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

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: GSM575432_pirrota_284_Input.137.CEL

source_name: Strain Oregon-R;Antibody H3K4me2 (target is H3K4me2);Developmental Stage 3rd Instar Larvae extraction5_array1 channel_1

value: 3rd Instar Larvae


title: H3K9me2-Ab2_(new_lot).2-4_hr_OR_embryo extraction1_array1

status: Public on Aug 10 2010

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is 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;

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: GSM575455_pirrota_935_Eearly2_Input_20cyc.690.CEL

label: biotin

molecule: genomic DNA

organism: Drosophila melanogaster

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

tag: strain

value: Oregon-R

tag: developmental stage

value: Embryo 2-4hr OR

tag: genotype

value: wild type


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

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: GSM575434_pirrota_298_S11_Input.143.CEL

source_name: Cell Line S2-DRSC;Antibody H3K79Me1 (target is H3K79me1) extraction1_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.

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

value: late embryonic stage

tag: sex

value: Male


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: GSM575430_pirrota_964_Larvae_Prep5_Input_14cyc.725.CEL

source_name: Strain Oregon-R;Antibody H3K4me2 (target is H3K4me2);Developmental Stage 3rd Instar Larvae extraction3_array1 channel_1

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


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: GSM575436_pirrota_303_S14_Input.148.CEL

source_name: Cell Line S2-DRSC;Antibody H3K79Me1 (target is H3K79me1) extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9acS10P (new lot); target name: H3K9acS10P; host: Rabbit; antigen: amino acids 7-20 corresponding to the N-terminus of human histone H3; clonal: Unknown; purified: Affinity; company: Abcam; catalog: ab12181; short description: rabbit polyclonal to Histone H3 (acetyl K9 phospho S10) - ChIP grade (ab12181);

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: GSM575440_pirrota_646_B3_Input2_20cycles.423.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) extraction3_array1 channel_1

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: H3K4me2.14-16_hr_OR_embryo 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: GSM575426_pirrota_263_E3_Input.108.CEL

value: Embryo 14-16hr OR


title: H3K4me2.14-16_hr_OR_embryo extraction1_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: GSM575424_pirrota_880_E_late_2_Input.651.CEL


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

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: GSM575420_pirrota_873_S15_Input-18cycles.644.CEL

source_name: Cell Line S2-DRSC;Antibody H3K4me2-Millipore (target is H3K4me2) 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: GSM575418_pirrota_620_B3_Input-18cycles.405.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me2-Millipore (target is H3K4me2) 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: GSM575422_pirrota_540_A12_Input18.362.CEL

source_name: Cell Line S2-DRSC;Antibody H3K4me2-Millipore (target is H3K4me2) 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: GSM575416_pirrota_621_B5_Input-18cycles.406.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me2-Millipore (target is H3K4me2) extraction1_array1 channel_1


title: H3K18Ac_(new_lot).2-4_hr_OR_embryo extraction3_array1

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

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: GSM575410_pirrota_879_E_early_1_Input.650.CEL


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K4me1 (new lot); 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; 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: GSM575414_pirrota_621_B5_Input-18cycles.406.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me1 (new lot) (target is 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: GSM575412_pirrota_916_B4_Input-18cycles.671.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me1 (new lot) (target is H3K4me1) extraction1_array1 channel_1


title: H3K18Ac_(new_lot).2-4_hr_OR_embryo extraction1_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: GSM575408_pirrota_935_Eearly2_Input_20cyc.690.CEL


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: GSM575406_pirrota_916_B4_Input-18cycles.671.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody GAF (target is 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: GSM575404_pirrota_437_B3_INPUT.253.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody GAF (target is GAF) extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Ez; target name: Ez; host: Rabbit; antigen: peptide amino acids 8-190; 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: GSM575402_pirrota_620_B3_Input-18cycles.405.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody Ez (target is 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: GSM575400_pirrota_916_B4_Input-18cycles.671.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody Ez (target is Ez) extraction1_array1 channel_1


title: H3K9me2-Ab2_(new_lot).2-4_hr_OR_embryo extraction7_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: GSM575461_pirrota_879_E_early_1_Input.650.CEL


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: GSM575428_pirrota_377_LarvaeTrial_Input.193.CEL

source_name: Strain Oregon-R;Antibody H3K4me2 (target is H3K4me2);Developmental Stage 3rd Instar Larvae extraction1_array1 channel_1


title: Chro(Chriz)BR.14-16_hr_OR_embryo extraction7_array1

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: GSM575398_pirrota_999_Elate4_Input_20cyc.738.CEL


title: Chro(Chriz)BR.14-16_hr_OR_embryo 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: GSM575394_pirrota_345_E7_Input.173.CEL


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: GSM575387_pirrota_725_Larvae_Prep3_Input_14cyc.489.CEL

source_name: Developmental Stage 3rd Instar Larvae;Antibody H3K9me3 (new lot) (target is H3K9me3);Strain Oregon-R extraction3_array1 channel_1


title: Chro(Chriz)BR.14-16_hr_OR_embryo extraction1_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: GSM575392_pirrota_824_E_late_1_inputDNA_20cyc.595.CEL


