title: expt.840 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: MLE Q4143;target name: MLE;host: Rabbit;antigen: Amino acid 2-101;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4143;short description: MLE;

source_name: expt.840 extraction1_array1 channel_1


title: expt.847 extraction4_array1

status: Public on Oct 13 2011

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;

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

label: biotin

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: expt.847 extraction4_array1 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: cell line

tag: tissue

value: embryo-derived cell-line

tag: developmental stage

value: late embryonic stage

tag: Sex

value: Male


title: expt.841 extraction3_array1

source_name: expt.841 extraction3_array1 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.


title: expt.846 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.846 extraction2_array1 channel_1


title: expt.1671 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1671 extraction2_array1 channel_1


title: expt.1896 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: MBD-R2(Q4167);target name: MBD-R2;host: Rabbit;antigen: Amino acid 511-610;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4167;short description: MBD-R2;

source_name: expt.1896 extraction3_array1 channel_1


title: expt.1904 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1904 extraction4_array1 channel_1


title: expt.1905 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1905 extraction2_array1 channel_1


title: expt.1897 extraction1_array1

source_name: expt.1897 extraction1_array1 channel_1


title: expt.1152 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1152 extraction4_array1 channel_1


title: expt.1829 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: LSD1 Q3430;target name: LSD1;host: Rabbit;antigen: aa 11-110 SKMTEPIEYVTLISDDSDGEPTPKRNVNHPPSALSAPNPGQKQKHPDEDSNDAPATSDERRTSRRNRPKVDYSNRPSGSGDTASNDKSGSASMGPNNQQA;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3430;short description: LSD1/Hdm/Su(var)3-3 CG17149;

source_name: expt.1829 extraction3_array1 channel_1


title: expt.1828 extraction1_array1

source_name: expt.1828 extraction1_array1 channel_1


title: expt.1876 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: mod2.2-VC;target name: MOD(MDG4)67.2;host: Rat;antigen: Polypeptide encoded by exons 5 and 6 of the corresponding mRNA isoform (Mongelard et al. 2002);clonal: Monoclonal;purified: Crude;company: Lab;catalog: Victor Corces;short description: Antibody against MOD(MDG4)67.2 protein;

source_name: expt.1876 extraction1_array1 channel_1


title: expt.1185 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1185 extraction2_array1 channel_1


title: expt.1643 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1643 extraction4_array1 channel_1


title: expt.624 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: JMJD2A-KDM4A Q2541;target name: JMJD2A/KDM4A;host: Rabbit;antigen: aa 350-449;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2541;short description: JMJD2A demethylase (CG15835) KDM4A;

source_name: expt.624 extraction3_array1 channel_1


title: expt.566 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.566 extraction4_array1 channel_1


title: expt.1831 extraction3_array1

source_name: expt.1831 extraction3_array1 channel_1


title: expt.1830 extraction1_array1

source_name: expt.1830 extraction1_array1 channel_1


title: expt.1642 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1642 extraction2_array1 channel_1


title: expt.417 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.417 extraction2_array1 channel_1


title: expt.1642 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1642 extraction4_array1 channel_1


title: expt.457 extraction1_array1

source_name: expt.457 extraction1_array1 channel_1


title: expt.1644 extraction3_array1

source_name: expt.1644 extraction3_array1 channel_1


title: expt.1645 extraction1_array1

source_name: expt.1645 extraction1_array1 channel_1


title: expt.1643 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1643 extraction2_array1 channel_1


title: expt.939 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.939 extraction2_array1 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: strain

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

value: 3rd Instar Larvae

tag: genotype

value: wild type


title: expt.1184 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1184 extraction4_array1 channel_1


title: expt.1387 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1387 extraction4_array1 channel_1


title: expt.1532 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1532 extraction2_array1 channel_1


title: expt.1491 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H4K16ac(M);target name: H4K16ac;host: Rabbit;antigen: Recognizes acetyl-histone H4 (Lys16) Mr ~10 kDa;clonal: Polyclonal;purified: Affinity;company: Upstate;catalog: 07-329;short description: Rabbit polyclonal to Histone H4K16ac. Recognizes acetyl-histone H4 (Lys16) Mr ~10 kDa;

source_name: expt.1491 extraction3_array1 channel_1


title: expt.1685 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1a hinge;target name: HP1a;host: Rabbit;antigen: KDRPSSSAKAKETQGRASSSTSTASKR; phosphorylated at aa 7 and 25;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Steve Henikoff;short description: Suppressor of variegation 205/HP1a;

source_name: expt.1685 extraction3_array1 channel_1


title: expt.1684 extraction1_array1

source_name: expt.1684 extraction1_array1 channel_1


title: expt.1386 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1386 extraction2_array1 channel_1


title: expt.1680 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP4 Q4072;target name: HP4;host: Rabbit;antigen: AA's 1-100;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4072;

source_name: expt.1680 extraction3_array1 channel_1


title: expt.1681 extraction1_array1

source_name: expt.1681 extraction1_array1 channel_1


title: expt.1418 extraction1_array1

source_name: expt.1418 extraction1_array1 channel_1


title: expt.1006 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1006 extraction4_array1 channel_1


title: expt.1531 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1531 extraction4_array1 channel_1


title: expt.986 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me2-Ab2 (new lot);target name: H3K9me2;host: Mouse;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 di methylated at K9.;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab1220;reference: http://www.abcam.com/Histone-H3-di-methyl-K9-antibody-mAbcam-1220-ChIP-Grade-ab1220.html;short description: mouse monoclonal to histone H3 di-methyl K9 chIP grade;

source_name: expt.986 extraction3_array1 channel_1


title: expt.973 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.973 extraction2_array1 channel_1


title: expt.966 extraction1_array1

source_name: expt.966 extraction1_array1 channel_1


title: expt.82 extraction5_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me1;target name: H3K9me1;host: Rabbit;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9045;short description: rabbit polyclonal against a synthetic peptide derived from residues 1-100 of human H3 mono methylated at K27;

source_name: expt.82 extraction5_array1 channel_1


title: expt.250 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.250 extraction4_array1 channel_1


title: expt.1704 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1704 extraction4_array1 channel_1


title: expt.41 extraction3_array1

source_name: expt.41 extraction3_array1 channel_1


title: expt.200 extraction1_array1

source_name: expt.200 extraction1_array1 channel_1


title: expt.85 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.85 extraction2_array1 channel_1


title: expt.270 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me1 (new lot);target name: H3K9me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 mono methylated at K9.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9045;reference: http://www.abcam.com/Histone-H3-mono-methyl-K9-antibody-ChIP-Grade-ab9045.html;short description: rabbit polyclonal to histone H3 mono-methyl K9 chIP grade;

source_name: expt.270 extraction3_array1 channel_1


title: expt.271 extraction1_array1

source_name: expt.271 extraction1_array1 channel_1


title: expt.46 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.46 extraction4_array1 channel_1


title: expt.251 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.251 extraction2_array1 channel_1


title: expt.1692 extraction1_array1

source_name: expt.1692 extraction1_array1 channel_1


title: expt.564 extraction6_array1

description: channel ch1 is input DNA;

