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;

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.

input sample: GSM521008 (pirrota_540_A12_Input18.362.CEL)

source_name: Cell Line S2-DRSC;Antibody CP190-HB extraction1_array1 channel_1

value: Male


status: Public on Mar 12 2010

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

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.

input sample: GSM521010 (pirrota_499_S14_Input18.320.CEL)

label: biotin

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Cell Line S2-DRSC;Antibody CP190-HB extraction3_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


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Su(Hw)-VC;target name: SU(HW);host: Rabbit;antigen: Not Available;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Victor Corces;short description: Antibody against SU(HW) protein;

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.

input sample: GSM520986 (pirrota_499_S14_Input18.320.CEL)

source_name: Cell Line S2-DRSC;Antibody Su(Hw)-VC 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.


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.

input sample: GSM520984 (pirrota_619_A14_Input-18cycles.404.CEL)

source_name: Cell Line S2-DRSC;Antibody Su(Hw)-VC extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: BEAF-70;target name: BEAF32A and B;host: Mouse;antigen: Not Available;clonal: Monoclonal;purified: Affinity;company: Lab;catalog: Paul Schedl Jason Blanton Greg Shanower;short description: Monoclonal antibody against BEAF32A and B.   The antibody recognizes the constant region of both BEAF 32A and B.;

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.

input sample: GSM520994 (pirrota_437_B3_INPUT.253.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody BEAF-70 extraction3_array1 channel_1

value: CNS-derived cell-line

value: third instar larval stage

tag: genotype

value: y v f mal

value: Unknown


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.

input sample: GSM521006 (pirrota_621_B5_Input-18cycles.406.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody CP190-HB extraction3_array1 channel_1


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.

input sample: GSM520998 (pirrota_441_A12_INPUT.267.CEL)

source_name: Cell Line S2-DRSC;Antibody BEAF-70 extraction3_array1 channel_1


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.

input sample: GSM521004 (pirrota_620_B3_Input-18cycles.405.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody CP190-HB extraction1_array1 channel_1


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.

input sample: GSM520996 (pirrota_499_S14_Input18.320.CEL)

source_name: Cell Line S2-DRSC;Antibody BEAF-70 extraction1_array1 channel_1


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;

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.

input sample: GSM520980 (pirrota_540_A12_Input18.362.CEL)

source_name: Cell Line S2-DRSC;Antibody SU(HW)-HB extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: RNA pol II (ALG);target name: PolII;host: Goat;antigen: Drosophila RNA polymerase II;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Arno L. Greenleaf;short description: Goat IgG against Drosophila RNA polymerase II (see Weeks et al. 1982 J.Biol.Chem257:5884-5891);

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.

input sample: GSM520976 (pirrota_212_A8_Input.62.CEL)

source_name: Cell Line S2-DRSC;Antibody RNA pol II (ALG) extraction1_array1 channel_1


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.

input sample: GSM520992 (pirrota_435_B4_INPUT.255.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody BEAF-70 extraction1_array1 channel_1


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.

input sample: GSM520978 (pirrota_292_A9_Input.136.CEL)

source_name: Cell Line S2-DRSC;Antibody RNA pol II (ALG) extraction3_array1 channel_1


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.

input sample: GSM520982 (pirrota_499_S14_Input18.320.CEL)

source_name: Cell Line S2-DRSC;Antibody SU(HW)-HB extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Pc;target name: Pc;host: Rabbit;antigen: Not Available;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: VP Lab;short description: Polyclonal Rabbit antibody against Polycomb protein.;

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.

input sample: GSM520962 (pirrota_365_B2_Input.208.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody Pc extraction3_array1 channel_1


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.

input sample: GSM520972 (pirrota_479_Kc-1_Input(14cyc).290.CEL)

source_name: Cell Line Kc167;Antibody RNA pol II (ALG) extraction1_array1 channel_1

value: se/e

value: Female


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.

input sample: GSM520968 (pirrota_477_C18-1_Input(14cyc).288.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody RNA pol II (ALG) extraction1_array1 channel_1

value: dorsal mesothoracic disc


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.

input sample: GSM520974 (pirrota_480_Kc-2_Input(14cyc).291.CEL)

source_name: Cell Line Kc167;Antibody RNA pol II (ALG) extraction3_array1 channel_1


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.

input sample: GSM520970 (pirrota_478_C18-2_Input(14cyc).289.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody RNA pol II (ALG) extraction3_array1 channel_1


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.

input sample: GSM520966 (pirrota_298_S11_Input.143.CEL)

source_name: Cell Line S2-DRSC;Antibody Pc extraction3_array1 channel_1


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.

input sample: GSM520964 (pirrota_264_S13_Input.116.CEL)

source_name: Cell Line S2-DRSC;Antibody Pc extraction1_array1 channel_1


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.

input sample: GSM520960 (pirrota_436_B5_INPUT.254.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody Pc extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: mod2.2-VC;target name: MOD(MDG4)67.2;host: Rat;antigen: Not Available;clonal: Monoclonal;purified: Crude;company: Lab;catalog: Victor Corces;short description: Antibody against MOD(MDG4)67.2 protein;

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.

input sample: GSM520956 (pirrota_620_B3_Input-18cycles.405.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody mod2.2-VC extraction1_array1 channel_1


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;

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.

input sample: GSM520954 (pirrota_292_A9_Input.136.CEL)

source_name: Cell Line S2-DRSC;Antibody H4K8ac extraction3_array1 channel_1


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;

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.

input sample: GSM520946 (pirrota_212_A8_Input.62.CEL)

source_name: Cell Line S2-DRSC;Antibody H4K16ac(M) extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H4K16ac(L);target name: H4K16ac;host: Rabbit;antigen: Peptide including acetil-lysine 16 of histon H4;clonal: Polyclonal;purified: Affinity;company: Lake Placid;catalog: AR-0107;short description: Rabbit polyclonal to Histone H4K16ac;

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.

input sample: GSM520942 (pirrota_212_A8_Input.62.CEL)

source_name: Cell Line S2-DRSC;Antibody H4K16ac(L) extraction3_array1 channel_1


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.

input sample: GSM520936 (pirrota_479_Kc-1_Input(14cyc).290.CEL)

source_name: Cell Line Kc167;Antibody H4K16ac(L) extraction1_array1 channel_1


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.

input sample: GSM520938 (pirrota_480_Kc-2_Input(14cyc).291.CEL)

source_name: Cell Line Kc167;Antibody H4K16ac(L) extraction3_array1 channel_1


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.

input sample: GSM520952 (pirrota_212_A8_Input.62.CEL)

source_name: Cell Line S2-DRSC;Antibody H4K8ac extraction1_array1 channel_1


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.

input sample: GSM520932 (pirrota_477_C18-1_Input(14cyc).288.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody H4K16ac(L) extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me3 (new lot);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;

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.

input sample: GSM520920 (pirrota_424_B1_Input.250.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9me3 (new lot) extraction1_array1 channel_1


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.