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: GSM575389_pirrota_363_E6_Input.206.CEL

source_name: Developmental Stage Embryo 2-4hr OR;Antibody H3K4Me3(LP) (target is H3K4me3);Strain Oregon-R extraction1_array1 channel_1


title: expt.141 extraction3_array1

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

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: GSM575375_pirrota_285_Input.138.CEL

source_name: expt.141 extraction3_array1 channel_1

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

value: Mixed Adult


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

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: GSM575377_pirrota_731_Larvae_Prep_3_Input_20cyc.495.CEL

source_name: Developmental Stage 3rd Instar Larvae;Antibody HP1 wa191 (target is HP1a);Strain Oregon-R 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: GSM575379_pirrota_732_Larvae_Prep_4_Input_20cyc.496.CEL

source_name: Developmental Stage 3rd Instar Larvae;Antibody HP1 wa191 (target is HP1a);Strain Oregon-R extraction3_array1 channel_1


title: expt.194 extraction1_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: GSM575373_pirrota_380_OR_HeadTrial_Input.197.CEL

source_name: expt.194 extraction1_array1 channel_1


title: expt.479 extraction1_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: GSM575381_pirrota_729_OR_Head_Prep3_Input_20cyc.493.CEL

source_name: expt.479 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: GSM575385_pirrota_726_Larvae_Prep4_Input_14cyc.490.CEL

source_name: Developmental Stage 3rd Instar Larvae;Antibody H3K9me3 (new lot) (target is H3K9me3);Strain Oregon-R extraction1_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: GSM575369_pirrota_354_E6_Input.182.CEL

source_name: Developmental Stage Embryo 2-4hr OR;Antibody H3K36me3 (target is H3K36me3);Strain Oregon-R 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: GSM575365_pirrota_344_E5_Input.172.CEL

source_name: Developmental Stage Embryo 14-16hr OR;Antibody H3K36me3 (target is H3K36me3);Strain Oregon-R extraction1_array1 channel_1


title: Chro(Chriz)BR.14-16_hr_OR_embryo 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: GSM575396_pirrota_344_E5_Input.172.CEL


title: expt.480 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: GSM575383_pirrota_730_OR_Head_Prep4_Input_20cyc.494.CEL

source_name: expt.480 extraction3_array1 channel_1


source_name: Developmental Stage Embryo 2-4hr OR;Antibody H3K4Me3(LP) (target is H3K4me3);Strain Oregon-R 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: GSM575371_pirrota_353_E4_Input.181.CEL

source_name: Developmental Stage Embryo 2-4hr OR;Antibody H3K36me3 (target is H3K36me3);Strain Oregon-R 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: GSM575367_pirrota_345_E7_Input.173.CEL

source_name: Developmental Stage Embryo 14-16hr OR;Antibody H3K36me3 (target is H3K36me3);Strain Oregon-R extraction3_array1 channel_1


title: Dmel_F_R2

status: Public on Jul 30 2010

type: RNA

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

country: USA

institute: NIDDK, NIH

hyb_protocol: Samples to be co-hybridized onto one microarray were pooled and precipitated with 120 µl DEPC treated H2O, 3 µl glycogen (1 mg/ml), 180 µl 5M ammonium acetate, and 900 µl cold 100% EtOH and by cold centrifugation at max speed for 20 min. Probe pellets were re-suspended in warm 2X hybridization buffer (250 µl formamide, 250 µl 20X SSC, 20 µl 10% SDS, 5 µl tRNA(2g/µl)) with Nimblegen feducial (Cy3 CPK6 and Cy5 CPK6) controls and heated to 95°C for 5 minutes. Nimblegen microarrays were fitted with X1 mixers according to standard protocols, warmed to 42°C on a MAUI hybridization station (BioMicro Systems, Salt Lake City, Utah), and 15 µl of hybridization cocktail was loaded onto microarrays through the X1 fill port. Vent and fill ports were sealed and arrays were loaded onto bays of the MAUI station. Mix mode B on the MAUI hybridization station was started and samples were hybridized for 18 hours at 42°C in low ozone conditions. Arrays were washed using the following modified Nimblegen protocol. An array with mixer was submerged for 10 seconds in warm (42°C) Buffer I (1000 ml H2O, 10 ml 20X SSC, 20 ml 10 % SDS, 100 µl 1 M DTT) and the mixer was removed. Arrays were placed in a fresh beaker of 42°C Buffer I and agitated for 2 minutes, submerged for 1 minute in room temperature Buffer II (1000 ml H2O, 10 ml 20X SSC, 100  µl 1 M DTT), followed by submerging for 15 sec in Buffer III (1000 ml H2O, 2.5 ml 20X SSC, 100 µl 1 M DTT). Arrays were placed in an ArrayIT Microarray Centrifuge and spun for 1 minute to dry. Dried arrays were paced in tubes and covered in aluminum foil until scanning.

scan_protocol: Arrays were scanned on a Axon GenePix® 4000B (Molecular Devices, Sunnyvale, California) scanner controlled by GenePix 6.0 software. Cy3 and Cy5 channels were balanced by visual inspection of histograms for Cy3 and Cy5 channels and by manually changing PMT settings for each laser. Each scan was saved as a TIFF file.

data_processing: Raw TIFF files for each microarray were processed using NimbleScan 2.4.27 (Roche NimbleGen, Inc. Madison, Wisconsin) software. We followed probe annotation defined in GEO platform ID GPL4629 for D. melanogaster, GPL4631 for D. pseudoobscura, and GPL4630 for D. mojavensis. This strategy created one measurement of gene expression by collapsing isoforms and should be conservative but doing so changes the number of probes assigned to gene models. The mean number of probes for D. melanogaster FBgn IDs was 27.3 (range: 20-520, N= 13446), for D. pseudobscurca the average number of probes was 25.3 per GLEANR ID (range:2 – 152 probes; N= 12901) and for D. mojavensis the average number of probes/GLEANR ID was 23.2 (range: 2-186; N=12648). All replicates for each species were hybridized together on the same day with the exception of D. mojavensis in which 3 of the 4 replicates were hybridized on one day and the fourth replicate was hybridized on a separate day. We co-hybridized male and female samples for each species on single arrays and subsequently extracted Cy3 and Cy5 channels for the replicates. Pair reports for each sample were generated using Nimblescan and individual channel pair files were loaded together and normalized using quantile normalization (Bolstad et al. 2003. Bioinformatics 19:185) and summarized using Robust Multiarray Averaging (RMA; Irizarray et al. 2003. Biostatistics 4:249) in Nimblescan software. All female and male samples were normalized together but RMA normalization was performed separately for each species.