source_name: expt.564 extraction6_array1 channel_1


title: expt.557 extraction5_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9ac;target name: H3K9ac;host: Rabbit;antigen: Peptide including acetyl-lysine 9 of histone 3;clonal: Polyclonal;purified: Crude;company: Lake Placid;catalog: AR-0102;short description: rabbit polyclonal against a peptide including acetyl-lysine 9 of histone H3.;

source_name: expt.557 extraction5_array1 channel_1


title: expt.247 extraction3_array1

source_name: expt.247 extraction3_array1 channel_1


title: expt.249 extraction1_array1

source_name: expt.249 extraction1_array1 channel_1


title: expt.1877 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K79Me2 AbCam;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: Antibody raised against H3 peptide containing K79 Di-methylated residue.;

source_name: expt.1877 extraction3_array1 channel_1


title: expt.1774 extraction1_array1

source_name: expt.1774 extraction1_array1 channel_1


title: expt.1773 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K79Me1;target name: H3K79me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 mono methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2886;reference: http://www.abcam.com/Histone-H3-mono-methyl-K79-antibody-ChIP-Grade-ab2886.html;short description: Rabbit antisera raised against H3 peptide mono-methylated at K79.;

source_name: expt.1773 extraction3_array1 channel_1


title: expt.1750 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1750 extraction2_array1 channel_1


title: expt.1776 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1776 extraction4_array1 channel_1


title: expt.1776 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1776 extraction2_array1 channel_1


title: expt.1693 extraction3_array1

source_name: expt.1693 extraction3_array1 channel_1


title: expt.1703 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1703 extraction2_array1 channel_1


title: expt.1784 extraction1_array1

source_name: expt.1784 extraction1_array1 channel_1


title: expt.1772 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K4me3 (ab8580 lot1);target name: H3K4me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 tri methylated at K4.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: 8580;reference: http://www.abcam.com/Histone-H3-tri-methyl-K4-antibody-ChIP-Grade-ab8580.html;short description: Histone H3 (tri methyl K4).;

source_name: expt.1772 extraction3_array1 channel_1


title: expt.1750 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1750 extraction4_array1 channel_1


title: expt.1757 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K4me1;target name: H3K4me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 mono methylated at K4.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8895;reference: http://www.abcam.com/Histone-H3-mono-methyl-K4-antibody-ChIP-Grade-ab8895.html;short description: Polyclonal rabbit antibody raised against synthetic peptide derived from residues 1-100 of H3 monomethylated at K4.;

source_name: expt.1757 extraction1_array1 channel_1


title: expt.1756 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1756 extraction2_array1 channel_1


title: expt.1783 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K27Ac;target name: H3K27ac;host: Rabbit;antigen: Peptide including acetyl-lysine 27 of H3;clonal: Polyclonal;purified: Crude;company: Lake Placid;catalog: AR-0105-50;short description: Rabbit antibody recognizing Acetylated K27 of H3.;

source_name: expt.1783 extraction3_array1 channel_1


title: expt.1762 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K27me2;target name: H3K27me2;host: Rabbit;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab24684;short description: Polyclonal rabbit antibody raised against a synthetic peptide derived from the first 100 AA of Histone H3 dimethylated at K27. Five ug of this antibody were used for ChIP experiments.;

source_name: expt.1762 extraction1_array1 channel_1


title: expt.1770 extraction3_array1

source_name: expt.1770 extraction3_array1 channel_1


title: expt.1759 extraction1_array1

source_name: expt.1759 extraction1_array1 channel_1


title: expt.1918 extraction3_array1

source_name: expt.1918 extraction3_array1 channel_1


title: expt.1874 extraction1_array1

source_name: expt.1874 extraction1_array1 channel_1


title: expt.787 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K23ac;target name: H3K23ac;host: Rabbit;antigen: Ovalbumin-conjugated synthetic peptide (KQLASAcKAARK-C) corresponding to amino acids 18-27 of yeast histone H3 acetylated on lysine 23 with a C-terminal cysteine added for conjugation purposes;clonal: Polyclonal;purified: Crude;company: Upstate;catalog: 07-355;reference: http://www.millipore.com/catalogue/item/07-355;short description: rabbit polyclonal against a synthetic peptide corresponding to aa 18-27 of yeast histone 3 with K23 acetylated;

source_name: expt.787 extraction1_array1 channel_1


title: expt.607 extraction6_array1

description: channel ch1 is input DNA;

source_name: expt.607 extraction6_array1 channel_1


title: expt.597 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.597 extraction2_array1 channel_1


title: expt.619 extraction3_array1

source_name: expt.619 extraction3_array1 channel_1


title: expt.608 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.608 extraction4_array1 channel_1


title: expt.1868 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: GAF;target name: GAF;host: Rabbit;antigen: Not Available;clonal: Polyclonal;purified: Crude;company: Lab;catalog: G. Cavalli;short description: Rabbit polyclonal antibody raised against recombinant GAGA factor protein (from G. Cavalli).  Serum used for ChIP (2ul);

source_name: expt.1868 extraction1_array1 channel_1


title: expt.1779 extraction3_array1

source_name: expt.1779 extraction3_array1 channel_1


title: expt.1750 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1750 extraction2_array1 channel_1


title: expt.630 extraction5_array1

source_name: expt.630 extraction5_array1 channel_1


title: expt.1760 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: EZ-Q3419;target name: E(Z);host: Rabbit;antigen: Peptide based on the aa190-289 of the E(Z) protein;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3419;short description: Rabbit polyclonal antibody raised against E(Z) protein;

source_name: expt.1760 extraction3_array1 channel_1


title: expt.1756 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1756 extraction4_array1 channel_1


title: expt.1765 extraction7_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: dSFMBT Q2642;target name: dSFMBT;host: Rabbit;antigen: aa 14-113 of dSFMBT protein;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2642;short description: Rabbit polyclonal Ab raised against the dSFMBT protein;

source_name: expt.1765 extraction7_array1 channel_1


title: expt.1764 extraction8_array1

description: channel ch1 is input DNA;

source_name: expt.1764 extraction8_array1 channel_1


title: expt.1321 extraction3_array1

source_name: expt.1321 extraction3_array1 channel_1


title: expt.1883 extraction6_array1

description: channel ch1 is input DNA;

source_name: expt.1883 extraction6_array1 channel_1


title: expt.1319 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1319 extraction4_array1 channel_1


title: expt.1917 extraction5_array1

source_name: expt.1917 extraction5_array1 channel_1


title: expt.1777 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: CTCF;target name: CTCF;host: Rabbit;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Marek Bartkuhn;short description: Rabbit polyclonal antibody raised against Drosphila CTCF obtained from Marek Bartkuhn.;

source_name: expt.1777 extraction1_array1 channel_1


title: expt.644 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.644 extraction2_array1 channel_1


title: expt.1872 extraction3_array1

source_name: expt.1872 extraction3_array1 channel_1


title: expt.1776 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1776 extraction4_array1 channel_1


title: expt.1674 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: dRING Q3200;target name: dRING;host: Rabbit;antigen: Peptide based on aa174-273 of the dRING protein;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3200;short description: Rabbit polyclonal Ab raised against the SCE/dRING protein;

source_name: expt.1674 extraction3_array1 channel_1


title: expt.1750 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1750 extraction4_array1 channel_1


title: expt.664 extraction1_array1

source_name: expt.664 extraction1_array1 channel_1


title: expt.1671 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1671 extraction4_array1 channel_1