input sample: GSM520944 (pirrota_292_A9_Input.136.CEL)

source_name: Cell Line S2-DRSC;Antibody H4K16ac(M) extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me3;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 against a synthetic peptide derived from residues 1-100 of human histone H3 tri-methylated at K9;

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.

input sample: GSM520924 (pirrota_242_S12_Input(14_cycles).85.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K9me3 extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H4K5ac;target name: H4K5ac;host: Rabbit;antigen: Synthetic peptide corresponding to amino acids 1-10 of yeast histone H4 acetylated on lysine 5 with a C-terminal cysteine added for conjugation purposes;clonal: Polyclonal;purified: Affinity;company: Millipore;catalog: 07-327;short description: Rabbit polyclonal to Histone H4 (acetyl K5);

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.

input sample: GSM520948 (pirrota_212_A8_Input.62.CEL)

source_name: Cell Line S2-DRSC;Antibody H4K5ac extraction1_array1 channel_1


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.

input sample: GSM520950 (10.pirrota_142_A3_Input_HD.CEL)

source_name: Cell Line S2-DRSC;Antibody H4K5ac extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me2 antibody2;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 against a synthetic peptide derived from within residues 1-100 of human H3 di methylated at K9;

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.

input sample: GSM520918 (pirrota_242_S12_Input(14_cycles).85.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K9me2 antibody2 extraction3_array1 channel_1


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.

input sample: GSM520940 (pirrota_292_A9_Input.136.CEL)

source_name: Cell Line S2-DRSC;Antibody H4K16ac(L) extraction1_array1 channel_1


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.

input sample: GSM520934 (pirrota_478_C18-2_Input(14cyc).289.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody H4K16ac(L) extraction3_array1 channel_1


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;

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.

input sample: GSM520914 (pirrota_424_B1_Input.250.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9me2-Ab2 (new lot) extraction3_array1 channel_1


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.

input sample: GSM520912 (pirrota_425_B2_Input.251.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9me2-Ab2 (new lot) extraction1_array1 channel_1


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.;

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.

input sample: GSM520910 (pirrota_242_S12_Input(14_cycles).85.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K9ac extraction3_array1 channel_1


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.

input sample: GSM520930 (pirrota_482_B2_Input(14cyc).293.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H4K16ac(L) extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K79Me2;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.;

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.

input sample: GSM520906 (40.pirrota_182_S8_Input_HD.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K79Me2 extraction3_array1 channel_1


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.

input sample: GSM520926 (pirrota_196_S9_Input.46.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K9me3 extraction3_array1 channel_1


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.

input sample: GSM520922 (pirrota_425_B2_Input.251.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9me3 (new lot) extraction3_array1 channel_1


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.

input sample: GSM520958 (pirrota_621_B5_Input-18cycles.406.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody mod2.2-VC extraction3_array1 channel_1


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.

input sample: GSM520916 (pirrota_196_S9_Input.46.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K9me2 antibody2 extraction1_array1 channel_1


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.

input sample: GSM520902 (pirrota_437_B3_INPUT.253.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K79Me2 extraction3_array1 channel_1


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.

input sample: GSM520904 (pirrota_208_S12_Input.58.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K79Me2 extraction1_array1 channel_1


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.

input sample: GSM520928 (pirrota_481_B1_Input(14cyc).292.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H4K16ac(L) extraction1_array1 channel_1


title: Antibody H3K4Me3(LP) extraction1_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K4Me3(LP);target name: H3K4me3;host: Rabbit;antigen: Antibody raised against a peptide containing trimethylated K4.;clonal: Polyclonal;purified: Crude;company: Lake Placid;catalog: AR-0169-50;short description: Polyclonal Rabbit antibody raised against a peptide containing trimethylated K4.;

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.

input sample: GSM520894 (40.pirrota_182_S8_Input_HD.CEL)

source_name: Antibody H3K4Me3(LP) extraction1_array1 channel_1


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.

input sample: GSM520900 (pirrota_365_B2_Input.208.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K79Me2 extraction1_array1 channel_1


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.

input sample: GSM520908 (pirrota_190_A3_Input.38.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K9ac extraction1_array1 channel_1


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.;

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.

input sample: GSM520892 (pirrota_540_A12_Input18.362.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K4me1 extraction5_array1 channel_1


title: Antibody H3K4Me3(LP) extraction5_array1

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.

input sample: GSM520898 (pirrota_208_S12_Input.58.CEL)

source_name: Antibody H3K4Me3(LP) extraction5_array1 channel_1


title: Antibody H3K4Me3(LP) extraction3_array1

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.

input sample: GSM520896 (pirrota_303_S14_Input.148.CEL)

source_name: Antibody H3K4Me3(LP) extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K36me3;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;

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.

input sample: GSM520884 (10.pirrota_142_A3_Input_HD.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K36me3 extraction1_array1 channel_1


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.

input sample: GSM520882 (pirrota_480_Kc-2_Input(14cyc).291.CEL)

source_name: Cell Line Kc167;Antibody H3K36me3 extraction3_array1 channel_1


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.

input sample: GSM520890 (pirrota_619_A14_Input-18cycles.404.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K4me1 extraction3_array1 channel_1


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.

input sample: GSM520888 (pirrota_208_S12_Input.58.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K4me1 extraction1_array1 channel_1


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.

input sample: GSM520880 (pirrota_479_Kc-1_Input(14cyc).290.CEL)

source_name: Cell Line Kc167;Antibody H3K36me3 extraction1_array1 channel_1


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.

input sample: GSM520886 (12.pirrota_144_A7_Input_HD.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K36me3 extraction3_array1 channel_1


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;

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.

input sample: GSM520874 (pirrota_482_B2_Input(14cyc).293.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K36me1 extraction3_array1 channel_1


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.

input sample: GSM520876 (pirrota_482_B2_Input(14cyc).293.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K36me3 extraction1_array1 channel_1


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.

input sample: GSM520878 (pirrota_481_B1_Input(14cyc).292.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K36me3 extraction3_array1 channel_1


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.;

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.

input sample: GSM520866 (pirrota_437_B3_INPUT.253.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K27Me3 (Abcam2) extraction3_array1 channel_1


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.;

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.

input sample: GSM520862 (pirrota_208_S12_Input.58.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K27Ac extraction3_array1 channel_1


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.

input sample: GSM520872 (pirrota_481_B1_Input(14cyc).292.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K36me1 extraction1_array1 channel_1


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.

input sample: GSM520868 (pirrota_298_S11_Input.143.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K27Me3 (Abcam2) extraction1_array1 channel_1


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.

input sample: GSM520870 (pirrota_499_S14_Input18.320.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K27Me3 (Abcam2) extraction3_array1 channel_1


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.

input sample: GSM520860 (40.pirrota_182_S8_Input_HD.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K27Ac extraction1_array1 channel_1


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;

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.

input sample: GSM520851 (pirrota_242_S12_Input(14_cycles).85.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K23ac extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K18ac;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 a synthetic peptide from within residues 1-100 of H3 acetylated at K18;

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.

input sample: GSM520845 (pirrota_242_S12_Input(14_cycles).85.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K18ac extraction3_array1 channel_1


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.

input sample: GSM520847 (pirrota_425_B2_Input.251.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K23ac extraction1_array1 channel_1