molecule: polyA RNA

source_name: Heads; 8 day old mated adults

label_protocol: Arrays were used in a two-color format with mRNA labeled with Cy3 or Cy5. Four biological replicate male and four biological replicate female heads, each dye-flipped to control for potential dye artifacts from each of the three species were used in microarray experiments. For each sample of mRNA, 600 ng was simultaneously reverse-transcribed and labeled with dye along with Arabidopsis spike-in controls. Reverse-transcription/labeling reactions consisted of 15 µl 5X First Strand Buffer (Invitrogen, Carlsbad, California), 3 µl 0.1 mM DTT (Invitrogen, Carlsbad, California), 9 µl of dye-mix containing Cy3 or Cy5 labeled nonamer primer (Trilink Biotechnologies, San Diego, California), 3 µl RNase inhibitor (Ambion, Austin, Texas), 15 µl H2O plus Arabidopsis spike-in controls, and 3 µl Super-script II reverse transcriptase (Invitrogen, Carlsbad, California). Labeling reactions were incubated at 37°C for 2 hours then stopped by heat termination at 85°C for 5 min. Labeling reactions were purified using Clonetech columns (TE-10), (Clonetech, Mountain View, California) following manufacture instructions.

growth_protocol: We examined gene expression in male and female head samples from Drosophila melanogaster (OreR), D. pseudobscura (Drosophila Species Stock Center (DSSC) 14011-0121.94), and D. mojavensis (DSSC 15081-1352.22). Flies were grown at 22°C, 60% relative humidity in standard vials containing cornmeal media, for D. melanogaster (http://flyfood.arl.arizona.edu/cornmeal.php3) or banana-opuntia for D. pseudobscura and D. mojavensis (http://flyfood.arl.arizona.edu/opuntia.php3).  All media was purchased from the Tucson Stock Center, Tucson, Arizona.  Newly eclosed flies of both females and males were housed together in vials at normal density and aged for 7 days.  On day 7, flies were anesthetized with CO2 and then females and males were sorted and placed into separate vials.  Same sex vials were then aged an additional 24 hours at 22°C, 60% relative humidity.  Whole flies were flash frozen on dry ice. Flash frozen flies were stored in -80°C before dissection and subsequent RNA extraction. Frozen fly heads were dissected using forceps from whole files on ceramic plates chilled on dry ice. All equipment used during dissections were wiped with RNAase Away (Molecular BioProducts, San Diego, California).

extract_protocol: Four biological replicate male and four biological replicate female samples were collected for each species. Each replicate consisted of a pooled sample of 400-500 fly heads. TRIzol (Invitrogen Inc, Carlsbad, California) was used to extract total RNA from heads following manufacture directions. Briefly, fly heads were immersed in 250 µl of TRIzol and thoroughly homogenized using a 1.5 ml RNAase free pestle (Kimble-Chase, Vineland, New Jersey) fitted to a Pellet Pestle Motor (Sigma-Aldrich, St. Louis, Missouri). After initial homogenization, 550 µl of TRIzol was added and the solution was further homogenized by hand. Chloroform (160 µl) was added to the homogenate and then the sample was centrifuged at 12,000 g for 15 minutes at 4°C. The aqueous layer was removed, precipitated with isopropyl alcohol and glycogen (8 µg), then centrifuged for 10 minutes at 4°C to pellet the RNA. The supernatant was removed and the RNA pellet was washed with fresh 75% ethanol. The pellet was dried briefly and then dissolved in 50 µl DEPC treated H2O. mRNA was enriched from total RNA by poly A+ selection using a Oligotex mRNA kit (QIAGEN Inc., Valencia, California) following manufacture instructions. mRNA was eluted from small spin columns twice with hot 30 µl buffer OEB. mRNA quality and quantity was determined by Bioanalyzer (Agilent, Santa Clara, California) and 260/280 ratio from Nanodrop ND-1000 UV spectrophotometer (Nanodrop, Wilmington, Delaware).

treatment_protocol: Frozen whole flies were placed on 10.8 x 10.8 cm ceramic plates frozen on dry ice. Forceps were used to dissect 400-500 heads/sex for subsequent RNA extraction.

tag: gender

value: female

value: OreR

value: head

value: 8 day old mated adult


title: Dmel_M_R3

value: male


title: Dmel_M_R4


title: Dmel_M_R2

description: mRNA-Seq was performed on this sample; these data are available at GSE20348 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20348) at GEO.


title: Dmel_F_R3


title: Dmel_F_R4


title: Dmel_M_R1


title: Dpse_M_R2

description: mRNA-Seq was performed on this sample; these data are available at GSE19989 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19989) in GEO.

organism: Drosophila pseudoobscura

value: D. pseudoobscura 14011-0121.94


title: Dpse_M_R4


title: Dpse_F_R4


title: Dpse_F_R1


title: Dmel_F_R1


title: Dpse_F_R3


title: Dpse_F_R2


title: Dpse_M_R1


title: Dpse_M_R3


title: Tumor_B_cells_H2AZ_1_(279939-3)

status: Public on Aug 09 2010

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: Chromatin immunoprecipitation (ChIP) profiling of tumor B cells harvested from the lymph node of a 6-week old mouse (B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc)).