title: expt.1235 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1235 extraction2_array1 channel_1

extract_protocol:
The template for the dsRNA synthesis was PCR amplified from Drosophila genomic DNA using specific primers extended with 5? T7-promoter tails. The sequence of the T7-promoter tails is as follows: 5?- CTAATACGACTCACTATAGGGAG-3?. The amplicon was selected such that it is contained within single exon. Following PCR the template was purified using PCR purification Kit from Qiagen. 2.5ug of purified template was used to synthesize dsRNA with Ribomax T7 RNA transcription kit from Promega. The dsRNA was precipitated with ethanol, dissolved in 300ul of pure water, denatured by heating to 65C for 30min and re-annealed by slow cooling to room temperature.2x10^6cells were treated with 50ug of dsRNA in 25cm2 T-flask for 1 hour in serum-free Schneider?s media. They were further brought up 6ml of Schneider?s media supplemented with 10% FBS and grown to confluence (~4 days). The cells were passaged to a 75cm2 T-flask and treated the second time with 200ug of dsRNA as described above. Following the treatment the cells were grown to confluence in 15ml Schneider?s media. 1ml of resulted culture was taken for preparation of nuclear and cytoplasmic protein extracts and the rest was in vivo crosslinked with formaldehyde. The protocol typically yields about 7x10^7 crosslinked cells, which is enough for about 7 ChIPs. And the RNAi treated cells were treated with formaldehyde as in normal cultured cell.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: expt.1228 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: CP190-HB;target name: CP190;host: Rabbit;antigen: Peptide based on the aa 606-742 of the CP-190 protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: VP Lab Huabing Li;short description: Polyclonal Ab against CP190 protein;

source_name: expt.1228 extraction3_array1 channel_1


title: expt.710 extraction5_array1

description: channel ch1 is input DNA;

source_name: expt.710 extraction5_array1 channel_1


title: expt.700 extraction4_array1

source_name: expt.700 extraction4_array1 channel_1


title: expt.1780 extraction1_array1

source_name: expt.1780 extraction1_array1 channel_1


title: expt.1776 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1776 extraction2_array1 channel_1


title: expt.1265 extraction1_array1

source_name: expt.1265 extraction1_array1 channel_1


title: expt.1752 extraction1_array1

source_name: expt.1752 extraction1_array1 channel_1


title: expt.1873 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: BEAF-HB;target name: BEAF32A and BEAF32B;host: Rabbit;antigen: Peptide based on aa 88-282 of the BEAF protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: VP Lab;short description: antibody against BEAF32A and BEAF32B;

source_name: expt.1873 extraction3_array1 channel_1


title: expt.1751 extraction1_array1

source_name: expt.1751 extraction1_array1 channel_1


title: expt.1781 extraction1_array1

source_name: expt.1781 extraction1_array1 channel_1


title: expt.1330 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1330 extraction4_array1 channel_1


title: expt.1331 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: ASH1 Q4177;target name: ASH1;host: Rabbit;antigen: peptide aa 1747-1846;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4177;short description: Antibody against ASH1 protein;

source_name: expt.1331 extraction3_array1 channel_1


title: expt.1870 extraction3_array1

source_name: expt.1870 extraction3_array1 channel_1


title: expt.1329 extraction1_array1

source_name: expt.1329 extraction1_array1 channel_1


title: expt.1303 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1303 extraction4_array1 channel_1


title: expt.1325 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1325 extraction2_array1 channel_1


title: expt.703 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: SU(HW)-HB;target name: SU(HW);host: Rabbit;antigen: Peptide based on aa 43-258 of the Su(HW) protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: VP Lab;short description: Polyclonal Ab against SU(HW) protein;

source_name: expt.703 extraction3_array1 channel_1


title: expt.497 extraction6_array1

description: channel ch1 is input DNA;

source_name: expt.497 extraction6_array1 channel_1


title: expt.1327 extraction1_array1

source_name: expt.1327 extraction1_array1 channel_1


title: expt.713 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.713 extraction4_array1 channel_1


title: expt.1381 extraction1_array1

source_name: expt.1381 extraction1_array1 channel_1


title: expt.715 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.715 extraction4_array1 channel_1


title: expt.1371 extraction3_array1

source_name: expt.1371 extraction3_array1 channel_1


title: expt.1372 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1372 extraction2_array1 channel_1


title: expt.1375 extraction1_array1

source_name: expt.1375 extraction1_array1 channel_1


title: expt.460 extraction5_array1

source_name: expt.460 extraction5_array1 channel_1


title: expt.468 extraction1_array1

source_name: expt.468 extraction1_array1 channel_1


title: expt.708 extraction3_array1

source_name: expt.708 extraction3_array1 channel_1


title: expt.499 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.499 extraction2_array1 channel_1


title: expt.1384 extraction3_array1

source_name: expt.1384 extraction3_array1 channel_1


title: expt.498 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.498 extraction2_array1 channel_1


title: expt.1189 extraction1_array1

source_name: expt.1189 extraction1_array1 channel_1


title: expt.1328 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1328 extraction2_array1 channel_1


title: expt.1295 extraction3_array1

source_name: expt.1295 extraction3_array1 channel_1


title: expt.1264 extraction3_array1

source_name: expt.1264 extraction3_array1 channel_1


title: expt.1235 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1235 extraction4_array1 channel_1


title: expt.710 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.710 extraction2_array1 channel_1


title: expt.1395 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1395 extraction4_array1 channel_1


title: expt.747 extraction1_array1

source_name: expt.747 extraction1_array1 channel_1


title: expt.1394 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1394 extraction2_array1 channel_1


title: expt.1380 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1380 extraction2_array1 channel_1


title: expt.1368 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1368 extraction4_array1 channel_1


title: expt.1393 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1393 extraction4_array1 channel_1


title: expt.1407 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: RNA Pol II (abcam);target name: PolII;host: Mouse;antigen: Synthetic peptide: YSPTSpPS (Human). The sequence is repeated multiple times in the C-terminal domain of RNA polymerase II.;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab5408;reference: http://www.abcam.com/RNA-polymerase-II-CTD-repeat-YSPTSPS-antibody-4H8-ChIP-Grade-ab5408.html;short description: Mouse Monoclonal (4H8) to RNA polymerase II CTD repeat YSPTSPS (ChIP grade);

source_name: expt.1407 extraction3_array1 channel_1


title: expt.1392 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1392 extraction2_array1 channel_1


title: expt.814 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.814 extraction4_array1 channel_1


title: expt.1473 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: POF (MO 459);target name: POF;host: Rabbit;antigen: aa1-150;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: MO 459;short description: Custom produced by Covance;

source_name: expt.1473 extraction3_array1 channel_1


title: expt.979 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.979 extraction2_array1 channel_1


title: expt.815 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.815 extraction2_array1 channel_1


title: expt.1406 extraction1_array1

source_name: expt.1406 extraction1_array1 channel_1


title: expt.1077 extraction3_array1

source_name: expt.1077 extraction3_array1 channel_1


title: expt.961 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.961 extraction4_array1 channel_1


title: expt.1076 extraction1_array1

source_name: expt.1076 extraction1_array1 channel_1


title: expt.1383 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1383 extraction4_array1 channel_1