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.

input sample: GSM520841 (pirrota_425_B2_Input.251.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K18ac extraction3_array1 channel_1


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.

input sample: GSM520853 (pirrota_190_A3_Input.38.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K23ac extraction3_array1 channel_1


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.

input sample: GSM520849 (pirrota_424_B1_Input.250.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K23ac extraction3_array1 channel_1


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.

input sample: GSM520858 (pirrota_437_B3_INPUT.253.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K27Ac extraction3_array1 channel_1


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.

input sample: GSM520856 (pirrota_436_B5_INPUT.254.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K27Ac extraction1_array1 channel_1


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: Isotype: IgG2a;

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.

input sample: GSM520837 (pirrota_292_A9_Input.136.CEL)

source_name: Cell Line S2-DRSC;Antibody H2B-ubiq (NRO3) extraction3_array1 channel_1


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.

input sample: no input (NA)

source_name: Cell Line S2-DRSC;Antibody H3K23ac extraction5_array1 channel_1


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.

input sample: GSM520839 (pirrota_424_B1_Input.250.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K18ac extraction1_array1 channel_1


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.

input sample: GSM520829 (pirrota_481_B1_Input(14cyc).292.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H2B-ubiq (NRO3) extraction3_array1 channel_1


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.

input sample: GSM520864 (pirrota_435_B4_INPUT.255.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K27Me3 (Abcam2) extraction1_array1 channel_1


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.

input sample: GSM520833 (pirrota_479_Kc-1_Input(14cyc).290.CEL)

source_name: Cell Line Kc167;Antibody H2B-ubiq (NRO3) extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Ez;target name: Ez;host: Rabbit;antigen: Not available;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: VP Lab;short description: Polyclonal rabbit antibody raised against recombinant Enhancer of Zeste protein.;

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.

input sample: GSM520821 (40.pirrota_182_S8_Input_HD.CEL)

source_name: Cell Line S2-DRSC;Antibody Ez extraction5_array1 channel_1


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.

input sample: GSM520843 (pirrota_190_A3_Input.38.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K18ac extraction1_array1 channel_1


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;

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.

input sample: GSM520815 (pirrota_499_S14_Input18.320.CEL)

source_name: Cell Line S2-DRSC;Antibody CTCF-VC extraction3_array1 channel_1


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.

input sample: GSM520819 (pirrota_264_S13_Input.116.CEL)

source_name: Cell Line S2-DRSC;Antibody Ez extraction3_array1 channel_1


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.

input sample: GSM520813 (pirrota_619_A14_Input-18cycles.404.CEL)

source_name: Cell Line S2-DRSC;Antibody CTCF-VC extraction1_array1 channel_1


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.

input sample: GSM520831 (pirrota_480_Kc-2_Input(14cyc).291.CEL)

source_name: Cell Line Kc167;Antibody H2B-ubiq (NRO3) extraction1_array1 channel_1


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);

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.

input sample: GSM520823 (pirrota_264_S13_Input.116.CEL)

source_name: Cell Line S2-DRSC;Antibody GAF extraction1_array1 channel_1


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.

input sample: GSM520809 (pirrota_621_B5_Input-18cycles.406.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody CTCF-VC extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: CP190-VC;target name: CP190;host: Guinea Pig;antigen: Not Available;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Victor Corces;short description: Antibody against CP190 protein;

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.

input sample: GSM520805 (pirrota_619_A14_Input-18cycles.404.CEL)

source_name: Cell Line S2-DRSC;Antibody CP190-VC extraction1_array1 channel_1


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.

input sample: GSM520817 (pirrota_499_S14_Input18.320.CEL)

source_name: Cell Line S2-DRSC;Antibody Ez extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Chro(Chriz)WR;target name: Chriz;host: Rabbit;antigen: Amino Acids 345-926;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: I.F. Zhimulev/H. Saumweber;short description: Rabbit antiserum  to CG10712. Gortchakov et al. 2005. Chromosoma.;

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.

input sample: GSM520803 (pirrota_292_A9_Input.136.CEL)

source_name: Cell Line S2-DRSC;Antibody Chro(Chriz)WR extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Chro(Chriz)BR;target name: Chriz;host: Rabbit;antigen: Amino Acids 345-926;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: I.F. Zhimulev/H. Saumweber;short description: Rabbit antiserum to CG10712. Gortchakov et al. 2005. Chromosoma.;

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.

input sample: GSM520797 (pirrota_292_A9_Input.136.CEL)

source_name: Cell Line S2-DRSC;Antibody Chro(Chriz)BR extraction1_array1 channel_1


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.

input sample: GSM520799 (pirrota_212_A8_Input.62.CEL)

source_name: Cell Line S2-DRSC;Antibody Chro(Chriz)BR extraction3_array1 channel_1


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.

input sample: GSM520835 (pirrota_212_A8_Input.62.CEL)

source_name: Cell Line S2-DRSC;Antibody H2B-ubiq (NRO3) extraction1_array1 channel_1


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.

input sample: GSM520825 (40.pirrota_182_S8_Input_HD.CEL)

source_name: Cell Line S2-DRSC;Antibody GAF extraction3_array1 channel_1


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.

input sample: GSM520793 (pirrota_479_Kc-1_Input(14cyc).290.CEL)

source_name: Cell Line Kc167;Antibody Chro(Chriz)BR extraction1_array1 channel_1


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.

input sample: GSM520811 (pirrota_620_B3_Input-18cycles.405.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody CTCF-VC extraction3_array1 channel_1


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.

input sample: GSM520807 (pirrota_499_S14_Input18.320.CEL)

source_name: Cell Line S2-DRSC;Antibody CP190-VC extraction3_array1 channel_1


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.

input sample: GSM520787 (pirrota_481_B1_Input(14cyc).292.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody Chro(Chriz)BR extraction3_array1 channel_1


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.

input sample: GSM520801 (pirrota_212_A8_Input.62.CEL)

source_name: Cell Line S2-DRSC;Antibody Chro(Chriz)WR extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H4AcTetra;target name: H4acTetra;host: Rabbit;antigen: Peptide containing the amino terminal region of Tetrahymena histone variant hv1 acetylated at multiple lysines.;clonal: Polyclonal;purified: Affinity;company: Lake Placid;catalog: AR-0109;short description: Polyclonal rabbit antibody raised against the N-termina region of Tetrahymena histone variant hv1 acetylated at multiple lysines.;

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.

input sample: GSM520776 (pirrota_208_S12_Input.58.CEL)

source_name: Cell Line S2-DRSC;Antibody H4AcTetra extraction1_array1 channel_1


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.

input sample: GSM520795 (pirrota_480_Kc-2_Input(14cyc).291.CEL)

source_name: Cell Line Kc167;Antibody Chro(Chriz)BR extraction3_array1 channel_1


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.

input sample: GSM520827 (pirrota_482_B2_Input(14cyc).293.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H2B-ubiq (NRO3) extraction1_array1 channel_1


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.

input sample: GSM520785 (pirrota_482_B2_Input(14cyc).293.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody Chro(Chriz)BR extraction1_array1 channel_1