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary gff and bedgraph files contain the bi-weight mean adjusted log base 2 ratios in MM8 coordinates.

organism: Mus musculus

source_name: Amplified H2A.Z Native ChIP

label_protocol: Standard NimbleGen protocol

extract_protocol: Nuclei from 10 million cells were treated with MNase to release mononucleosomes. Soluble chromatin was extracted in 150 mM NaCl. An antibody against H2A.Z was used to pull down H2A.Z containing nucleosomes and the IPed DNA was purified by phenol chloroform extraction. Purified DNA was amplified using Sigma's whole genome amplification kit (WGA2).

value: B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc)

tag: age

value: 6 weeks

value: lymph node

tag: cell type

value: tumor B cells

source_name: Fragmented and amplified genomic DNA

extract_protocol: Nuclei from 10 million cells were treated with MNase to release mononucleosomes. Soluble chromatin was extracted in 150 mM NaCl and the DNA was purified by phenol chloroform extraction. Purified DNA was amplified using Sigma's whole genome amplification kit (WGA2).


title: Dmoj_F_R2

organism: Drosophila mojavensis

value: D. mojavensis wrigleyi 15081-1352.22


title: Dmoj_F_R3

description: mRNA-Seq was performed on this sample; these data are available at GSE20882 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20882) in GEO.


title: Dmoj_M_R4


title: Dmoj_M_R2


title: Dmoj_F_R1


title: Dmoj_M_R3


title: Dmoj_M_R1


title: WT_pre-B_cells_600mM_(381542-2)

description: Profiling of 600 mM salt-soluble chromatin of wild type CD54+ pre-B cells harvested from the bone marrows of three 6-week old mice (C57BL/6J).

source_name: Amplified 600 mM salt-soluble MNased DNA

extract_protocol: Nuclei from 10 million cells were treated with MNase to release mononucleosomes. Soluble chromatin was extracted in 600 mM NaCl and DNA was purified by phenol chloroform extraction. Purified DNA was amplified using Sigma's whole genome amplification kit (WGA2).

value: bone marrow

value: CD45+ pre-B cells

source_name: Amplified total MNased DNA

extract_protocol: Nuclei from 10 million cells were treated with MNase to release mononucleosomes. Total chromatin was extracted and purified by phenol chloroform. Purified DNA was amplified using Sigma's whole genome amplification kit (WGA2).


title: Myc_pre-B_cells_H2AZ_2_(280283)

description: Chromatin immunoprecipitation (ChIP) profiling of Myc over-expressing CD45+ pre-B cells harvested from the bone marrows of 3 6-week old mice (B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc)).

extract_protocol: Nuclei from 10 million cells were treated with MNase to release mononucleosomes. Soluble chromatin was extracted in 150 mM NaCl. An antibody against H2A.Z was used to pull down H2A.Z containing nucleosomes and the IPd DNA was purified by phenol chloroform extraction. Purified DNA was amplified using Sigma's whole genome amplification kit (WGA2).


title: Tumor_B_cells_DNA_Methylation_1_(381304)

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary gff and bedgraph files contain the bi-weight mean adjusted log base 2 ratios in MM9 coordinates.

source_name: Amplified MeDIP DNA

extract_protocol: 10 million cells were divided into two aliquots and DNA was isolated via Qiagen's DNeasy blood and tissue kit (Qiagen, Inc) following the manufactures directions. DNA was sonicated to an average size of 600 bp and denatured with heat. An antibody against methylated DNA was used to pull down methylated DNA fragments and the MeDIP DNA was purified by phenol chloroform extraction. Purified DNA was amplified using Sigma's whole genome amplification kit (WGA2).

source_name: Sonicated and amplified genomic DNA

extract_protocol: 10 million cells were divided into two aliquots and DNA was isolated via Qiagen's DNeasy blood and tissue kit (Qiagen, Inc) following the manufactures directions. DNA was sonicated to an average size of 600 bp and denatured with heat. Purified DNA was amplified using Sigma's whole genome amplification kit (WGA2).


title: Tumor_B_cells_150mM_(426513_3)

description: Profiling of 150 mM salt-soluble chromatin of wild type CD54+ pre-B cells harvested from the lymph nodess of three 6-week old mice (B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc)).

source_name: Amplified 150 mM salt-soluble MNased DNA

extract_protocol: Nuclei from 10 million cells were treated with MNase to release mononucleosomes. Soluble chromatin was extracted in 150 mM NaCl and DNA was purified by phenol chloroform extraction. Purified DNA was amplified using Sigma's whole genome amplification kit (WGA2).

value: B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc))


title: Dmoj_F_R4


title: WT_pre-B_cells_H2AZ_2_(280214-3)

description: Chromatin immunoprecipitation (ChIP) profiling of wild type CD45+ pre-B cells harvested from the bone marrows of 4 6-week old mice (C57BL/6J).


title: Myc_pre-B_cells_150mM_(426554-3)

description: Profiling of 150 mM salt-soluble chromatin of Myc over-expressing CD54+ pre-B cells harvested from the bone marrows of three 6-week old mice (B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc)).


title: WT_pre-B_cells_H2AZ_1_(270812-2)


title: Myc_pre-B_cells_H2AZ_1_(277575-2)


title: WT_pre-B_cells_DNA_Methylation_1_(381552)

description: Methylated DNA immunoprecipitation (MeDIP) profiling of wild type CD45+ pre-B cells harvested from the bone marrows of 5 6-week old mice (C57BL/6J).


title: WT_pre-B_cells_150mM_(427074-3)

description: Profiling of 150 mM salt-soluble chromatin of wild type CD54+ pre-B cells harvested from the bone marrows of three 6-week old mice (C57BL/6J).


title: Tumor_B_cells_600mM_(381526-3)

description: Profiling of 600 mM salt-soluble chromatin of wild type CD54+ pre-B cells harvested from the lymph nodess of three 6-week old mice (B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc)).


title: Myc_pre-B_cells_DNA_Methylation-1_(381504)


title: Myc_pre-B_cells_600mM_(387888-3)

description: Profiling of 600 mM salt-soluble chromatin of Myc over-expressing CD54+ pre-B cells harvested from the bone marrows of three 6-week old mice (B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc)).


title: WT_EXP_2_(369194)

status: Public on Jun 14 2010

type: mixed

description: Expression profiling of total RNA from the root hair zone.