title: expt.1409 extraction3_array1

source_name: expt.1409 extraction3_array1 channel_1


title: expt.1461 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: JHDM1 Q2634;target name: JHDM1;host: Rabbit;antigen: aa 418-517 DLPPQKKNVPSLVLDPVALIKDVRSLVERHCKDQQDLAITGVSVLKSPPGSQPPFLLYDRTRVKQEIKQEIARKNAEVIREQQQLEAGRAREAESDTSQS;clonal: Unknown;purified: Affinity;company: SDI;catalog: Q2634;short description: JHDM1 demethylase (CG11033);

source_name: expt.1461 extraction1_array1 channel_1


title: expt.1395 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1395 extraction4_array1 channel_1


title: expt.1185 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1185 extraction2_array1 channel_1


title: expt.1611 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1 wa191;target name: HP1a;host: Rabbit;antigen: CYAVEKIIDRRVRKGKVEYYLKWKG;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Elgin;short description: Rabbit polyclonal;

source_name: expt.1611 extraction3_array1 channel_1


title: expt.977 extraction3_array1

source_name: expt.977 extraction3_array1 channel_1


title: expt.1312 extraction3_array1

source_name: expt.1312 extraction3_array1 channel_1


title: expt.1394 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1394 extraction2_array1 channel_1


title: expt.1610 extraction1_array1

source_name: expt.1610 extraction1_array1 channel_1


title: expt.891 extraction1_array1

source_name: expt.891 extraction1_array1 channel_1


title: expt.979 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.979 extraction4_array1 channel_1


title: expt.1408 extraction1_array1

source_name: expt.1408 extraction1_array1 channel_1


title: expt.890 extraction3_array1

source_name: expt.890 extraction3_array1 channel_1


title: expt.976 extraction1_array1

source_name: expt.976 extraction1_array1 channel_1


title: expt.1474 extraction1_array1

source_name: expt.1474 extraction1_array1 channel_1


title: expt.978 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.978 extraction2_array1 channel_1


title: expt.1403 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1a 552;target name: HP1a;host: Rabbit;antigen: CKWKGYPETENTWEPENN;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Elgin;short description: rabbit polyclonal;

source_name: expt.1403 extraction3_array1 channel_1


title: expt.1387 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1387 extraction4_array1 channel_1


title: expt.1402 extraction1_array1

source_name: expt.1402 extraction1_array1 channel_1


title: expt.1386 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1386 extraction2_array1 channel_1


title: expt.1578 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H4K20me (2nd lot);target name: H4K20me;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of Human Histone H4 mono methylated at K20.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9051;reference: http://www.abcam.com/histone-h4-mono-methyl-k20-antibody-chip-grade-ab9051.html;short description: H4K20me antibody;

source_name: expt.1578 extraction1_array1 channel_1


title: expt.965 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me2-Ab2 (new lot);target name: H3K9me2;host: Mouse;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 di methylated at K9.;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab1220;reference: http://www.abcam.com/Histone-H3-di-methyl-K9-antibody-mAbcam-1220-ChIP-Grade-ab1220.html;short description: mouse monoclonal to histone H3 di-methyl K9 chIP grade;

source_name: expt.965 extraction3_array1 channel_1


title: expt.972 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.972 extraction4_array1 channel_1


title: expt.1571 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1571 extraction4_array1 channel_1


title: expt.1577 extraction3_array1

source_name: expt.1577 extraction3_array1 channel_1


title: expt.1005 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1005 extraction2_array1 channel_1


title: expt.961 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.961 extraction2_array1 channel_1


title: expt.960 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.960 extraction4_array1 channel_1


title: expt.985 extraction1_array1

source_name: expt.985 extraction1_array1 channel_1


title: expt.1006 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1006 extraction4_array1 channel_1


title: expt.462 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K4me3 (ab8580 lot1);target name: H3K4me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 tri methylated at K4.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: 8580;reference: http://www.abcam.com/Histone-H3-tri-methyl-K4-antibody-ChIP-Grade-ab8580.html;short description: Histone H3 (tri methyl K4).;

source_name: expt.462 extraction3_array1 channel_1


title: expt.497 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.497 extraction4_array1 channel_1


title: expt.1080 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K4me2 JBC 1360331;target name: H3K4me2;host: Rabbit;antigen: KLH conjugated synthetic peptide (ARTMe2KQTAR-GC) corresponding to amino acids 1-8 of human Histone H3.;clonal: Polyclonal;purified: Crude;company: Upstate;catalog: 07-030;short description: Anti dimethyl Histone H3 (Lys4);

source_name: expt.1080 extraction1_array1 channel_1


title: expt.754 extraction1_array1

source_name: expt.754 extraction1_array1 channel_1


title: expt.973 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.973 extraction2_array1 channel_1


title: expt.1081 extraction3_array1

source_name: expt.1081 extraction3_array1 channel_1


title: expt.713 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.713 extraction2_array1 channel_1


title: expt.1572 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1572 extraction2_array1 channel_1


title: expt.713 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.713 extraction4_array1 channel_1


title: expt.1532 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1532 extraction2_array1 channel_1


title: expt.1078 extraction3_array1

source_name: expt.1078 extraction3_array1 channel_1


title: expt.1526 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K36me3 abcam;target name: H3K36me3;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;reference: http://www.abcam.com/histone-h3-tri-methyl-k36-antibody-chip-grade-ab9050.html;short description: rabbit polyclonal to Histone H3 (tri methyl K36) ChIP grade;

source_name: expt.1526 extraction1_array1 channel_1


title: expt.1525 extraction3_array1

source_name: expt.1525 extraction3_array1 channel_1


title: expt.1005 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1005 extraction2_array1 channel_1


title: expt.1079 extraction1_array1

source_name: expt.1079 extraction1_array1 channel_1


title: expt.972 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.972 extraction4_array1 channel_1


title: expt.1531 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1531 extraction4_array1 channel_1


title: expt.499 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.499 extraction4_array1 channel_1


title: expt.470 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K27Me3 (Abcam2);target name: H3K27Me3;host: Mouse;antigen: Synthetic peptide derived from residues 1 - 100 of Human Histone H3 tri methylated at K27;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab6002;reference: http://www.abcam.com/Histone-H3-tri-methyl-K27-antibody-mAbcam-6002-ChIP-Grade-ab6002.html;short description: Monoclonal antibody raised against synthetic peptide tri-methylated at K27.;

source_name: expt.470 extraction3_array1 channel_1


title: expt.750 extraction1_array1

source_name: expt.750 extraction1_array1 channel_1


title: expt.461 extraction1_array1

source_name: expt.461 extraction1_array1 channel_1


title: expt.498 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.498 extraction4_array1 channel_1


title: expt.465 extraction3_array1

source_name: expt.465 extraction3_array1 channel_1


title: expt.714 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.714 extraction2_array1 channel_1


title: expt.752 extraction1_array1

source_name: expt.752 extraction1_array1 channel_1


title: expt.746 extraction3_array1

source_name: expt.746 extraction3_array1 channel_1


title: expt.1235 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1235 extraction2_array1 channel_1


title: expt.1232 extraction3_array1

source_name: expt.1232 extraction3_array1 channel_1


title: expt.1236 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1236 extraction4_array1 channel_1