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;

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.

input sample: GSM520781 (pirrota_499_S14_Input18.320.CEL)

source_name: Cell Line S2-DRSC;Antibody BEAF-HB extraction1_array1 channel_1


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.

input sample: no input (NA)

source_name: Cell Line S2-DRSC;Antibody H4AcTetra extraction5_array1 channel_1


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.

input sample: GSM520778 (pirrota_303_S14_Input.148.CEL)

source_name: Cell Line S2-DRSC;Antibody H4AcTetra extraction3_array1 channel_1


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.

input sample: GSM520791 (pirrota_478_C18-2_Input(14cyc).289.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody Chro(Chriz)BR extraction3_array1 channel_1


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.

input sample: GSM520789 (pirrota_477_C18-1_Input(14cyc).288.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody Chro(Chriz)BR extraction1_array1 channel_1


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.

input sample: GSM520783 (pirrota_540_A12_Input18.362.CEL)

source_name: Cell Line S2-DRSC;Antibody BEAF-HB extraction3_array1 channel_1


title: Drosophila_S2_WT_Mock_ChIP_rep2

status: Public on Jan 11 2010

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

country: USA

institute: NIDDK, NIH

description: ChIP-chip of Mock in Drosophila S2 WT cells

hyb_protocol: Hybridizations of samples to the microarrays were performed at 60°C, followed by washes exactly as described  (Parisi M, 2004, Genome Biol 5:R40).

scan_protocol: Arrays were scanned on an Axon GenePix 4000B (Molecular Devices Corporation, Sunnyvale, CA) and signal for each array elements were extracted with GenePix v.5.1 image acquisition software (Molecular Devices Corporation).

data_processing: All microarray data were processed and analyzed in R/Bioconductor.  The arrays were normalized using quantile normalization based on the input channel as common reference across slides.

source_name: Input, Drosophila melanogaster S2 cells

label_protocol: 600 ng of amplified DNA (ChIP enriched DNA or input DNA) were then labeled using the Cy3- or Cy5-labeled random nonamers (Trilink Biosciences, San Diego, USA) with Klenow enzymes.

growth_protocol: Drosophila S2 cells were grown at 25°C in Schneider's Drosophila Medium (Invitrogen, Carlsbad, CA) supplemented with 10% Fetal Bovine serum (SAFC Biosciences, Lenexa, KS) and Penicillin-Streptomycin.

extract_protocol: 5-10 x 106 S2 cells with dsRNA or mock treatment were fixed with 1% formaldehyde in tissue culture media for 10 min at room temperature. After washing, the cells were disrupted by cell lysis and nuclei lysis. The nuclear extraction was then sheared to 200-1000bp by sonication using a Misonix Sonicator 3000 and the soluble chromatin was collected for IPs. Specific antibodies were added to the chromatin extract for two hours and then were bound to protein A agarose beads at 4°C overnight. After washes and elution, the immunoprecipitated DNA was extracted and purified. DNA amplification was performed using a Ligation-mediated PCR (LM-PCR) protocol from FlyChip (http://www.flychip.org.uk/protocols/chip/lm_pcr.php).

tag: cell type

value: S2 cells

tag: sample type

value: input

source_name: Mock ChIP, Drosophila melanogaster S2 cells

tag: antibody

value: Mock


title: Drosophila_S2_msl2-RNAi-treated_H4AcK16_ChIP_rep1

description: ChIP-chip of H4AcK16 in Drosophila S2 msl2-RNAi-treated cells

source_name: H4AcK16 ChIP, Drosophila melanogaster S2 cells


title: Drosophila_S2_msl2-RNAi-treated_H4AcK16_ChIP_rep3

source_name: input, Drosophila melanogaster S2 cells


title: Drosophila_S2_mof-RNAi-treated_Mock_ChIP_rep2

description: ChIP-chip of Mock in Drosophila S2 mof-RNAi-treated cells


title: Drosophila_S2_mof-RNAi-treated_Mock_ChIP_rep1


title: Drosophila_S2_WT_H4AcK16_ChIP_rep1

description: ChIP-chip of H4AcK16 in Drosophila S2 WT cells


title: Drosophila_S2_mof-RNAi-treated_H4AcK16_ChIP_rep1

description: ChIP-chip of H4AcK16 in Drosophila S2 mof-RNAi-treated cells


title: Drosophila_S2_msl2-RNAi-treated_H4AcK16_ChIP_rep2


title: Drosophila_S2_mof-RNAi-treated_H4AcK16_ChIP_rep2


title: Drosophila_S2_msl2-RNAi-treated_H3diMeK4_ChIP_rep2

description: ChIP-chip of H3diMeK4 in Drosophila S2 msl2-RNAi-treated cells

source_name: H3diMeK4 ChIP, Drosophila melanogaster S2 cells


title: Drosophila_S2_WT_Mock_ChIP_rep3


title: Drosophila_S2_mof-RNAi-treated_H3diMeK4_ChIP_rep3

description: ChIP-chip of H3diMeK4 in Drosophila S2 mof-RNAi-treated cells


title: Drosophila_S2_WT_Mock_ChIP_rep1


title: Drosophila_S2_WT_H4AcK16_ChIP_rep2


title: Drosophila_S2_msl2-RNAi-treated_Mock_ChIP_rep3

description: ChIP-chip of Mock in Drosophila S2 msl2-RNAi-treated cells


title: Drosophila_S2_mof-RNAi-treated_H4AcK16_ChIP_rep3


title: Drosophila_S2_mof-RNAi-treated_Mock_ChIP_rep3


title: Drosophila_S2_WT_H3diMeK4_ChIP_rep2

description: ChIP-chip of H3diMeK4 in Drosophila S2 WT cells


title: Drosophila_S2_mof-RNAi-treated_H3diMeK4_ChIP_rep1


title: Drosophila_S2_WT_H3diMeK4_ChIP_rep1


title: Drosophila_S2_mof-RNAi-treated_H3diMeK4_ChIP_rep2


title: Drosophila_S2_msl2-RNAi-treated_Mock_ChIP_rep2


title: Drosophila_S2_msl2-RNAi-treated_H3diMeK4_ChIP_rep1


title: Drosophila_S2_WT_H4AcK16_ChIP_rep3


title: Drosophila_S2_WT_H3diMeK4_ChIP_rep3


title: Dmel_adult_H3diMeK4_ChIP_female_rep2

description: ChIP-chip of H3diMeK4 in Drosophila adult female flies

data_processing: All microarray data were processed and analyzed in R/Bioconductor.  The arrays were median centered (subtracting the weighted median from M-values for each array) and then normalized using quantile normalization based on the input channel as common reference across slides.

source_name: input, Drosophila melanogaster adult female

growth_protocol: Flies were grown at 25°C on standard cornmeal media. Wildtype flies for chromatin immunoprecipitaion were aged for 5-7 days post-eclosion, sexed and flash frozen.

extract_protocol: About 0.5 g of sex-sorted adult flies was cross-linked with 1.8% for 20 minutes at room temperature. After washing, the flies were completely homogenized and the cells were disrupted by cell lysis and nuclei lysis. The nuclear extraction was then sheared to 200-1000bp by sonication using a Misonix Sonicator 3000 and the soluble chromatin was collected for IPs. Specific antibodies were added to the chromatin extract for two hours and then were bound to protein A agarose beads at 4°C overnight. After washes and elution, the immunoprecipitated DNA was extracted and purified. DNA amplification was performed using a Ligation-mediated PCR (LM-PCR) protocol from FlyChip (http://www.flychip.org.uk/protocols/chip/lm_pcr.php).

tag: gender

value: female

tag: reference

value: Input, 5-7 day aged adult flies

source_name: H3diMeK4 ChIP, Drosophila melanogaster adult female

tag: test

value: ChIP, 5-7 day aged adult flies


title: Dmel_adult_H3diMeK4_ChIP_male_rep1

description: ChIP-chip of H3diMeK4 in Drosophila adult male flies

source_name: input, Drosophila melanogaster adult male

value: male

source_name: H3diMeK4 ChIP, Drosophila melanogaster adult male


title: Dmel_adult_H3diMeK4_ChIP_male_rep2


title: Dmel_adult_H4AcK16_ChIP_male_rep4

description: ChIP-chip of H4AcK16 in Drosophila adult male flies

source_name: H4AcK16 ChIP, Drosophila melanogaster adult male


title: Dmel_adult_H3PS10_ChIP_male_rep1

description: ChIP-chip of H3PS10 in Drosophila adult male flies

source_name: H3PS10 ChIP, Drosophila melanogaster adult male


title: LeftVentricleEndothelialCells_sedentary3

status: Public on Dec 18 2009

type: RNA

city: Brisbane

first: Aya

last: Matsumoto

state: Qld

address: Blair Drive

department: Hunan Movement Studies

country: Australia

institute: University of Queensland

hyb_protocol: To 10µl sample, the following were added in order: 1µl of 10µg/µl poly dA, 8µl of 20x SSC, 20µl of deionised formamide and 1µl of 20% w/v SDS. After heat denaturing at  95oC for 5 min followed by equilibration at 45oC for 60 min 38µl of hybridization mixture hybridization mixture was added to prewarmed microarray slides. The hybridization was allowed to proceed for 22 hrs at  45oC in hybrization chambers saturated with 40µl of formamide/MilliQ.. After hybridsation slides were washed sequentially in the dark for in 1x SSC in 0.1% w/v SDS, 0.5x SSC and 0.2x SSC at 450C for 10 min each, dried and scanned immediately.

scan_protocol: Microarray slides were scanned using a high resolution Agilent scanner and scanned images were processed with ImaGene 6.0 software.

data_processing: Signals of all arrays were normalized per spot and per chip using intensity-dependent Lowess fit normalization in GeneSpring.

molecule: total RNA

organism: Rattus norvegicus

source_name: Left ventricle endothelial cells, sedentary

label_protocol: cDNA was labeled using a SuperScript Plus Direct Labeling System according to the manufacturer's instructions.

growth_protocol:
Rats were housed 2-3 per cage,
maintained on a 12-12h light/dark cycle,
provided with rat chow and tap water ad libitum

extract_protocol: Endothelial cells were extracted from left ventricles using Dynabeads. Total RNA was then extracted using a Quigen Rneasy Micro Kit according to the manufacturer's instructions.

value: heart

value: endothelial

tag: strain

value: Wistar

tag: Sex

tag: age

value: 24wk old

source_name: Left ventricle endothelial cells, reference

extract_protocol: Endothelial cells were extracted from left ventricle using Dynabeads. Total RNA was then extracted using a Quigen Rneasy Micro Kit according to the manufacturer's instructions.


title: Drosophila_S2_expression_mof-RNAi_rep2

description: Gene expression profile of Drosophila S2 mof-RNAi cells

hyb_protocol: Nimblegen sample tracking control, CPK6 50mer fiducial oligo control and hybridization buffer were added to the labeled samples. The samples were applied to microarrays on MAUI hybridization station (BioMicro Systems, Salt Lake City, UT ) and were hybridized for 16 hours at 42°C. Slides were then washed according to the protocol described by Nimblegen (Madison, WI) and dried by centrifugation.

scan_protocol: Arrays were scanned on an Axon GenePix 4200AL scanner (Molecular Devices Corporation, Sunnyvale, CA) and data was captured using NimbleScan 2.1 (NimbleGen Systems, Madison, WI).

data_processing: All microarray data were processed and analyzed in R/Bioconductor.  The arrays were normalized using loess and quantile normalization.

molecule: polyA RNA

source_name: Drosophila melanogaster S2 cells WT

label_protocol: 200ng adult poly(A)+ RNA was labeled with Cy3 or Cy5 random nonamer primer oligonucleotides (TriLink Biotechnologies, San Diego, CA) by reversed transcription in the presence of SuperScript II Reverse Transcriptase (Invitrogen). The labeled sample was purified with Chroma Spin column TE-10 (Clontech, Mountain View, CA).

extract_protocol: Total RNA was extracted using Trizol procedure, followed by mRNA isolation using an Oligotex mRNA Kit (Qiagen, Valencia, CA).

source_name: Drosophila melanogaster S2 cells mof-RNAi


title: Dmel_adult_H3PS10_ChIP_female_rep2

description: ChIP-chip of H3PS10 in Drosophila adult female flies

source_name: H3PS10 ChIP, Drosophila melanogaster adult female


title: Dmel_adult_H4AcK16_ChIP_female_rep1

description: ChIP-chip of H4AcK16 in Drosophila adult female flies

source_name: H4AcK16 ChIP, Drosophila melanogaster adult female


title: Dmel_adult_H3PS10_ChIP_male_rep2


title: Dmel_adult_H3PS10_ChIP_female_rep1


title: Dmel_adult_H4AcK16_ChIP_male_rep3


title: Dmel_adult_H4AcK16_ChIP_male_rep2


title: Drosophila_S2_msl2-RNAi-treated_H3diMeK4_ChIP_rep3


title: LeftVentricleEndothelialCells_AntioxidantandExercised2

source_name: Left ventricle endothelial cells, antioxidant supplemented and exercised

treatment_protocol:
Antioxidant supplementation for 14 weeks:
1000IU vitamin E /kg diet
1.6g alpha lipoic acid /kg diet
Endurance training on treadmill for 14 wks


title: Dmel_adult_H4AcK16_ChIP_female_rep3


title: LeftVentricleEndothelialCells_sedentary1


title: Dmel_adult_H4AcK16_ChIP_female_rep2


title: LeftVentricleEndothelialCells_sedentary4


title: Dmel_adult_H3diMeK4_ChIP_female_rep1


title: LeftVentricleEndothelialCells_sedentary2


title: Drosophila_S2_expression_msl2-RNAi_rep1

description: Gene expression profile of Drosophila S2 msl2-RNAi cells

source_name: Drosophila melanogaster S2 cells msl2-RNAi


title: Dmel_adult_H4AcK16_ChIP_male_rep1


title: LeftVentricleEndothelialCells_AntioxidantandExercised3


title: Drosophila_S2_expression_mof-RNAi_rep1


title: LeftVentricleEndothelialCells_AntioxidantandExercised1


title: Drosophila_S2_expression_msl2-RNAi_rep2


title: LeftVentricleEndothelialCells_AntioxidantandExercised4


title: LeftVentricleEndothelialCells_Antioxidant4

source_name: Left ventricle endothelial cells, antioxidant supplemented

treatment_protocol:
Antioxidant supplementation for 14 weeks:
1000IU vitamin E /kg diet
1.6g alpha lipoic acid /kg diet


title: Drosophila_S2_msl2-RNAi-treated_Mock_ChIP_rep1

source_name: Input, Drosophila melanogaster S2 cells

source_name: Mock ChIP, Drosophila melanogaster S2 cells


title: LeftVentricleEndothelialCells_Antioxidant1


title: LeftVentricleEndothelialCells_Antioxidant2


title: CoronaryArteryEndothelialCells_sedentary1

source_name: Coronary artery endothelial cells, sedentary

extract_protocol: Endothelial cells were extracted from coronary artery using Dynabeads. Total RNA was then extracted using a Quigen Rneasy Micro Kit according to the manufacturer's instructions.

source_name: Coronary artery endothelial cells, reference


title: LeftVentricleEndothelialCells_Exercise4

source_name: Left ventricle endothelial cells, exercised

treatment_protocol: Endurance training on treadmill for 14 wks


title: CoronaryArteryEndothelialCells_Antioxidant1

source_name: Coronary artery endothelial cells, antioxidant supplemented


title: LeftVentricleEndothelialCells_Exercise2


title: CoronaryArteryEndothelialCells_Exercise3

source_name: Coronary artery endothelial cells, exercised


title: CoronaryArteryEndothelialCells_AntioxidantandExercised2

source_name: Coronary artery endothelial cells, antioxidant supplemented and exercised


title: CoronaryArteryEndothelialCells_AntioxidantandExercised1


title: LeftVentricleEndothelialCells_Antioxidant3


title: CoronaryArteryEndothelialCells_sedentary3


title: CoronaryArteryEndothelialCells_AntioxidantandExercised3


title: LeftVentricleEndothelialCells_Exercise3


title: CoronaryArteryEndothelialCells_Exercise2


title: LeftVentricleEndothelialCells_Exercise1


title: CoronaryArteryEndothelialCells_sedentary2


title: CoronaryArteryEndothelialCells_Exercise1


title: CoronaryArteryEndothelialCells_Antioxidant3


title: CoronaryArteryEndothelialCells_Antioxidant2


title: Expression_(SOH10)

status: Public on Jan 12 2010

type: mixed

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: PolyA-tailed N2 mixed stage worm RNA expression profile over sonicated N2 genomic DNA

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing: The biweight mean was subtracted from the log base 2 ratios of Cy3/Cy5. Then the adjusted log ratios for all exonic probes of WS190 genes were averaged to give a single expression value for each gene in the supplementary file SOH10_expression.txt. These values were divided into quintiles for genes with both the 5-prime and 3-prime ends annotated in WS190.

organism: Caenorhabditis elegans

source_name: cDNA arising from oligo-dT primer reverse-transcribed total RNA

label_protocol: Standard NimbleGen protocol.

extract_protocol: RNA Trizol was used to prepare total RNA.

value: mixed stage

value: N2 (Bristol)

source_name: sonicated genomic DNA

extract_protocol: Genomic DNA was extracted with phenol-chloroform using the standard worm genomic DNA extraction protocol.


title: Chip-23 Endodormant Crown Bud rep-2 blue-2 & Non Flowering Competent Ecodormant Crown Bud rep-2 red-2

status: Public on Dec 01 2009

city: Fargo

first: Munevver

last: Dogramaci

state: ND

address: 1605 Albrecht Blvd N

institute: USDA-ARS

description:
Induction of endodormancy in crown buds was accomplished by subjecting greenhouse grown and growth chamber acclimated plants to a ramp down (RD) treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as previously established by Foley et al. (2009). These conditions mimic the average seasonal environmental conditions experienced in Fargo, ND (46°54′ N, 96°48′ W) during the transition from para- to endo-dormancy (Anderson et al. 2005).
Greenhouse-grown and one week growth chamber acclimated plants were subjected directly to an prolonged cold treatment for 11 weeks at 5-7°C, under constant 8 h:16 h day:night cycle; light fluencies were approximately 250 μmol m-2 s-1.
See Dogramaci et al. (2010, Plant Molecular Biology) for more details.

hyb_protocol: For microarray hybridizations, labeled cDNAs were prepared from 30 µg of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer's protocols. Labeled cDNAs were hybridized to a custom made 23K element microarray that contained 19,808 unigenes from a leafy spurge EST database (Anderson et al. 2007) and an additional 4,129 unigenes from a cassava EST database (Lokko et al. 2007). Comparison of gene expression between samples was accomplished using a rolling circle dye swap hybridization scheme (Churchill 2002) to provide every biological replicate with technical replicates. In our microarray analyses experiment, each of the four biological replicates included four technical replicates using two different dyes, resulting in a total of 16 technical replicates for each treatment.

scan_protocol: Microarray hybridization was visualized using a GenePix 4000B scanner and probe intensities and background were quantified using GenePix 6.0 software (Molecular Devices, Sunnyvale, California, USA).

data_processing: A quality control value of “1” was assigned to all probes that had intensity values greater than 2 times the standard deviation over average of the negative control and empty probe intensities (after deletion of 1% of the most intense negative/empty probe values). GeneMaths XT 5.1 software (Applied Maths Inc., Austin, TX, USA) was used for statistical analysis and clustering of the dataset. Hybridization intensities were log2 transformed, and arrays were centered and normalized against each other; technical replicates within each biological replicate were averaged.

organism: Euphorbia esula

source_name: Endodormant Crown Bud

growth_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype 1984-ND001 and maintained in a greenhouse as described by Anderson and Davis (2004). Shoot cuttings were grown in No. 1 Ray Leach Cone-tainers (Stuewe and Sons Inc. Corvallis, OR, USA) in the greenhouse for three months prior to application of experimental treatments. The greenhouse was set at 25°C with a 16 h:8 h day:night photoperiod. Average daily light fluencies were approximately 350 μmol m-2 s-1 and 400 W high-pressure sodium lamps were used as to extend the day-length. Thirty plants per biological replication were exposed to each of the four environmental treatments (Fig. 1) and each environmental treatment was replicated four times. Prior to the start of each experiment, plants were randomly chosen from the greenhouse and acclimated in a growth chamber (PGR15 Model of Conviron, Winnipeg, Canada) for one week at 27°C, 16 h:8 h day:night photoperiod. All crown buds samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation.

extract_protocol: At the end of each treatment, crown bud samples were collected, flash froze in liquid N2, and stored at -80°C until RNA extraction. Crown bud samples were ground to a fine powder in liquid N2, and RNA was extracted from approximately one gram of tissue according to the pine tree RNA extraction protocol (Chang et al. 1993). RNA quality and quantity was confirmed by spectrophotometry and agarose gel electrophoresis.

value: Endodormant Crown Bud


title: Chip-27 Endodormant Crown Bud rep-3 blue-2 & Non Flowering Competent Ecodormant Crown Bud rep-3 red-2

label_protocol: For microarray hybridizations, labeled cDNAs were prepared from 30 µg of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer's protocols. Labeled cDNAs were hybridized to a custom made 23K element microarray that contained 19,808 unigenes from a leafy spurge EST database (Anderson et al. 2007) and an additional 4,129 unigenes from a cassava EST database (Lokko et al. 2007). Comparison of gene expression between samples was accomplished using a rolling circle dye swap hybridization scheme (Churchill 2002) to provide every biological replicate with technical replicates. In our microarray analyses experiment, each of the four biological replicates included four technical replicates using two different dyes, resulting in a total of 16 technical replicates for each treatment.

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype 1984-ND001 and maintained in a greenhouse as described by Anderson and Davis (2004). Shoot cuttings were grown in No. 1 Ray Leach Cone-tainers (Stuewe and Sons Inc. Corvallis, OR, USA) in the greenhouse for three months prior to application of experimental treatments. The greenhouse was set at 25°C with a 16 h:8 h day:night photoperiod. Average daily light fluencies were approximately 350 μmol m-2 s-1 and 400 W high-pressure sodium lamps were used as to extend the day-length. Thirty plants per biological replication were exposed to each of the four environmental treatments (Fig. 1) and each environmental treatment was replicated four times. Prior to the start of each experiment, plants were randomly chosen from the greenhouse and acclimated in a growth chamber (PGR15 Model of Conviron, Winnipeg, Canada) for one week at 27°C, 16 h:8 h day:night photoperiod. All crown buds samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation.


title: Chip-31 Endodormant Crown Bud rep-4 blue-2 & Non Flowering Competent Ecodormant Crown Bud rep-4 red-2


title: Chip-28 Flowering Competent Ecodormant Crown Bud rep-3 blue-2 & Endodormant Crown Bud rep-3 red-2

description:
After induction of endodormancy in crown buds by a ramp down (RD) treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light), to induce a transition of crown buds from endo- to FC eco-dormancy, plants were subjected to a prolonged cold treatment for 11 weeks at 5-7°C, under constant 8 h:16 h day:night cycle; light fluencies were approximately 250 μmol m-2 s-1.
Induction of endodormancy in crown buds was accomplished by subjecting greenhouse grown and growth chamber acclimated plants to a ramp down (RD) treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as previously established by Foley et al. (2009). These conditions mimic the average seasonal environmental conditions experienced in Fargo, ND (46°54′ N, 96°48′ W) during the transition from para- to endo-dormancy (Anderson et al. 2005).
See Dogramaci et al. (2010, Plant Molecular Biology) for more details.


title: Chip-32 Flowering Competent Ecodormant Crown Bud rep-4 blue-2 & Endodormant Crown Bud rep-4 red-2


title: Chip-25 Paradormant Crown Bud rep-3 blue-2 & Flowering Competent Ecodormant Crown Bud rep-3 red-2

description:
Paradormant crown buds from three-month old greenhouse plants were collected after one week of acclimation under growth chamber conditions.
After induction of endodormancy in crown buds by a ramp down (RD) treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light), to induce a transition of crown buds from endo- to FC eco-dormancy, plants were subjected to a prolonged cold treatment for 11 weeks at 5-7°C, under constant 8 h:16 h day:night cycle; light fluencies were approximately 250 μmol m-2 s-1.
See Dogramaci et al. (2010, Plant Molecular Biology) for more details.

source_name: Paradormant Crown Bud

value: Paradormant Crown Bud


title: Chip-24 Flowering Competent Ecodormant Crown Bud rep-2 blue-2 & Endodormant Crown Bud rep-2 red-2


title: Chip-30 Non Flowering Competent Ecodormant Crown Bud rep-4 blue-2 & Paradormant Crown Bud rep-4 red-2

description:
Greenhouse-grown and one week growth chamber acclimated plants were subjected directly to an prolonged cold treatment for 11 weeks at 5-7°C, under constant 8 h:16 h day:night cycle; light fluencies were approximately 250 μmol m-2 s-1.
Paradormant crown buds from three-month old greenhouse plants were collected after one week of acclimation under growth chamber conditions.
See Dogramaci et al. (2010, Plant Molecular Biology) for more details.


title: Chip-22 Non Flowering Competent Ecodormant Crown Bud rep-2 blue-2 & Paradormant Crown Bud rep-2 red-2


title: Chip-29 Paradormant Crown Bud rep-4 blue-2 & Flowering Competent Ecodormant Crown Bud rep-4 red-2


title: Chip-26 Non Flowering Competent Ecodormant Crown Bud rep-3 blue-2 & Paradormant Crown Bud rep-3 red-2


title: Chip-20 Flowering Competent Ecodormant Crown Bud rep-1 blue-2 & Endodormant Crown Bud rep-1 red-2


title: Chip-18 Non Flowering Competent Ecodormant Crown Bud rep-1 blue-2 & Paradormant Crown Bud rep-1 red-2


title: Chip-19 Endodormant Crown Bud rep-1 blue-2 & Non Flowering Competent Ecodormant Crown Bud rep-1 red-2


title: Chip-16 Flowering Competent Ecodormant Crown Bud rep-4 blue-1 & Endodormant Crown Bud rep-4 red-1


title: Chip-12 Flowering Competent Ecodormant Crown Bud rep-3 blue-1 & Endodormant Crown Bud rep-3 red-1


title: Chip-14 Non Flowering Competent Ecodormant Crown Bud rep-4 blue-1 & Paradormant Crown Bud rep-4 red-1


title: Chip-15 Endodormant Crown Bud rep-4 blue-1 & Non Flowering Competent Ecodormant Crown Bud  rep-4 red-1


title: Chip-21 Paradormant Crown Bud rep-2 blue-2 & Flowering Competent Ecodormant Crown Bud rep-2 red-2


title: Chip-11 Endodormant Crown Bud rep-3 blue-1 & Non Flowering Competent Ecodormant Crown Bud rep-3 red-1


title: Chip-17 Paradormant Crown Bud rep-1 blue-2 & Flowering Competent Ecodormant Crown Bud rep-1 red-2


title: Chip-10 Non Flowering Competent Ecodormant Crown Bud rep-3 blue-1 & Paradormant Crown Bud rep-3 red-1


title: Chip-13 Paradormant Crown Bud rep-4 blue-1 & Flowering Competent Ecodormant Crown Bud rep-4 red-1


title: Chip-9 Paradormant Crown Bud rep-3 blue-1 & Flowering Competent Ecodormant Crown Bud rep-3 red-1


title: Chip-8 Flowering Competent Ecodormant Crown Bud rep-2 blue-1 & Endodormant Crown Bud rep-2 red-1


title: Chip-2 Non Flowering Competent Ecodormant Crown Bud rep-1 blue-1 & Paradormant Crown Bud rep-1 red-1

growth_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype 1984-ND001 and maintained in a greenhouse as described by Anderson and Davis (2004). Shoot cuttings were grown in No. 1 Ray Leach Cone-tainers (Stuewe and Sons Inc. Corvallis, OR, USA) in the greenhouse for three months prior to application of experimental treatments. The greenhouse was set at 25°C with a 16 h:8 h day:night photoperiod. Average daily light fluencies were approximately 350 μmol m-2 s-1 and 400 W high-pressure sodium lamps were used as to extend the day-length. Thirty plants per biological replication were exposed to each of the four environmental treatments. Prior to the start of each experiment, plants were randomly chosen from the greenhouse and acclimated in a growth chamber (PGR15 Model of Conviron, Winnipeg, Canada) for one week at 27°C, 16 h:8 h day:night photoperiod. All crown buds samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation.


title: Chip-7 Endodormant Crown Bud rep-2 blue-1 & Non Flowering Competent Ecodormant Crown Bud rep-2 red-1


title: Chip-6 Non Flowering Competent Ecodormant Crown Bud rep-2 blue-1 & Paradormant Crown Bud rep-2 red-1


title: Chip-4 Flowering Competent Ecodormant Crown Bud rep-1 blue-1 & Endodormant Crown Bud rep-1 red-1


title: Chip-5 Paradormant Crown Bud rep-2 blue-1 & Flowering Competent Ecodormant Crown Bud rep-2 red-1


title: Chip-1 Paradormant Crown Bud rep-1 blue-1 & Flowering Competent Ecodormant Crown Bud rep-1 red-1

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype 1984-ND001 and maintained in a greenhouse as described by Anderson and Davis (2004). Shoot cuttings were grown in No. 1 Ray Leach Cone-tainers (Stuewe and Sons Inc. Corvallis, OR, USA) in the greenhouse for three months prior to application of experimental treatments. The greenhouse was set at 25°C with a 16 h:8 h day:night photoperiod. Average daily light fluencies were approximately 350 μmol m-2 s-1 and 400 W high-pressure sodium lamps were used as to extend the day-length. Thirty plants per biological replication were exposed to each of the four environmental treatments. Prior to the start of each experiment, plants were randomly chosen from the greenhouse and acclimated in a growth chamber (PGR15 Model of Conviron, Winnipeg, Canada) for one week at 27°C, 16 h:8 h day:night photoperiod. All crown buds samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation.

treatment_protocol: Induction of endodormancy in crown buds was accomplished by subjecting greenhouse grown and growth chamber acclimated plants to a ramp down (RD) treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as previously established by Foley et al. (2009). These conditions mimic the average seasonal environmental conditions experienced in Fargo, ND (46°54′ N, 96°48′ W) during the transition from para- to endo-dormancy (Anderson et al. 2005). To induce a transition of crown buds from endo- to eco-dormancy, plants subjected to the RD treatment were given prolonged cold treatment for 11 weeks at 5-7°C, under constant 8 h:16 h day:night cycle; light fluencies were approximately 250 μmol m-2 s-1.


title: 600mM_salt_pellet_1_(SOH40)

status: Public on Dec 08 2009

description: Nucleosomes were obtained using extraction of intact MNase-digested nuclei with 600mM salt and the remaining insoluble pellet profiled.

data_processing: Adjusted log base 2 ratios of Cy3/Cy5 were computed using the method of Peng, et al (BMC Bioinformatics, 2007,8:219,PMID 17592629). The adjusted log ratios were converted to standard deviates by subtracting their mean and dividing by their standard deviation. (NOTE: the supplementary files have the adjusted log ratios, not their standard deviates.)

source_name: H3.3 DNA salt pellet

extract_protocol: 600mM pellet (salt insoluble) compared to MNAse treated starting material. Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc

value: embryos

source_name: H3.3 DNA nuc


title: Mononucleosomes_embryos_3_(SOH59)

data_processing: Adjusted log base 2 ratios of Cy3/Cy5 were computed using the method of Peng, et al (BMC Bioinformatics,2007,8:219,PMID 17592629). The adjusted log ratios were converted to standard deviates by subtracting their mean and dividing by their standard deviation. (NOTE: the supplementary files have the adjusted log ratios, not their standard deviates.)

source_name: DNA gel-purified mononucleosomes

label_protocol: Modified NimbleGen protocol described in Henikoff, et al (Genome Res,2009,19:460-469,PMID 19088306).

extract_protocol: GEl-Extracted mononucleosomes compared to MNAse treated starting material. Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc

source_name: DNA nucleosomes


title: Mononucleosomes_embryos_1_(SOH52)

source_name: DNA Gel purified mononucleosomes

source_name: DNA Nucleosomes

extract_protocol: Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc


title: 80mM_salt_fraction_2_(SOH36)

description: 80mM NaCl-exracted chromatin.

source_name: H3.3 DNA salt 80mM cut

extract_protocol: Nucleosomes were obtained using extraction of intact MNase-digested nuclei with 80mM NaCl. 80mM salt soluble fraction compared to MNAse treated starting material. Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc


title: H3.3_600mM_salt_fraction_2_(SOH41)

description: 600mM NaCl-extracted chromatin

source_name: H3.3 DNA pull-down

extract_protocol: H3.3 Streptavidin pulldown from 600 mM salt soluble fraction compared to the 600 mM salt soluble fraction. Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc

source_name: H3.3 DNA input


title: Mononucleosomes_embryos_2_(SOH53)


title: H3.3_350mM_salt_extract_(SOH54)

description: 350mM NaCl-extracted chromatin

extract_protocol: H3.3 Streptavidin pulldown from 350 mM salt soluble fraction compared to the 350 mM salt soluble fraction. Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc


title: H3.3_350mM_salt_fraction_(SOH12)

description: 350mM NaCl-extracted chromatin


title: Mononucleosomes_adult_1_(SOH28)

value: adults


title: Chip-3 Endodormant Crown Bud rep-1 blue-1 & Non Flowering Competent  Ecodormant Crown Bud rep-1 red-1


title: Mononucleosomes_adult_2b_(SOH35)


title: Mononucleosomes_adult_2a_(SOH34)


title: 600mM_salt_pellet_2_(SOH44)


title: 600mM_salt_fraction_2_(SOH39)

description: 600mM NaCl-exracted chromatin.

source_name: H3.3 DNA salt 600mM cut

extract_protocol: Nucleosomes were obtained using extraction of intact MNase-digested nuclei with 600mM NaCl. 600mM salt soluble fraction compared to MNAase treated starting material. Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc


title: H3.3_80mM_salt_fraction_2_(SOH37)

description: 80mM NaCl-extracted chromatin

extract_protocol: H3.3 Streptavidin pulldown from 80 mM salt soluble fraction compared to the 80 mM salt soluble fraction. Detailed protocol at http://nettie.fhcrc.org/modencode/protocols/Worm_Protocol.doc


title: H3.3_600mM_salt_fraction_1_(SOH21)

description: 600mM NaCl-extracted chromatin


title: 80mM_salt_fraction_1_(SOH18)

description: 80mM NaCl-exracted chromatin.


title: H3.3_80mM_salt_fraction_1_(SOH25)

description: 80mM NaCl-extracted chromatin