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy3/Cy5 were computed. Then the log ratios for up to 100 exonic probes starting from the 3' ends of TAIR8 genes were averaged to give a single expression value for each gene in the supplementary file WT_EXP_2.dat . The supplementary files WT_EXP_2.gff and WT_EXP_2.bedgraph contain the bi-weight mean adjusted log base 2 ratios.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: amplified root cDNA.

label_protocol: Standard NimbleGen protocol using 5 hour labeling reaction rather than 2 hour reaction.

extract_protocol: RNA isolation was done with Qiagen RNeasy micro kit. cDNA preparation and amplification were done with the Sigma WTA2 kit.

value: root (root hair zone)

source_name: Fragmented genomic DNA.

extract_protocol: DNA was isolated with the Qiagen Plant Dneasy mini kit and fragmented by sonication.


title: WT_EXP_1_(369196-2)

description: Expression profiling of total RNA from the root hair zone

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy3/Cy5 were computed. Then the log ratios for up to 100 exonic probes starting from the 3' ends of TAIR8 genes were averaged to give a single expression value for each gene in the supplementary file WT_EXP_1.dat . The supplementary files WT_EXP_1.gff and WT_EXP_1.bedgraph contain the bi-weight mean adjusted log base 2 ratios.

source_name: amplified root cDNA


title: Baculovirus_FLAG_H2Av_(010410_FAvN_3I5PD_382963)

status: Public on Jul 12 2010

description: S2 cells transduced with Baculovirus-encoded FLAG-tagged H2Av

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed.

source_name: Pulldown DNA

label_protocol: Protocol included in Strand-displacement_labeling_808.txt

extract_protocol: Protocol included in file N-Chip_BH2Av_FH2Av.txt

tag: assay

source_name: Input DNA


title: GL2_K4_1_(294553-2)

description: Chromatin immunoprecipitation (ChIP) profiling of the H3K4me3 modification in INTACT-purified nuclei from Arabidopsis root non-hair cells.

source_name: Amplified H3K4me3 ChIP.

extract_protocol: Amplification of ChIP DNA was done with Sigma WGA4 kit. Detailed protocol is located on the Series record.

value: root epidermis non-hair cell nuclei

source_name: Amplified H3 ChIP.


title: BLRP_H2Av_(010410_BAvN_3I5PD_382848-2)

description: Stably transformed BLRP-H2Av S2 cells


title: geminin RNAi 48h exp2 vs. control exp2

status: Public on Mar 18 2010

city: Durham

first: David

middle: M

last: MacAlpine

state: NC

address: Box 3813 DUMC

department: Pharmacology and Cancer Biology

institute: Duke University Medical Center

description: CGH comparison of geminin RNAi depleted cells to control cells

hyb_protocol: Differentially labelled experimental and control samples were hybrisized onto the arrays overnight at 65⁰C.

scan_protocol: The slides were washed and scanned as per Agilent recommendations.

data_processing: Data for each slide was loess normalized using the LIMMA package in R.  The normalized and loess smoothed data were output as a wiggle track using Flybase 5.x coordinates for all experiments.

source_name: geminin depletion 2

label_protocol: 1µg of isolated DNA was sheared and labeled with either fluorescent Cy5- or Cy3-conjugated dUTP (GE Healthcare Bio-Sci Corp.) using sequenase (US Biochemicals) and a random nonamer oligo (IDT). The labeled DNA was purified using Microcon YM-30 filters (Millipore).

growth_protocol: The Drosophila Kc167 cells were cultured at 25°C in Schneider’s Insect Cell Medium (Invitrogen) supplemented with 10% fetal bovine serum and 1% penicillin / streptomycin / glutamine (Invitrogen).

extract_protocol: For each experiment, 2 plates of cells (~2×107) were collected and washed once in cold 1xPBS. The cells were then suspended in 0.7ml 10mM Tris (pH 9.5), 0.7ml NDS and 100µl 20mg/ml proteinase K. Mix and incubate at 37⁰C for two hours. Add 1.5ml TE and extract the solution twice with phenol/chloroform. precipitate the DNA with 2.5 volumes of ethanol. Resuspend the pelleted DNA in TE/RNase and incubate at 37⁰C for one hour. Precipitate the DNA with 3M NaOAC and 2.5 volumes of ethanol, and resuspend it in TE.

treatment_protocol: For each RNAi experiment, cells were washed with and diluted in serum-free medium to a final concentration of 2×106 cells/ml. 15µg dsRNA (geminin dsRNA, and pUC dsRNA as the control)  was added per 1×106 cells, gently mixed, and incubated for one hour.  After the incubation,  2× medium was added resulting in a final  concentration of 1×106 cells/ml. The cells were incubated for 1-2 days before harvesting.

tag: protocol

value: geminin depletion 2

source_name: control 2

value: control 2


title: geminin RNAi 48h exp1 vs. control exp1

source_name: geminin depletion 1

value: geminin depletion 1

source_name: control 1

value: control 1


title: NUC_EXP_1_(369174)

description: Expression profiling of nuclear RNA from the root hair zone

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy3/Cy5 were computed. Then the log ratios for up to 100 exonic probes starting from the 3' ends of TAIR8 genes were averaged to give a single expression value for each gene in the supplementary file NUC_EXP_1.dat . The supplementary files NUC_EXP_1.gff and NUC_EXP_1.bedgraph contain the bi-weight mean adjusted log base 2 ratios.

molecule: nuclear RNA

source_name: amplified nuclear cDNA.

extract_protocol: DNA was isolated with the Qiagen Plant Dneasy mini kit and fragmented by sonication


status: Public on Mar 12 2010

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

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: GSM521107 (pirrota_436_B5_INPUT.254.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me3 (ab8580 lot1) 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).

value: CNS-derived cell-line

value: third instar larval stage

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: GSM521105 (pirrota_365_B2_Input.208.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me3 (ab8580 lot1) extraction1_array1 channel_1


title: NUC_EXP_2_(369136)

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy3/Cy5 were computed. Then the log ratios for up to 100 exonic probes starting from the 3' ends of TAIR8 genes were averaged to give a single expression value for each gene in the supplementary file NUC_EXP_2.dat . The supplementary files NUC_EXP_2.gff and NUC_EXP_2.bedgraph contain the bi-weight mean adjusted log base 2 ratios.

extract_protocol: DNA was isolated with Qiagen Plant DNeasy Mini kit and fragmented by sonication.


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

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: GSM521103 (pirrota_540_A12_Input18.362.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K4me2 extraction3_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: control exp1 vs. control exp2

description: CGH comparison independent replicate control samples


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: GSM521099 (pirrota_836_CL8-1_Input_DNA(14cyc).607.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9ac extraction3_array1 channel_1

value: dorsal mesothoracic disc


title: GL2_K27_1_(294543-2)

description: Chromatin immunoprecipitation (ChIP) profiling of the H3K27me3 modification in INTACT-purified nuclei from Arabidopsis root non-hair cells.

source_name: Amplified H3K27me3 ChIP.


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: GSM521097 (pirrota_837_CL8-2_Input_DNA(14cyc).608.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9ac extraction1_array1 channel_1


title: GL2_K4_2_(294553-2)


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: GSM521101 (pirrota_196_S9_Input.46.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K4me2 extraction1_array1 channel_1


title: GL2_EXP_1_(294548)

description: Expression profiling of nuclear RNA from INTACT-purified Arabidopsis non-hair cell nuclei.

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy3/Cy5 were computed. Then the log ratios for up to 100 exonic probes starting from the 3' ends of TAIR8 genes were averaged to give a single expression value for each gene in the supplementary file GL2_EXP_1.dat . The supplementary files GL2_EXP_1.gff and GL2_EXP_1.bedgraph contain the bi-weight mean adjusted log base 2 ratios.

source_name: INTACT-derived amplified nuclear cDNA.

extract_protocol: RNA isolation was done with Qiagen RNeasy micro kit. cDNA preparation ond amplification were done with the Sigma WTA2 kit. Detailed protocol is located on the Series record.

source_name: Fragmented genomic DNA.

extract_protocol: DNA isolation was done with the Qiagen DNeasy Plant Kit and was not amplified.

value: total root


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

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: GSM521093 (pirrota_298_S11_Input.143.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K79Me1 extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Su(var)3-9;target name: Su(var)3-9;host: Rabbit;antigen: Purified bacterial GST-SU(VAR)3-9 aa275-480;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Reuter Lab;reference: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list uids=11867540;short description: rabbit polyclonal antibody; purified by absorption against embryo extract from Su(var)3-9-06 homozygous mutant embryos by the Reuter lab.;

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: GSM521085 (pirrota_646_B3_Input2(20cycles).423.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody Su(var)3-9 extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: WDS Q2691;target name: WDS;host: Rabbit;antigen: LDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNMVYIWNLQSKEVVQKLQGHTDTVLCTACHPTENIIASAALENDKTIKLWKSD (261-360 of the WDS protein);clonal: Unknown;purified: Affinity;company: SDI;catalog: Q2691;short description: WDS (CG17437);

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: GSM521091 (pirrota_641_S12_input_gk2.417.CEL)

source_name: Cell Line S2-DRSC;Antibody WDS Q2691 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: GSM521089 (pirrota_803_A14.input.566.CEL)

source_name: Cell Line S2-DRSC;Antibody WDS Q2691 extraction1_array1 channel_1


title: ADF_EXP_1_(294548)

description: Expression profiling of nuclear RNA from INTACT-purified Arabidopsis hair-cell nuclei.

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy3/Cy5 were computed. Then the log ratios for up to 100 exonic probes starting from the 3' ends of TAIR8 genes were averaged to give a single expression value for each gene in the supplementary file ADF_EXP_1.dat . The supplementary files ADF_EXP_1.gff and ADF_EXP_1.bedgraph contain the bi-weight mean adjusted log base 2 ratios.

value: root epidermis hair cell nuclei


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: GSM521079 (pirrota_482_B2_Input(14cyc).293.CEL)

source_name: Cell Line ML-DmBG3-c2;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: GSM521087 (pirrota_602_B5_Input(20cycles).391.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody Su(var)3-9 extraction3_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: GSM521081 (pirrota_621_B5_Input-18cycles.406.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody SU(HW)-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: GSM521077 (pirrota_481_B1_Input(14cyc).292.CEL)

source_name: Cell Line ML-DmBG3-c2;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: GSM521095 (pirrota_303_S14_Input.148.CEL)

source_name: Cell Line S2-DRSC;Antibody H3K79Me1 extraction3_array1 channel_1


title: time_course_40_1_(TC1-40_283996-2)

status: Public on May 27 2010

description: CATCH-IT profiling of Drosophila S2 cells using 40 minute azidohomoalanine treatment, replicate 1.

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed.

source_name: Amplified CATCH-IT pulldown DNA.

extract_protocol: Detailed protocol at http://nettie.fhcrc.org/labuser/protocols/CATCH-IT_protocol.doc

tag: time point

value: 40 minute

tag: agent

value: azidohomoalanine

tag: replicate

source_name: Amplified input DNA.

tag: reference

value: Amplified input DNA


title: ADF_K27_2_(293003-2)

description: Chromatin immunoprecipitation (ChIP) profiling of the H3K27me3 modification in INTACT-purified nuclei from Arabidopsis root hair cells.

source_name: Amplified H3 ChIP.


title: chase_1_(521-3H-C_283713-2)

description: CATCH-IT profiling of Drosophila S2 cells treated with azidohomoalanine for 3 hours (pulse) followed by a 1.5 hour treatment with Methionine (chase).

value: azidohomoalanine/Methionine (chase)

value: 3 hours (pulse) followed by a 15 hour treatment with Methionine (chase)


title: GL2_EXP_2_(294548)

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy3/Cy5 were computed. Then the log ratios for up to 100 exonic probes starting from the 3' ends of TAIR8 genes were averaged to give a single expression value for each gene in the supplementary file GL2_EXP_2.dat . The supplementary files GL2_EXP_2.gff and GL2_EXP_2.bedgraph contain the bi-weight mean adjusted log base 2 ratios.

value: root epidermis non-hair cell nuclei


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: GSM521083 (pirrota_620_B3_Input-18cycles.405.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody SU(HW)-HB extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: PIWI-Q2569;target name: PIWI;host: Rabbit;antigen: AA's 454-553;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2569;short description: Affinity Purfied antibodies from 80ml Rabbit antisera;

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 Kc167;Antibody PIWI-Q2569 extraction5_array1 channel_1

value: se/e

value: Female


title: ADF_K4_1_(294553-2)

description: Chromatin immunoprecipitation (ChIP) profiling of the H3K4me3 modification in INTACT-purified nuclei from Arabidopsis root hair cells.

source_name: Amplified H3K4me3 ChIP.


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: GSM521074 (pirrota_600_Kc1_Input(20cycles).389.CEL)

source_name: Cell Line Kc167;Antibody PIWI-Q2569 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: GSM521072 (pirrota_647_Kc2_Input(20cycles).424.CEL)

source_name: Cell Line Kc167;Antibody PIWI-Q2569 extraction1_array1 channel_1


title: ADF_EXP_2_(294543)

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy3/Cy5 were computed. Then the log ratios for up to 100 exonic probes starting from the 3' ends of TAIR8 genes were averaged to give a single expression value for each gene in the supplementary file ADF_EXP_2.dat . The supplementary files ADF_EXP_2.gff and ADF_EXP_2.bedgraph contain the bi-weight mean adjusted log base 2 ratios.

source_name: INTACT-derived amplified nuclear cDNA.

source_name: Fragmented genomic DNA.


title: ADF_K27_1_(294548-2)

source_name: Amplified H3K27me3 ChIP.


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: PCL Q3412;target name: PCL;host: Rabbit;antigen: Peptide based on the aa 681-780 of the PCL protein;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3412;short description: Rabbit polyclonal Ab raised against the PCL 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: GSM521070 (pirrota_621_B5_Input-18cycles.406.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody PCL Q3412 extraction3_array1 channel_1

value: CNS-derived cell-line

value: third instar larval stage


title: time_course_20_2_(TC3-20_353394-4)

description: CATCH-IT profiling of Drosophila S2 cells using 20 minute azidohomoalanine treatment, replicate 2.

value: 20 minute


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: GSM521068 (pirrota_620_B3_Input-18cycles.405.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody PCL Q3412 extraction1_array1 channel_1

value: y v f mal

value: Unknown


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: NURF301 Q2602;target name: NURF301;host: Rabbit;antigen: Amino Acids 1155-1254;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2602;short description: Accession Number : AAN11431. Description: NURF301 -Nucleosome-remodeling factor subunit. Histone-binding component of NURF (nucleosome remodeling factor) a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Specifically recognizes H3 tails trimethylated on 'Lys-4' (H3-K4Me3);

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: GSM521064 (pirrota_761_A18_Input.531.CEL)

source_name: Cell Line S2-DRSC;Antibody NURF301 Q2602 extraction1_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: time_course_20_1_(TC1-20_283997-2)

description: CATCH-IT profiling of Drosophila S2 cells using 20 minute azidohomoalanine treatment, replicate 1.


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: MBD-R2 Q2567;target name: MBD-R2;host: Rabbit;antigen: Amino Acids 783-882;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2567;short description: Accession number: AAF54781. Has a Zinc-fingerdomain DNA binding; protein binding; zinc ion binding. The biological processes in which it is involved are not known. Since MOF and MBD-R2 robustly coimmunoprecipitate we next tested the effect of its depletion on the localization of MSL proteins on the male X chromosome in SL-2 cells. MBD-R2 protein appeared nuclear in control EGFP dsRNA-treated cells. We could deplete 90% of MBD-R2 protein as detected by Western blot analysis However localization of MSL1 MSL-3 and MOF appeared unaffected in these cells;

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: GSM521062 (pirrota_760_A17_Input.530.CEL)

source_name: Cell Line S2-DRSC;Antibody MBD-R2 Q2567 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: GSM521060 (pirrota_761_A18_Input.531.CEL)

source_name: Cell Line S2-DRSC;Antibody MBD-R2 Q2567 extraction1_array1 channel_1


title: GL2_K27_2_(294543-3)

description: Chromatin immunoprecipitation (ChIP) profiling of the H3K27me3 modification in INTACT-purified nuclei from Arabidopsis root non-hair cells.


title: ADF_K4_2_(294346-2)

value: root epidermis hair cell nuclei


title: time_course_60_1_(TC1-60_283426-3)

description: CATCH-IT profiling of Drosophila S2 cells using 60 minute azidohomoalanine treatment, replicate 1.

value: 60 minute


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: JIL1 Q3433;target name: JIL1;host: Rabbit;antigen: Amino Acids: 919-1018;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3433;short description: JIL1. Accession number AAV11898   JIL-1 isoform A;

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: GSM521058 (pirrota_760_A17_Input.530.CEL)

source_name: Cell Line S2-DRSC;Antibody JIL1 Q3433 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: GSM521056 (pirrota_761_A18_Input.531.CEL)

source_name: Cell Line S2-DRSC;Antibody JIL1 Q3433 extraction1_array1 channel_1


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

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: GSM521054 (pirrota_683_A11_Input.452.CEL)

source_name: Cell Line S2-DRSC;Antibody HP2 (Ab2-90) 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: GSM521052 (pirrota_684_A15_Input.453.CEL)

source_name: Cell Line S2-DRSC;Antibody HP2 (Ab2-90) extraction1_array1 channel_1


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

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: GSM521044 (pirrota_602_B5_Input(20cycles).391.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody HP1c (MO 462) 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: GSM521048 (pirrota_684_A15_Input.453.CEL)

source_name: Cell Line S2-DRSC;Antibody HP1c (MO 462) extraction1_array1 channel_1


title: pulse_1_(521-3H_283426-2)

description: CATCH-IT profiling of Drosophila S2 cells treated with azidohomoalanine for 3 hours (pulse).