title: expt.755 extraction3_array1

source_name: expt.755 extraction3_array1 channel_1


title: expt.1229 extraction1_array1

source_name: expt.1229 extraction1_array1 channel_1


title: expt.497 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.497 extraction2_array1 channel_1


title: expt.715 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.715 extraction2_array1 channel_1


title: expt.756 extraction1_array1

source_name: expt.756 extraction1_array1 channel_1


title: expt.1571 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1571 extraction4_array1 channel_1


title: expt.712 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.712 extraction2_array1 channel_1


title: expt.1241 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: dMi-2(Q4443);target name: dMi-2;host: Rabbit;antigen: Amino Acid 4120-209;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4443;short description: dMi-2;

source_name: expt.1241 extraction3_array1 channel_1


title: expt.847 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.847 extraction4_array1 channel_1


title: expt.846 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.846 extraction2_array1 channel_1


title: expt.1572 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1572 extraction2_array1 channel_1


title: expt.1574 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H2AV 9751;target name: H2AV;host: Rabbit;antigen: QDPQRKGNVILSQAY;clonal: Polyclonal;purified: Affinity;company: Lake Placid;catalog: Rabbit 9751;short description: Raised against peptide;

source_name: expt.1574 extraction1_array1 channel_1


title: expt.1573 extraction3_array1

source_name: expt.1573 extraction3_array1 channel_1


title: expt.1242 extraction1_array1

source_name: expt.1242 extraction1_array1 channel_1


title: expt.1113 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1113 extraction4_array1 channel_1


title: expt.1114 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1114 extraction2_array1 channel_1


title: expt.1588 extraction1_array1

source_name: expt.1588 extraction1_array1 channel_1


title: expt.710 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.710 extraction4_array1 channel_1


title: expt.499 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.499 extraction4_array1 channel_1


title: expt.1188 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: CTCF-VC;target name: CTCF;host: Guinea Pig;antigen: Not Available;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Victor Corces;short description: Polyclonal antibody against CTCF protein;

source_name: expt.1188 extraction1_array1 channel_1


title: expt.715 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.715 extraction2_array1 channel_1


title: expt.1383 extraction6_array1

description: channel ch1 is input DNA;

source_name: expt.1383 extraction6_array1 channel_1


title: expt.469 extraction3_array1

source_name: expt.469 extraction3_array1 channel_1


title: expt.497 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.497 extraction2_array1 channel_1


title: expt.709 extraction1_array1

source_name: expt.709 extraction1_array1 channel_1


title: expt.1587 extraction3_array1

source_name: expt.1587 extraction3_array1 channel_1


title: expt.1385 extraction5_array1

source_name: expt.1385 extraction5_array1 channel_1


title: expt.714 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.714 extraction4_array1 channel_1


title: expt.498 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.498 extraction2_array1 channel_1


title: expt.464 extraction1_array1

source_name: expt.464 extraction1_array1 channel_1


title: expt.1380 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1380 extraction4_array1 channel_1


title: expt.757 extraction3_array1

source_name: expt.757 extraction3_array1 channel_1


title: expt.1235 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1235 extraction2_array1 channel_1


title: expt.1382 extraction3_array1

source_name: expt.1382 extraction3_array1 channel_1


title: expt.1226 extraction1_array1

source_name: expt.1226 extraction1_array1 channel_1


title: expt.710 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.710 extraction4_array1 channel_1


title: expt.758 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: CP190-HB;target name: CP190;host: Rabbit;antigen: Peptide based on the aa 606-742 of the CP-190 protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: VP Lab Huabing Li;short description: Polyclonal Ab against CP190 protein;

source_name: expt.758 extraction3_array1 channel_1


title: expt.1370 extraction3_array1

source_name: expt.1370 extraction3_array1 channel_1


title: expt.713 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.713 extraction4_array1 channel_1


title: expt.463 extraction1_array1

source_name: expt.463 extraction1_array1 channel_1


title: expt.497 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.497 extraction2_array1 channel_1


title: expt.1374 extraction1_array1

source_name: expt.1374 extraction1_array1 channel_1


title: expt.1372 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1372 extraction2_array1 channel_1


title: expt.704 extraction3_array1

source_name: expt.704 extraction3_array1 channel_1


title: expt.705 extraction5_array1

source_name: expt.705 extraction5_array1 channel_1


title: expt.1300 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1300 extraction4_array1 channel_1


title: expt.1290 extraction3_array1

source_name: expt.1290 extraction3_array1 channel_1


title: expt.499 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.499 extraction2_array1 channel_1


title: expt.753 extraction3_array1

source_name: expt.753 extraction3_array1 channel_1


title: expt.714 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.714 extraction4_array1 channel_1


title: expt.498 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.498 extraction2_array1 channel_1


title: expt.472 extraction1_array1

source_name: expt.472 extraction1_array1 channel_1


title: expt.467 extraction1_array1

source_name: expt.467 extraction1_array1 channel_1


title: expt.712 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.712 extraction4_array1 channel_1


title: expt.1187 extraction3_array1

source_name: expt.1187 extraction3_array1 channel_1


title: expt.1368 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1368 extraction4_array1 channel_1


title: expt.1231 extraction1_array1

source_name: expt.1231 extraction1_array1 channel_1


title: expt.1236 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1236 extraction2_array1 channel_1


title: expt.715 extraction6_array1

description: channel ch1 is input DNA;

source_name: expt.715 extraction6_array1 channel_1


title: expt.1291 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: BEAF-HB;target name: BEAF32A and BEAF32B;host: Rabbit;antigen: Peptide based on aa 88-282 of the BEAF protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: VP Lab;short description: antibody against BEAF32A and BEAF32B;

source_name: expt.1291 extraction3_array1 channel_1


title: expt.1235 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1235 extraction4_array1 channel_1


title: expt.715 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.715 extraction2_array1 channel_1


title: expt.707 extraction1_array1

source_name: expt.707 extraction1_array1 channel_1


title: expt.1227 extraction3_array1

source_name: expt.1227 extraction3_array1 channel_1


title: expt.748 extraction1_array1

source_name: expt.748 extraction1_array1 channel_1


title: expt.710 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.710 extraction2_array1 channel_1


title: expt.714 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.714 extraction4_array1 channel_1


title: expt.702 extraction1_array1

source_name: expt.702 extraction1_array1 channel_1


title: expt.1236 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1236 extraction4_array1 channel_1


title: expt.751 extraction3_array1

source_name: expt.751 extraction3_array1 channel_1


title: expt.1230 extraction3_array1

source_name: expt.1230 extraction3_array1 channel_1


title: expt.712 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.712 extraction2_array1 channel_1


title: expt.466 extraction1_array1

source_name: expt.466 extraction1_array1 channel_1


title: expt.110 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.110 extraction4_array1 channel_1


title: expt.498 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.498 extraction2_array1 channel_1


title: expt.279 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H4;target name: H4;host: Rabbit;antigen: KLH-conjugated synthetic peptide corresponding to amino acids 17-28 of Histone H4. Epitope has been mapped to residues 25-28;clonal: Monoclonal;purified: Affinity;company: Upstate;catalog: 05-858;reference: http://www.millipore.com/catalogue/item/05-858;short description: Anti-histone H4 pan;

source_name: expt.279 extraction3_array1 channel_1


title: expt.330 extraction1_array1

source_name: expt.330 extraction1_array1 channel_1


title: expt.112 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.112 extraction2_array1 channel_1


title: expt.331 extraction3_array1

source_name: expt.331 extraction3_array1 channel_1


title: expt.332 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.332 extraction4_array1 channel_1


title: expt.315 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.315 extraction2_array1 channel_1


title: expt.314 extraction1_array1

source_name: expt.314 extraction1_array1 channel_1


title: expt.564 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.564 extraction4_array1 channel_1


title: expt.943 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3 antibody3;target name: H3;host: Rabbit;antigen: C-terminal peptide of histone H3;clonal: Polyclonal;purified: Crude;company: Active Motif;catalog: 39163;reference: http://www.activemotif.com/catalog/details/39163.html;short description: Rabbit polyclonal antibody against a C-terminal peptide of H3;

source_name: expt.943 extraction3_array1 channel_1


title: expt.1000 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1000 extraction2_array1 channel_1


title: expt.942 extraction1_array1

source_name: expt.942 extraction1_array1 channel_1


title: expt.136 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.136 extraction4_array1 channel_1


title: expt.62 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.62 extraction2_array1 channel_1


title: expt.309 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H1;target name: H1;host: Rabbit;antigen: Drosophila histone H1;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Jim Kadonaga;short description: Polyclonal rabbit antibodies against Drosophila histone H1;

source_name: expt.309 extraction3_array1 channel_1


title: expt.308 extraction1_array1

source_name: expt.308 extraction1_array1 channel_1


title: expt.293 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.293 extraction4_array1 channel_1


title: expt.292 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.292 extraction2_array1 channel_1


title: expt.340 extraction1_array1

source_name: expt.340 extraction1_array1 channel_1


title: expt.1128 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Su(var)3-7-Q3448;target name: Su(var)3-7;host: Rabbit;antigen: AA's 329-428;clonal: Unknown;purified: Affinity;company: SDI;catalog: Q3448;short description: Affinity purified antibodies from 80mL rabbit antisera;

source_name: expt.1128 extraction3_array1 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Embryo 14-16hr OR


title: expt.341 extraction3_array1

source_name: expt.341 extraction3_array1 channel_1


title: expt.974 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.974 extraction2_array1 channel_1


title: expt.975 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.975 extraction4_array1 channel_1


title: expt.1127 extraction1_array1

source_name: expt.1127 extraction1_array1 channel_1


title: expt.815 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.815 extraction2_array1 channel_1

value: se/e

value: Female


title: expt.814 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.814 extraction4_array1 channel_1


title: expt.1138 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: RPD3-Q3451;target name: RPD3;host: Rabbit;antigen: AA's 385-484;clonal: Unknown;purified: Affinity;company: SDI;catalog: Q3451;short description: Affinity purified antibodies from 80mL rabbit antisera;

source_name: expt.1138 extraction3_array1 channel_1


title: expt.1139 extraction1_array1

source_name: expt.1139 extraction1_array1 channel_1


title: expt.774 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.774 extraction2_array1 channel_1


title: expt.773 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.773 extraction4_array1 channel_1


title: expt.1168 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: RNA Pol II (abcam);target name: PolII;host: Mouse;antigen: Synthetic peptide: YSPTSpPS (Human). The sequence is repeated multiple times in the C-terminal domain of RNA polymerase II.;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab5408;reference: http://www.abcam.com/RNA-polymerase-II-CTD-repeat-YSPTSPS-antibody-4H8-ChIP-Grade-ab5408.html;short description: Mouse Monoclonal (4H8) to RNA polymerase II CTD repeat YSPTSPS (ChIP grade);

source_name: expt.1168 extraction1_array1 channel_1


title: expt.1167 extraction3_array1

source_name: expt.1167 extraction3_array1 channel_1


title: expt.847 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.847 extraction4_array1 channel_1


title: expt.939 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.939 extraction4_array1 channel_1


title: expt.285 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: POF;target name: POF;host: Rabbit;antigen: TDDQDKEASGGDGSQC;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Jan Larsson;

source_name: expt.285 extraction3_array1 channel_1


title: expt.1238 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: MSL-1(Q4453);target name: MSL-1;host: Rabbit;antigen: Amino Acid 599-698;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4453;short description: MSL-1 (biological process: dosage compensation);

source_name: expt.1238 extraction1_array1 channel_1


title: expt.328 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.328 extraction4_array1 channel_1


title: expt.846 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.846 extraction2_array1 channel_1


title: expt.86 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.86 extraction2_array1 channel_1


title: expt.1237 extraction3_array1

source_name: expt.1237 extraction3_array1 channel_1


title: expt.284 extraction1_array1

source_name: expt.284 extraction1_array1 channel_1


title: expt.919 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: JIL1 Q3433;target name: JIL1;host: Rabbit;antigen: Amino Acids: 919-1018;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3433;short description: JIL1

source_name: expt.919 extraction3_array1 channel_1


title: expt.1184 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1184 extraction2_array1 channel_1


title: expt.1178 extraction1_array1

source_name: expt.1178 extraction1_array1 channel_1


title: expt.1210 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1b Q4114;target name: HP1b;host: Rabbit;antigen: AA's 151-240;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4114;short description: affinity purified antibody from 80mL rabbit antisera;

source_name: expt.1210 extraction3_array1 channel_1


title: expt.1209 extraction1_array1

source_name: expt.1209 extraction1_array1 channel_1


title: expt.975 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.975 extraction4_array1 channel_1


title: expt.1271 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1c Q4064;target name: HP1c;host: Rabbit;antigen: AA's 1-100;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4064;

source_name: expt.1271 extraction1_array1 channel_1


title: expt.1114 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1114 extraction4_array1 channel_1


title: expt.1250 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H4K8ac;target name: H4K8ac;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H4 acetylated at K8.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab15823;reference: http://www.abcam.com/Histone-H4-acetyl-K8-antibody-ChIP-Grade-ab15823.html;short description: Rabbit polyclonal to Histone H4 (acetyl K8) - ChIP Grade. Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H4 acetylated at K8.;

source_name: expt.1250 extraction3_array1 channel_1

value: dorsal mesothoracic disc


title: expt.1113 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1113 extraction2_array1 channel_1


title: expt.1246 extraction3_array1

source_name: expt.1246 extraction3_array1 channel_1


title: expt.289 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.289 extraction4_array1 channel_1


title: expt.1249 extraction1_array1

source_name: expt.1249 extraction1_array1 channel_1


title: expt.1185 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1185 extraction4_array1 channel_1


title: expt.1245 extraction1_array1

source_name: expt.1245 extraction1_array1 channel_1


title: expt.288 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.288 extraction2_array1 channel_1


title: expt.1280 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1280 extraction2_array1 channel_1


title: expt.1281 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1281 extraction4_array1 channel_1


title: expt.1221 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H4K20me (2nd lot);target name: H4K20me;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of Human Histone H4 mono methylated at K20.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9051;reference: http://www.abcam.com/histone-h4-mono-methyl-k20-antibody-chip-grade-ab9051.html;short description: H4K20me antibody;

source_name: expt.1221 extraction3_array1 channel_1


title: expt.1155 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1155 extraction4_array1 channel_1


title: expt.1216 extraction3_array1

source_name: expt.1216 extraction3_array1 channel_1


title: expt.1218 extraction3_array1

source_name: expt.1218 extraction3_array1 channel_1


title: expt.1154 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1154 extraction2_array1 channel_1


title: expt.1272 extraction3_array1

source_name: expt.1272 extraction3_array1 channel_1


title: expt.1220 extraction1_array1

source_name: expt.1220 extraction1_array1 channel_1


title: expt.1156 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1156 extraction2_array1 channel_1


title: expt.974 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.974 extraction2_array1 channel_1


title: expt.939 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.939 extraction4_array1 channel_1


title: expt.1153 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1153 extraction4_array1 channel_1


title: expt.1152 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1152 extraction2_array1 channel_1


title: expt.62 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.62 extraction4_array1 channel_1


title: expt.1217 extraction1_array1

source_name: expt.1217 extraction1_array1 channel_1


title: expt.1184 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1184 extraction2_array1 channel_1


title: expt.924 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H2B-ubiq (NRO3);target name: H2Bubi;host: Mouse;antigen: This antibody was raised against a branched peptide corresponding to the conjugation site of ubiquitin on human histone H2B.;clonal: Monoclonal;purified: Affinity;company: Medimabs;catalog: #MM-0029;short description: Ubiquitinated Histone H2B Mouse Monoclonal Antibody:

source_name: expt.924 extraction3_array1 channel_1


title: expt.65 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H2BK5ac;target name: H2BK5ac;host: Rabbit;antigen: Synthetic acetylated peptide corresponding to residues surrounding Lys 5 of Histone H2B.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: 40886;reference: http://www.abcam.com/Histone-H2B-acetyl-K5-antibody-EP857Y-ChIP-Grade-ab40886.html;short description: Rabbit monoclonal [EP857Y] to Histone H2B (acetyl K5) - ChIP Grade;

source_name: expt.65 extraction3_array1 channel_1


title: expt.1152 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1152 extraction4_array1 channel_1


title: expt.136 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.136 extraction2_array1 channel_1


title: expt.1219 extraction1_array1

source_name: expt.1219 extraction1_array1 channel_1


title: expt.904 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.904 extraction2_array1 channel_1


title: expt.1146 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H2AV 9751;target name: H2AV;host: Rabbit;antigen: QDPQRKGNVILSQAY;clonal: Polyclonal;purified: Affinity;company: Lake Placid;catalog: Rabbit 9751;short description: Raised against peptide;

source_name: expt.1146 extraction1_array1 channel_1


title: expt.131 extraction1_array1

source_name: expt.131 extraction1_array1 channel_1


title: expt.1150 extraction3_array1

source_name: expt.1150 extraction3_array1 channel_1


title: expt.148 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.148 extraction4_array1 channel_1


title: expt.234 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: CTCF;target name: CTCF;host: Rabbit;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Marek Bartkuhn;short description: Rabbit polyclonal antibody raised against Drosphila CTCF obtained from Marek Bartkuhn.;

source_name: expt.234 extraction1_array1 channel_1


title: expt.58 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.58 extraction2_array1 channel_1


title: expt.150 extraction3_array1

source_name: expt.150 extraction3_array1 channel_1


title: expt.671 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.671 extraction4_array1 channel_1


title: expt.235 extraction1_array1

source_name: expt.235 extraction1_array1 channel_1


title: expt.819 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: ASH1 Q4177;target name: ASH1;host: Rabbit;antigen: peptide aa 1747-1846;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4177;short description: Antibody against ASH1 protein;

source_name: expt.819 extraction1_array1 channel_1


title: expt.730 extraction3_array1

source_name: expt.730 extraction3_array1 channel_1


title: expt.823 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.823 extraction2_array1 channel_1


title: expt.253 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.253 extraction4_array1 channel_1


title: expt.207 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.207 extraction2_array1 channel_1


title: expt.258 extraction3_array1

source_name: expt.258 extraction3_array1 channel_1


title: expt.1004 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1004 extraction4_array1 channel_1


title: expt.1177 extraction1_array1

source_name: expt.1177 extraction1_array1 channel_1


title: expt.1058 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: POF (MO 459);target name: POF;host: Rabbit;antigen: aa1-150;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: MO 459;short description: Custom produced by Covance;

source_name: expt.1058 extraction3_array1 channel_1


title: expt.1115 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1115 extraction4_array1 channel_1


title: expt.1057 extraction1_array1

source_name: expt.1057 extraction1_array1 channel_1


title: expt.1003 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1003 extraction2_array1 channel_1


title: expt.1109 extraction3_array1

source_name: expt.1109 extraction3_array1 channel_1


title: expt.1110 extraction1_array1

source_name: expt.1110 extraction1_array1 channel_1


title: expt.1116 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1116 extraction2_array1 channel_1


title: expt.974 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.974 extraction2_array1 channel_1


title: expt.964 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1 wa191;target name: HP1a;host: Rabbit;antigen: CYAVEKIIDRRVRKGKVEYYLKWKG;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Elgin;short description: Rabbit polyclonal;

source_name: expt.964 extraction3_array1 channel_1


title: expt.975 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.975 extraction4_array1 channel_1


title: expt.1124 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP2 (Ab2-90);target name: HP2;host: Rabbit;antigen: cDNA identified in Y2H that corresponds to C-terminal end;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Elgin Ab2-90;short description: rabbit polyclonal;

source_name: expt.1124 extraction3_array1 channel_1


title: expt.968 extraction1_array1

source_name: expt.968 extraction1_array1 channel_1


title: expt.967 extraction3_array1

source_name: expt.967 extraction3_array1 channel_1


title: expt.971 extraction1_array1

source_name: expt.971 extraction1_array1 channel_1


title: expt.1123 extraction1_array1

source_name: expt.1123 extraction1_array1 channel_1


title: expt.799 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.799 extraction2_array1 channel_1


title: expt.876 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1c (MO 462);target name: HP1c;host: Rabbit;antigen: aa135-237;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: MO 462;short description: E.coli produced protein fragment was used to inocculate rabbit.;

source_name: expt.876 extraction3_array1 channel_1


title: expt.798 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.798 extraction4_array1 channel_1


title: expt.877 extraction1_array1

source_name: expt.877 extraction1_array1 channel_1


title: expt.690 extraction5_array1

description: channel ch1 is input DNA;

source_name: expt.690 extraction5_array1 channel_1

value: Embryo 2-4hr OR


title: expt.855 extraction4_array1

source_name: expt.855 extraction4_array1 channel_1


title: expt.791 extraction3_array1

source_name: expt.791 extraction3_array1 channel_1


title: expt.974 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.974 extraction4_array1 channel_1


title: expt.1045 extraction1_array1

source_name: expt.1045 extraction1_array1 channel_1


title: expt.800 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.800 extraction2_array1 channel_1


title: expt.1083 extraction3_array1

source_name: expt.1083 extraction3_array1 channel_1


title: expt.975 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.975 extraction2_array1 channel_1


title: expt.1093 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1b (Henikoff);target name: HP1b;host: Rabbit;antigen: CASPIGSINQDENIKPDESSELDN;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Henikoff;short description: HP1b antibody from Henikoff lab;

source_name: expt.1093 extraction3_array1 channel_1


title: expt.1084 extraction1_array1

source_name: expt.1084 extraction1_array1 channel_1


title: expt.1094 extraction1_array1

source_name: expt.1094 extraction1_array1 channel_1


title: expt.858 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me3 abcam;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;reference: http://www.abcam.com/Histone-H3-tri-methyl-K9-antibody-ChIP-Grade-ab8898.html;short description: rabbit polyclonal to Histone H3 (tri methyl K9) ChIP grade;

source_name: expt.858 extraction3_array1 channel_1


title: expt.903 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.903 extraction4_array1 channel_1


title: expt.207 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.207 extraction4_array1 channel_1


title: expt.213 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K79Me1;target name: H3K79me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 mono methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2886;reference: http://www.abcam.com/Histone-H3-mono-methyl-K79-antibody-ChIP-Grade-ab2886.html;short description: Rabbit antisera raised against H3 peptide mono-methylated at K79.;

source_name: expt.213 extraction3_array1 channel_1


title: expt.937 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.937 extraction2_array1 channel_1


title: expt.859 extraction1_array1

source_name: expt.859 extraction1_array1 channel_1


title: expt.221 extraction1_array1

source_name: expt.221 extraction1_array1 channel_1


title: expt.902 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.902 extraction2_array1 channel_1


title: expt.860 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9ac;target name: H3K9ac;host: Rabbit;antigen: Peptide including acetyl-lysine 9 of histone 3;clonal: Polyclonal;purified: Crude;company: Lake Placid;catalog: AR-0102;short description: rabbit polyclonal against a peptide including acetyl-lysine 9 of histone H3.;

source_name: expt.860 extraction1_array1 channel_1


title: expt.938 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.938 extraction4_array1 channel_1


title: expt.929 extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K36me1;target name: H3K36me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 mono methylated at K36.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9048;reference: http://www.abcam.com/Histone-H3-mono-methyl-K36-antibody-ChIP-Grade-ab9048.html;short description: Rabbit polyclonal to Histone H3 (mono methyl K36) - ChIP Grade;

source_name: expt.929 extraction1_array1 channel_1


title: expt.861 extraction3_array1

source_name: expt.861 extraction3_array1 channel_1


title: expt.930 extraction3_array1

source_name: expt.930 extraction3_array1 channel_1


title: expt.1065 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1065 extraction2_array1 channel_1


title: expt.1087 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K23ac;target name: H3K23ac;host: Rabbit;antigen: Ovalbumin-conjugated synthetic peptide (KQLASAcKAARK-C) corresponding to amino acids 18-27 of yeast histone H3 acetylated on lysine 23 with a C-terminal cysteine added for conjugation purposes;clonal: Polyclonal;purified: Crude;company: Upstate;catalog: 07-355;reference: http://www.millipore.com/catalogue/item/07-355;short description: rabbit polyclonal against a synthetic peptide corresponding to aa 18-27 of yeast histone 3 with K23 acetylated;

source_name: expt.1087 extraction3_array1 channel_1


title: expt.1088 extraction1_array1

source_name: expt.1088 extraction1_array1 channel_1


title: expt.923 extraction3_array1

source_name: expt.923 extraction3_array1 channel_1


title: expt.922 extraction1_array1

source_name: expt.922 extraction1_array1 channel_1


title: expt.690 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.690 extraction4_array1 channel_1


title: expt.1112 extraction3_array1

source_name: expt.1112 extraction3_array1 channel_1


title: expt.208 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.208 extraction2_array1 channel_1


title: expt.1064 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1064 extraction4_array1 channel_1


title: expt.865 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K18Ac (new lot);target name: H3K18Ac;host: Rabbit;antigen: Synthetic peptide derived from within residues 1 - 100 Histone H3 acetylated at K18.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab1191;reference: http://www.abcam.com/Histone-H3-acetyl-K18-antibody-ChIP-Grade-ab1191.html;short description: rabbit polyclonal to Histone H3K18ac ChIP grade;

source_name: expt.865 extraction3_array1 channel_1


title: expt.864 extraction1_array1

source_name: expt.864 extraction1_array1 channel_1


title: expt.1111 extraction1_array1

source_name: expt.1111 extraction1_array1 channel_1


title: expt.909 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.909 extraction4_array1 channel_1


title: expt.1148 extraction3_array1

source_name: expt.1148 extraction3_array1 channel_1


title: expt.1145 extraction1_array1

source_name: expt.1145 extraction1_array1 channel_1


title: expt.910 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.910 extraction2_array1 channel_1


title: expt.1156 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1156 extraction4_array1 channel_1


title: expt.85 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.85 extraction4_array1 channel_1


title: expt.1149 extraction1_array1

source_name: expt.1149 extraction1_array1 channel_1


title: expt.1155 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1155 extraction2_array1 channel_1


title: expt.281 extraction1_array1

source_name: expt.281 extraction1_array1 channel_1


title: expt.280 extraction3_array1

source_name: expt.280 extraction3_array1 channel_1


title: expt.1116 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1116 extraction2_array1 channel_1


title: expt.240 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.240 extraction2_array1 channel_1


title: expt.1131 extraction3_array1

source_name: expt.1131 extraction3_array1 channel_1


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 15

type: RNA

city: Rotterdam

first: Jill

last: Spijkers-Hagelstein

address: Dr Molewaterplein 50

department: Pediatric Oncology

country: Netherlands

institute: ErasmusMC - Sophia's Childrens Hospital

description:
sens_15
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix HU133plus 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The CEL files represent the raw (unscaled; scaling factor = 1) gene expression data. Raw (unscaled) array data was collectively normalized using variance-stabilizing normalization (VSN), performed in the statistical environment R (version 2.10.1) using Bioconductor packages.

molecule: total RNA

organism: Homo sapiens

source_name: Primary infant ALL cells at diagnosis (untreated) (>90% blasts)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted form leukemic cells using TRIzol reagent (Invitrogen) according to the manufacturer's protocol

treatment_protocol: Primary ALL samples were obtained at diagnosis (before treatment) and processed within 24 hours after sampling. All samples contained >90% leukemic blasts.

tag: disease state

value: Precursor B-cell acute lymphoblastic leukemia (ALL)

tag: cell type

value: MLL-rearranged

tag: age

value: < 1 year of age

tag: prednisolone sensitivity

value: sensitive


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 12

description:
sens_12
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels

value: Primary infant ALL cells at diagnosis (untreated) (>90% blasts)


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 7

description:
sens_7
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 14

description:
sens_14
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 10

description:
sens_10
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 24

description:
res_24
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels

value: resistant


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 11

description:
sens_11
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 16

description:
res_16
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 17

description:
sens_17
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 18

description:
sens_18
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 1

description:
sens_1
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 2

description:
sens_2
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 19

description:
res_19
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 16

description:
sens_16
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 19

description:
sens_19
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 3

description:
sens_3
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 13

description:
sens_13
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 9

description:
sens_9
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 20

description:
res_20
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 6

description:
sens_6
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 5

description:
sens_5
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 23

description:
res_23
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 17

description:
res_17
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 22

description:
res_22
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 8

description:
sens_8
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro sensitive to prednisolone 4

description:
sens_4
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 15

description:
res_15
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 18

description:
res_18
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 21

description:
res_21
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 10

description:
res_10
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels