVKWYDAIICHCKEELTQAIVDAFPLNAITKNKETSHVAMENGDDEAMLSDTSDNQMSTTDYQMPKNICRNSE);clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDI;short description: Antibody was produced by Strategic Diagnostics Inc. SDI to indicated antigen.;


title: H3K27Me3_replicates 1,2,3

description:
test CEL files: H3K27Me3_18.CEL H3K27Me3_9.CEL H3K27Me3.CEL
control CEL files: H3K27me3_Input_1.CEL H3K27me3_input_3.31.CEL H3K27me3_Input_3.CEL
H3K27Me3_replicates 1,2,3


title: Pol_II_replicates 1,2,3

description:
test CEL files: pol II.CEL Pol II 14.CEL Pol II 7.CEL
control CEL files: input 3.31.CEL Input 2.CEL Input 1.CEL
Pol_II_replicates 1,2,3

value: PolII


title: su(Hw)_ab2_replicates 1,2,3

description:
test CEL files: suHw_ab2_A1_pam.CEL suHw_ab2_A2_pam.CEL suHw_ab2_A3_pam.CEL
control CEL files: suHw_ab2_Input_A_pam.CEL suHw_ab2_Input_B_pam.CEL suHw_ab2_Input_C_pam.CEL
su(Hw)_ab2_replicates 1,2,3


title: H3K4me3_Kc_replicates 1,2,3

description:
test CEL files: KC NOE 1.CEL KC NOE 2.CEL KC NOE 3.CEL
control CEL files: Input KC NOE 1.CEL Input KC NOE 2.CEL Input KC NOE 3.CEL
H3K4me3_Kc_replicate1


title: GAF_replicates 1,2,3

description:
test CEL files: GAF_A2_3558.CEL GAF_B2_3558.CEL GAF_ss8_3558.CEL
control CEL files: GAF_A2_input.CEL GAF_B2_input_2.CEL GAF_ss2_input.CEL
GAF_replicates 1,2,3

value: GAF


title: H3K4me3_S2_replicates 1,2,3

description:
test CEL files: H3K4me3_NOE_S2_R1.CEL H3K4me3_NOE_S2_R2.CEL H3K4me3_NOE_S2_R3.CEL
control CEL files: Input_NOE_S2_R1.CEL Input_NOE_S2_R2.CEL Input_NOE_S2_R3.CEL
H3K4me3_S2_replicate1


title: H3K4Me3_replicates 1,2,3

description:
test CEL files: H3K4me3_A2.CEL H3K4Me3_C2_1.CEL H3K4me3_C2_2.CEL
control CEL files: H3K4me3_A2_Mock.CEL H3K4me3_C2_Mock1.CEL H3K4me3_C2_Mock2.CEL
H3K4Me3_replicates 1,2,3


title: CTCF_C_replicates 1,2,3

description:
test CEL files: CTCF_C1_10.CEL CTCF_C1_15.CEL CTCF_C1_3.CEL
control CEL files: CTCF_C_Input_1.CEL CTCF_C_Input_2.CEL CTCF_C_Input_3.CEL
CTCF_C_replicates 1,2,3


title: CP190_replicates 1,2,3

description:
test CEL files: CP190_12.CEL CP190_17.CEL CP190_6.CEL
control CEL files: CP190_Input_1.CEL CP190_Input_2.CEL CP190_Input_3.CEL
CP190_replicates 1,2,3


title: CTCF_N_replicates 1,2,3

description:
test CEL files: CTCF_N_11.CEL CTCF_N1_5.CEL CTCF_N_16.CEL
control CEL files: CTCF_N_Input_1.CEL CTCF_N_Input_2.CEL CTCF_N_Input_3.CEL
CTCF_N_replicates 1,2,3

value: CTCF-N


title: brm_pupae

status: Public on May 12 2009

description:
brm_pupae
test: brm_1.CEL
test: brm_2.CEL
test: brm_3.CEL
reference: input_pupae.CEL

data_processing:
.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks.
.bed and .bar were generated with MAT.

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.  2. For a collection of pupae at 1-2 days APF (after puparium formation), new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles.  3. Pupae are collected 2 days after the first pupa formed on the wall of the bottle. They are collected with a brush humidified with EWB and placed into an eppendorf tube. They are rinsed extensively with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.

treatment_protocol: No Treatment

value: brm

tag: tissue

value: pupae

source_name: input

tag: reference

value: input


title: end300_E7-24h

description:
end300_E7-24h
test: en_14.CEL
test: en_2_5.CEL
test: en_3_6.CEL
reference: input_7-24h_15.CEL

value: Embryos

tag: time point


title: UBX7701_E3-8h

description:
UBX7701_E3-8h
test: 3-8h_7701.CEL
test: A1_7701_3-8h.CEL
test: A2_7701_3-8h.CEL
reference: 3-8h_Input.CEL
reference: Input_A_3-8h.CEL
reference: Input_B_3-8h.CEL


title: UBX2_E3-8h

description:
UBX2_E3-8h
test: 3-8h_Ubx_2.CEL
test: A3_Ubx_2_3-8h.CEL
test: A4_Ubx_2_3-8h.CEL
reference: 3-8h_Input.CEL
reference: Input_A_3-8h.CEL
reference: Input_B_3-8h.CEL


title: snr1_Pupae

description:
snr1_Pupae
test: snr_1.CEL
test: snr_2.CEL
test: snr_3.CEL
reference: input_pupae.CEL

value: Pupae


title: UBX1_E3-8h

description:
UBX1_E3-8h
test: 3-8h_Ubx.CEL
test: B1_Ubx_1_3-8h.CEL
test: B2_Ubx_1_3-8h.CEL
reference: 3-8h_Input.CEL
reference: Input_A_3-8h.CEL
reference: Input_B_3-8h.CEL


title: CTCF_S2_replicates 1,2,3

description:
test CEL files: CTCF_S2_1.CEL CTCF_S2_2.CEL CTCF.CEL
control CEL files: CTCF_S2_Mock.CEL Input-S2.CEL
CTCF_S2_replicates 1,2,3


title: gsbnpurif_E7-24h

status: Public on May 13 2009

description:
gsbnpurif_E7-24h
test: gsbn_1.CEL
test: gsbn_2.CEL
test: gsbn_3.CEL
reference: input_7-24h_15.CEL

extract_protocol: Drosophila embryos are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.

value: gsbnpurif


title: su(Hw)_ab1_replicates 1,2,3

description:
test CEL files: suHw_ab1_A1.CEL suHw_ab1_ss1.CEL suHw_ab1_ss5.CEL
control CEL files: suHw_ab1_A1_Input.CEL suHw_ab1_A2_input.CEL suHw_ab1_ss2_input.CEL
su(Hw)_ab1_replicates 1,2,3


title: BEAF-32_replicates 1,2,3

description:
test CEL files: beaf_321.CEL beaf_322.CEL beaf_323.CEL
control CEL file: beaf_input0-13_1.CEL
BEAF-32_replicates 1,2,3


title: TTK_E0-12h

description:
TTK_E0-12h
test: 91.CEL
test: A1_TTK.CEL
test: B1_TTK.CEL
reference: B1_Mock.CEL
reference: I.CEL
reference: S_A1_Mock.CEL

value: TTK


title: UBX7701_E0-12h

description:
UBX7701_E0-12h
test: 7701.CEL
test: A1_7701.CEL
test: B3.2_7701.CEL
reference: A1_Input.CEL
reference: B3.2_Mock.CEL
reference: input_0-12h_3%.CEL


title: ZFH1_E-0-12h

description:
ZFH1_E-0-12h
test: 84.CEL
test: A1_ZFH1.CEL
test: B1_ZFH1.CEL
reference: B1_Mock.CEL
reference: I.CEL
reference: S_A1_Mock.CEL


title: RUN7659_E0-12h

description:
RUN7659_E0-12h
test: 0-12h_7659.CEL
test: 59.CEL
test: B2_7659.CEL
reference: 0-12h_Input.CEL
reference: B2_Mock.CEL
reference: I.CEL


title: H3K9me3_E0-12h

description:
H3K9me3_E0-12h
test: A1_K9Me3.CEL
test: A2_K9Me3.CEL
test: A3_K9Me3.CEL
reference:  Input_K9Me3.CEL

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

tag: antibody lot number


title: INV7657_E-0-12h

description:
INV7657_E-0-12h
test: 0-12h_7657.CEL
test: 57.CEL
test: B2_7657.CEL
reference: 0-12h_Input.CEL
reference: B2_Mock.CEL
reference: I.CEL


title: H3K36me3_E0-12h

description:
H3K36me3_E0-12h
test: K36_1.CEL
test: K36_2.CEL
test: K36_3.CEL
reference: KW_Input_1.CEL
reference: KW_Input_2.CEL
reference: KW_Input_3.CEL


title: H3K4me3_E0-12h

description:
H3K4me3_E0-12h
test: A2_H3K4me3.CEL
test: C2_H3K4Me31.CEL
test: C2_H3K4Me32.CEL
reference: A2_Mock.CEL
reference: C2_Mock1.CEL
reference: C2_Mock2.CEL


title: Gro3_E0-12h

description:
Gro3_E0-12h
test: A1_gro_3%.CEL
test: A2_gro_3%.CEL
test: A3_gro_3%.CEL
reference: Input_3%_gro.CEL


title: KN_E0-12h

description:
test: 94.CEL
test: A1_KN.CEL
test: B1_KN.CEL
reference: B1_Mock.CEL
reference: I.CEL
reference: S_A1_Mock.CEL
KN_E0-12h

value: KN


title: GROAviva

description:
GROAviva
test: A1gro.CEL
test: A2__GRO.CEL
test: B2_GRO.CEL
test: B3.3_gro-aviva.CEL
test: s_gro.CEL
reference: A1_Input.CEL
reference: input_0-12h_3%.CEL
reference: Input_B3.2.CEL
reference: S_A2_Mock.CEL
reference: S_B2_Mock.CEL

value: embryos

value: GROAviva