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed.

source_name: Amplified CATCH-IT pulldown DNA.

value: azidohomoalanine

value: 3 hours (pulse)

source_name: Amplified input DNA.


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

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: GSM521042 (pirrota_684_A15_Input.453.CEL)

source_name: Cell Line S2-DRSC;Antibody HP1b (Henikoff) 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: GSM521050 (pirrota_683_A11_Input.452.CEL)

source_name: Cell Line S2-DRSC;Antibody HP1c (MO 462) 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: GSM521046 (pirrota_646_B3_Input2(20cycles).423.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody HP1c (MO 462) extraction3_array1 channel_1


title: time_course_60_2_(TC3-60_353629-3)

description: CATCH-IT profiling of Drosophila S2 cells using 60 minute azidohomoalanine treatment, replicate 2.

value: Amplified input DNA


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: GSM521040 (pirrota_683_A11_Input.452.CEL)

source_name: Cell Line S2-DRSC;Antibody HP1b (Henikoff) 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: GSM521038 (pirrota_836_CL8-1_Input_DNA(14cyc).607.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9me3 (new lot) extraction3_array1 channel_1

value: dorsal mesothoracic disc


title: MET_1_(MET_cy5-cy3)

description: CATCH-IT profiling of Drosophila S2 cells treated with methionine (instead of azidohomoalanine) for 6 hours.

value: 6 hours


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: GSM521036 (pirrota_837_CL8-2_Input_DNA(14cyc).608.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9me3 (new lot) extraction1_array1 channel_1


title: time_course_40_2_(TC3-40_353352)

description: CATCH-IT profiling of Drosophila S2 cells using 40 minute azidohomoalanine treatment, replicate 2.

value: 40 minute


title: AHA_6hr_1_(AHA_cy5-cy3_284230)

description: CATCH-IT profiling of Drosophila S2 cells treated with azidohomoalanine for 6 hours.


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

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: GSM521022 (pirrota_540_A12_Input18.362.CEL)

source_name: Cell Line S2-DRSC;Antibody dRING Q3200 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: GSM521028 (pirrota_837_CL8-2_Input_DNA(14cyc).608.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K9me2-Ab2 (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: GSM521030 (pirrota_836_CL8-1_Input_DNA(14cyc).607.CEL)

source_name: Cell Line CME-W1-Cl.8+;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: GSM521034 (pirrota_682_KC2_Input(14cycles).451.CEL)

source_name: Cell Line Kc167;Antibody H3K9me2-Ab2 (new lot) extraction3_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: GSM521032 (pirrota_681_KC1_Input(14cycles).450.CEL)

source_name: Cell Line Kc167;Antibody H3K9me2-Ab2 (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: GSM521020 (pirrota_277_S12_Input.122.CEL)

source_name: Cell Line S2-DRSC;Antibody dRING Q3200 extraction1_array1 channel_1


title: AHA_3hr_2_(CSB_277840-3)

description: CATCH-IT profiling of Drosophila S2 cells treated with azidohomoalanine for 3 hours, replicate 2.

value: 3 hours


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: GSM521018 (pirrota_620_B3_Input-18cycles.405.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody dRING Q3200 extraction3_array1 channel_1

value: CNS-derived cell-line

value: third instar larval stage


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

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: GSM521024 (pirrota_836_CL8-1_Input_DNA(14cyc).607.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K18Ac (new lot) extraction1_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: NURF301 Q2602;target name: NURF301;host: Rabbit;antigen: Amino Acids 1155-1254;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2602;short description: Accession Number : AAN11431. Description: NURF301 -Nucleosome-remodeling factor subunit. Histone-binding component of NURF (nucleosome remodeling factor) a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Specifically recognizes H3 tails trimethylated on 'Lys-4' (H3-K4Me3);

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: GSM521066 (pirrota_760_A17_Input.530.CEL)

source_name: Cell Line S2-DRSC;Antibody NURF301 Q2602 extraction3_array1 channel_1


title: AHA_3hr_1_(3C_382774)

description: CATCH-IT profiling of Drosophila S2 cells treated with azidohomoalanine for 3 hours, replicate 1.

source_name: Amplified CATCH-IT pulldown DNA.


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: GSM521026 (pirrota_837_CL8-2_Input_DNA(14cyc).608.CEL)

source_name: Cell Line CME-W1-Cl.8+;Antibody H3K18Ac (new lot) extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: dMi-2 Q2626;target name: dMi-2;host: Rabbit;antigen: Amino Acids 1518-1617;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2626;short description: Accession Number: AAX52739. Chromodomain-helicase-DNA-binding protein Mi-2 homolog. Vital role in development. Protein binds to a portion of Hunchback (HB) protein that is critical for repression of bithorax complex (BXC) genes. May also function in polycomb group (PcG) repression of Hox genes. Belongs to the SNF2/RAD54 helicase family.Contains 2 chromo domains. Contains 1 helicase ATP-binding domain.Contains 1 helicase C-terminal domain. Contains 2 PHD-type zinc fingers.

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: GSM521014 (pirrota_761_A18_Input.531.CEL)

source_name: Cell Line S2-DRSC;Antibody dMi-2 Q2626 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: GSM521016 (pirrota_621_B5_Input-18cycles.406.CEL)

source_name: Cell Line ML-DmBG3-c2;Antibody dRING Q3200 extraction1_array1 channel_1

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: GSM521012 (pirrota_760_A17_Input.530.CEL)

source_name: Cell Line S2-DRSC;Antibody dMi-2 Q2626 extraction1_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage