title: expt.854 extraction3_array1

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

Input: pirrota_1038_Kc4_Input_14cyc_812.CEL

source_name: expt.854 extraction3_array1 channel_1


title: Chip-23 Day14 Rep4 Blue & Day0 Rep4 Red

status: Public on Apr 05 2011

type: RNA

city: Fargo

first: Munevver

last: Dogramaci

state: ND

address: 1605 Albrecht Blvd N

country: USA

institute: USDA-ARS

description: See Dogramaci et al. Plant Molecular Biology 2010 (PMID 20340040) for more details.

hyb_protocol: Labeled cDNAs were hybridized to a custom-made 23K element microarray that contained 19,808 UniGenes from a leafy spurge EST database (Anderson et al. 2007) and an additional 4,129 UniGenes from a cassava EST database (Lokko et al. 2007). Comparison of gene expression between samples was accomplished using a rolling circle dye-swap hybridization scheme (Churchill 2002) to provide every biological replicate with technical replicates. In this experiment, each of the four biological replicates included two technical replicates.

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

data_processing: A quality control value of “1” was assigned to all probes that had intensity values greater than 2 times the standard deviation over average of the negative control and empty probe intensities (after deleting 1% of the most intense negative/empty probe values). Intensity values of control spots (a total of 1455 spots including 3X SSC, blanks, and mouse) from MA chips were removed before bioinformatics. In this submission, the original “GPR” files include information for the control spots, while the Sample data tables include information only for the spots that were used for data analyses (a total of: 23937). Raw signal intensities of all DNA-containing spots were up-loaded into the GeneMaths XT 5.1 microarray data analysis program (Applied Maths Inc., Austin, TX, USA) for normalization following the "Layer/Normalization/Arrays" path with default settings (Offset: Average; Scaling: Standard deviation), and for statistical analysis and clustering of the dataset. Hybridization intensities were log2 transformed, and arrays were centered and normalized against each other; technical replicates within each biological replicate were averaged.

molecule: total RNA

organism: Euphorbia esula

source_name: 14-day dehydration-stressed endodormant crown buds

label_protocol: For microarray hybridizations, labeled cDNAs were prepared from 30 µg of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer's protocols.

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

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

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype and maintained in a greenhouse. Induction of endodormancy in crown buds was accomplished by subjecting paradormant plants to a ramp down treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as described by Dogramaci et al. (2010); plants were watered daily. After endodormancy induction, water was withheld from these plants for 14 days to study effect of dehydration stress on transcriptome profiles and dormancy status.

tag: biotype

tag: tissue

value: crown bud

tag: treatment

value: dehydration stress

tag: treatment time

value: 14 days

source_name: 0-day dehydration-stressed endodormant crown buds

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype and maintained in a greenhouse. Induction of endodormancy in crown buds was accomplished by subjecting paradormant plants to a ramp down treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as described by Dogramaci et al. (2010); plants were watered daily. In this study, endodormant crown buds were used as controls, and referred as Day-0 dehydration.

value: 0 days


title: expt.928 extraction3_array1

status: Public on Mar 09 2011

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

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

Input: pirrota_478_C18-2_Input_14cyc_289.CEL

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

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

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

label: biotin

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: expt.928 extraction3_array1 channel_1

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

tag: cell line

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage

tag: Sex

value: Male


title: expt.947 extraction1_array1

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

Input: pirrota_1041_Kc5_Input_20cyc_815.CEL

source_name: expt.947 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.

value: embryo-derived cell-line

value: late embryonic stage

tag: genotype

value: se/e

value: Female


title: expt.666 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K27me2-TJ;target name: H3K27me2;host: Rabbit;antigen: H3K27me2 antigen (aa 22-33) containing two TKAARK(Me)2SAPATG fingers;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Thomas Jenuwein;short description: Polyclonal rabbit antibody raised against H3K27me2;

Input: pirrota_915_A17_Input-18cycles.670.CEL

source_name: expt.666 extraction3_array1 channel_1


title: expt.667 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K27me2-TJ;target name: H3K27me2;host: Rabbit;antigen: H3K27me2 antigen (aa 22-33) containing two TKAARK(Me)2SAPATG fingers;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Thomas Jenuwein;short description: Polyclonal rabbit antibody raised against H3K27me2;

Input: pirrota_873_S15_Input-18cycles.644.CEL

source_name: expt.667 extraction1_array1 channel_1


title: expt.437 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K27me2-TJ;target name: H3K27me2;host: Rabbit;antigen: H3K27me2 antigen (aa 22-33) containing two TKAARK(Me)2SAPATG fingers;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Thomas Jenuwein;short description: Polyclonal rabbit antibody raised against H3K27me2;

Input: pirrota_620_B3_Input-18cycles.405.CEL

source_name: expt.437 extraction1_array1 channel_1

value: CNS-derived cell-line

value: y v f mal

value: Unknown


title: expt.1055 extraction3_array1

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

Input: pirrota_1038_Kc4_Input_14cyc_812.CEL

source_name: expt.1055 extraction3_array1 channel_1


title: expt.668 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K27me2-TJ;target name: H3K27me2;host: Rabbit;antigen: H3K27me2 antigen (aa 22-33) containing two TKAARK(Me)2SAPATG fingers;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Thomas Jenuwein;short description: Polyclonal rabbit antibody raised against H3K27me2;

Input: pirrota_916_B4_Input-18cycles.671.CEL

source_name: expt.668 extraction3_array1 channel_1


title: haploid ES cell line HTG1 p11 vs male somatic C57B/6 gDNA

status: Public on Jul 23 2011

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: CNV analysis of HTG1 haploid ES cell line vs C57B/6 male

hyb_protocol: hybridization were performed by a commercial provider; Imagenes, Berlin

scan_protocol: scanning were performed by a commercial provider; Imagenes, Berlin

organism: Mus musculus

source_name: gDNA from HTG1

label_protocol: sample processing, labelling and data processing were performed by a commercial provider; Imagenes, Berlin

growth_protocol: male kidney

extract_protocol: gDNA was extracted using the Quiagen Gentra Puregene Kit

treatment_protocol: ES cells were established and cultured in 2i medium

tag: strain

value: mixed transgenic

tag: dna source

value: haploid ES cells

source_name: C57B/6 male kidney control

label_protocol: labelling were performed by a commercial provider; Imagenes, Berlin

growth_protocol: gDNA extracted from male kidney

treatment_protocol: kidney was collected from an inbred C57B/6 mouse

value: male somatic kidney


title: expt.906 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: WDS Q2691;target name: WDS;host: Rabbit;antigen: LDNTLKLWDY SKGKCLKTYT GHKNEKYCIF ANFSVTGGKW IVSGSEDNMV YIWNLQSKEV VQKLQGHTDT VLCTACHPTE NIIASAALEN DKTIKLWKSD  (261-360 of the WDS protein); clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2691;short description: WDS (CG17437). FLYBASE:FBgn0040066. The essential Drosophila melanogaster gene wds (will die slowly) codes for a WD-repeat protein with seven repeats.;

Input: pirrota_1220_Kc4_Input.904.CEL

source_name: expt.906 extraction1_array1 channel_1


title: CBA male somatic vs male somatic C57B/6 gDNA

description: CNV analysis of CBA male vs C57B/6 male

data_processing: data processing were performed by a commercial provider; Imagenes, Berlin

source_name: gDNA from CBA somatic control

treatment_protocol: kidney was collected from an inbred CBA mouse

value: CBA


title: haploid ES cell line HAP2 p18 vs male somatic C57B/6 gDNA

description: CNV analysis of HAP2 haploid ES cell line vs C57B/6 male

source_name: gDNA from HAP2

value: F1 CBAxB6


title: expt.946 extraction3_array1

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

Input: pirrota_1040_Kc4_Input_20cyc_814.CEL

source_name: expt.946 extraction3_array1 channel_1


title: expt.853 extraction1_array1

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

Input: pirrota_1039_Kc5_Input_14cyc_813.CEL

source_name: expt.853 extraction1_array1 channel_1


title: expt.907 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: WDS Q2691;target name: WDS;host: Rabbit;antigen: LDNTLKLWDY SKGKCLKTYT GHKNEKYCIF ANFSVTGGKW IVSGSEDNMV YIWNLQSKEV VQKLQGHTDT VLCTACHPTE NIIASAALEN DKTIKLWKSD  (261-360 of the WDS protein); clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2691;short description: WDS (CG17437). FLYBASE:FBgn0040066. The essential Drosophila melanogaster gene wds (will die slowly) codes for a WD-repeat protein with seven repeats.;

Input: pirrota_1221_Kc5_Input.905.CEL

source_name: expt.907 extraction3_array1 channel_1


title: expt.843 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MLE Q4142;target name: MLE;host: Rabbit;antigen: Amino acid 2-101;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4142;short description: MLE;

Input: pirrota_1089_A20_Input.847.CEL

source_name: expt.843 extraction3_array1 channel_1


title: expt.956 extraction1_array1

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

Input: pirrota_1040_Kc4_Input_20cyc_814.CEL

source_name: expt.956 extraction1_array1 channel_1


title: expt.994 extraction3_array1

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

Input: pirrota_1012_A21_Input_20cyc_774.CEL

source_name: expt.994 extraction3_array1 channel_1


title: expt.993 extraction1_array1

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

Input: pirrota_1011_A20_Input_20cyc_773.CEL

source_name: expt.993 extraction1_array1 channel_1


title: expt.842 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MLE Q4142;target name: MLE;host: Rabbit;antigen: Amino acid 2-101;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4142;short description: MLE;

Input: pirrota_1088_A21_Input.846.CEL

source_name: expt.842 extraction1_array1 channel_1


title: expt.825 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JIL-1(Q4170);target name: JIL-1;host: Rabbit;antigen: Amino acid 566-665;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4170;short description: JIL-1;

Input: pirrota_761_A18_Input.531.CEL

source_name: expt.825 extraction3_array1 channel_1


title: haploid ES cell line HTG2 p11 vs male somatic C57B/6 gDNA

description: CNV analysis of HTG2 haploid ES cell line vs C57B/6 male

source_name: gDNA from HTG2


title: expt.636 extraction1_array1

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;

Input: pirrota_499_S14_Input18.320.CEL

source_name: expt.636 extraction1_array1 channel_1


title: expt.576 extraction3_array1

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;

Input: pirrota_619_A14_Input-18cycles.404.CEL

source_name: expt.576 extraction3_array1 channel_1


title: haploid ES cell line HAP1 p25 vs male somatic C57B/6 gDNA

description: CNV analysis of HAP1 haploid ES cell line vs C57B/6 male

source_name: gDNA from HAP1


title: expt.917 extraction3_array1

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

Input: pirrota_1204_B3_Input.935.CEL

source_name: expt.917 extraction3_array1 channel_1


title: expt.918 extraction1_array1

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

Input: pirrota_1205_B5_Input.936.CEL

source_name: expt.918 extraction1_array1 channel_1


title: expt.1089 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ISWI Q4095;target name: ISWI;host: Rabbit;antigen: Amino acid 589-688;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4095;short description: ISWI;

Input: pirrota_1361_Kc-4_Input.1113.CEL

source_name: expt.1089 extraction3_array1 channel_1


title: expt.824 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JIL-1(Q4170);target name: JIL-1;host: Rabbit;antigen: Amino acid 566-665;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4170;short description: JIL-1;

Input: pirrota_760_A17_Input.530.CEL

source_name: expt.824 extraction1_array1 channel_1


title: expt.832 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ISWI Q4095;target name: ISWI;host: Rabbit;antigen: Amino acid 589-688;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4095;short description: ISWI;

Input: pirrota_1088_A21_Input.846.CEL

source_name: expt.832 extraction3_array1 channel_1


title: expt.833 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ISWI Q4095;target name: ISWI;host: Rabbit;antigen: Amino acid 589-688;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4095;short description: ISWI;

Input: pirrota_1089_A20_Input.847.CEL

source_name: expt.833 extraction1_array1 channel_1


title: expt.957 extraction3_array1

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

Input: pirrota_1041_Kc5_Input_20cyc_815.CEL

source_name: expt.957 extraction3_array1 channel_1


title: NA19209 replicate-1

status: Public on Jan 05 2011

city: London

first: Jordana

last: Bell

address: St Thomas' Hospital, Westminster Bridge Rd

department: Department of Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: BeadArray

data_processing: BeadStudio software

label: Cy5 and Cy3

organism: Homo sapiens

source_name: HapMap Yoruba lymphoblastoid cell line

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from LCLs according to standard recommended Illumina protocol for genome DNA extraction using the EZ DNA Methylation-Gold Kit (from Zymo Research).

tag: gender

value: HapMap Yoruba lymphoblastoid cell line

tag: coriell catalog id

tag: replicate


title: NA19201 replicate-1


title: NA19238 replicate-1


title: NA19239 replicate-1


title: NA19210 replicate-1


title: NA19172 replicate-1


title: NA19257 replicate-1


title: NA19153 replicate-1


title: NA19190 replicate-1


title: NA19225 replicate-1


title: NA19204 replicate-1


title: NA19159 replicate-1


title: NA19200 replicate-1


title: NA19203 replicate-1


title: NA19207 replicate-1


title: NA19222 replicate-1


title: NA19192 replicate-1


title: NA19223 replicate-1


title: NA19147 replicate-1


title: NA19206 replicate-1


title: NA19160 replicate-1


title: NA19141 replicate-1


title: NA19171 replicate-1


title: NA19193 replicate-1


title: NA19152 replicate-1


title: NA19143 replicate-1


title: NA19140 replicate-1


title: NA19138 replicate-1


title: NA19144 replicate-1


title: NA19137 replicate-1


title: NA19102 replicate-1


title: NA19131 replicate-1


title: NA19116 replicate-1


title: NA19119 replicate-1


title: NA19128 replicate-1


title: NA19101 replicate-1


title: NA19127 replicate-1


title: NA19108 replicate-1


title: NA18916 replicate-1


title: NA19093 replicate-1


title: NA19099 replicate-1


title: NA19130 replicate-1


title: NA18913 replicate-1


title: NA19092 replicate-1


title: NA18907 replicate-1


title: NA18870 replicate-1


title: NA19114 replicate-1


title: NA18871 replicate-1


title: NA19098 replicate-1


title: NA18858 replicate-1


title: NA18909 replicate-1


title: NA18852 replicate-1


title: NA18912 replicate-1


title: NA18856 replicate-1


title: NA18862 replicate-1


title: NA18861 replicate-1


title: NA18853 replicate-1


title: NA18855 replicate-1


title: NA18859 replicate-1


title: NA18516 replicate-1


title: NA18520 replicate-1


title: NA18505 replicate-1


title: NA18523 replicate-1


title: NA18510 replicate-1


title: NA18522 replicate-1


title: NA18498 replicate-1


title: NA18517 replicate-1


title: NA18507 replicate-1


title: NA18504 replicate-1


title: NA18499 replicate-1


title: NA19127 replicate-3


title: NA18871 replicate-2


title: NA18502 replicate-1


title: NA19257 replicate-2


title: NA19099 replicate-3


title: NA19225 replicate-2


title: NA18508 replicate-1


title: NA19193 replicate-2


title: NA19200 replicate-3


title: NA18501 replicate-1


title: NA19190 replicate-2


title: NA19153 replicate-2


title: NA19200 replicate-4


title: NA19223 replicate-2


title: NA18511 replicate-1


title: NA19192 replicate-2


title: NA18489 replicate-1


title: NA19147 replicate-2


title: NA18916 replicate-2


title: NA19108 replicate-2


title: NA19140 replicate-2


title: NA19130 replicate-2


title: NA19114 replicate-2


title: NA18909 replicate-2


title: NA18907 replicate-2


title: NA18855 replicate-2


title: NA18853 replicate-2


title: NA19127 replicate-2


title: NA19128 replicate-2


title: NA18852 replicate-2


title: NA18523 replicate-2


title: NA18520 replicate-2


title: NA18499 replicate-2


title: NA18510 replicate-2


title: NA18511 replicate-2


title: NA19238 replicate-2


title: NA19238 replicate-3


title: NA19239 replicate-2


title: NA18519 replicate-2


title: NA18486 replicate-2


title: NA19210 replicate-2


title: NA19222 replicate-2


title: NA18489 replicate-2


title: NA19209 replicate-2


title: NA18519 replicate-1


title: NA19201 replicate-2


title: NA19160 replicate-2


title: NA19200 replicate-2


title: NA19206 replicate-2


title: NA19203 replicate-2


title: NA19207 replicate-2


title: NA19144 replicate-2


title: NA19152 replicate-2


title: NA19159 replicate-2


title: NA19172 replicate-2


title: NA19171 replicate-2


title: NA19204 replicate-2


title: NA19131 replicate-2


title: NA19137 replicate-2


title: NA19099 replicate-2


title: NA19141 replicate-2


title: NA19116 replicate-2


title: NA19119 replicate-2


title: NA19098 replicate-2


title: NA19101 replicate-2


title: NA18498 replicate-2


title: NA19102 replicate-2


title: NA19143 replicate-2


title: NA19093 replicate-2


title: NA19092 replicate-2


title: NA18913 replicate-2


title: NA18862 replicate-2


title: NA18507 replicate-3


title: NA18861 replicate-2


title: NA18856 replicate-2


title: NA18522 replicate-2


title: H3K36me1.S2 extraction3_array1

status: Public on Nov 18 2010

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

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

input: GSM624683_pirrota_142_A3_Input_HD.10.CEL


title: NA18517 replicate-2


title: NA18859 replicate-2


title: NA19138 replicate-2


title: NA18505 replicate-2


title: NA18507 replicate-2


title: NA18858 replicate-2


title: ZW5.BG3 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: ZW5;target name: ZW5;host: Rabbit;antigen: GST fusion of aa 5-110 of ZW5 protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Vincent Pirrotta;short description: Rabbit antibody raised against GST fusion protein containing Zeste white 5 sequence.;

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: GSM624679_pirrota_365_B2_Input.208.CEL

source_name: ZW5.BG3 extraction3_array1 channel_1


title: NA18508 replicate-2


title: NA18502 replicate-2


title: NA18516 replicate-2


title: ZW5.BG3 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: GSM624677_pirrota_364_B1_Input.207.CEL

source_name: ZW5.BG3 extraction1_array1 channel_1


title: NA18504 replicate-2


title: shMYB Day 5 of diff, rep 1

status: Public on Jan 03 2011

city: Boston

first: Vijay

middle: G.

last: Sankaran

state: MA

address: 300 Longwood Avenue

department: Department of Medicine

institute: Children's Hospital Boston

description: Expression data from total RNA of CD34-derived erythroid progenitors

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on to the GeneChip array. GeneChips were washed and stained in the Affymetrix Fluidics Station.  Details are available at: http://jura.wi.mit.edu/genomecorewiki/index.php/Main_Page.

scan_protocol: GeneChips were scanned using the GeneChip Scanner.  Details are available at: http://jura.wi.mit.edu/genomecorewiki/index.php/Main_Page.

data_processing: Array data were normalized with the Robust Multichip Averaging (RMA) protocol using the affy package in BioConductor.

source_name: shMYB lentivirus transduced CD34 cells at day 5 of differentiation, replicate 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 ug total RNA (3' IVT Express Kit manual, 2008, Affymetrix).

growth_protocol: CD34 cells were grown in a two-phase culture as has been described in detail previously (Sankaran et al., Science, 2008) and is described in the accompanying manuscript.

extract_protocol: Total RNA was extracted using the miRNAeasy Mini Kit from Qiagen and following the standard protocol.

treatment_protocol: CD34 cells were transduced with control or MYB shRNAs using lentiviral transduction prior to differentiation.

tag: cell type

value: CD34-derived erythroid progenitors

value: MYB shRNA Knockdown


title: H3K36me1.S2 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: GSM624681_pirrota_212_A8_Input.62.CEL


title: NA18486 replicate-1


title: Control Day 5 of diff, rep 2

source_name: Control lentivirus transduced CD34 cells at day 5 of differentiation, replicate 2

value: control


title: shMYB Day 5 of diff, rep 4

source_name: shMYB lentivirus transduced CD34 cells at day 5 of differentiation, replicate 4


title: NA18912 replicate-2


title: Control Day 5 of diff, rep 4

source_name: Control lentivirus transduced CD34 cells at day 5 of differentiation, replicate 4


title: shMYB Day 5 of diff, rep 2

source_name: shMYB lentivirus transduced CD34 cells at day 5 of differentiation, replicate 2


title: Control Day 5 of diff, rep 1

source_name: Control lentivirus transduced CD34 cells at day 5 of differentiation, replicate 1


title: SPT16_Q2583.S2 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: SPT16 Q2583;target name: SPT16;host: Rabbit;antigen: Amino Acid 105-204;clonal: Unknown;purified: Affinity;company: SDI;catalog: Q2583;short description: Annotation symbol CG1828; Component of the FACT( Facilitates chromatin transcription ) complex It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the Nucleosome. The FACT complex is required for expression of Hox genes.

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: GSM624675_pirrota_1088_A21_Input.846.CEL

value: Male


title: SPT16_Q2583.S2 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: GSM624673_pirrota_1089_A20_Input.847.CEL

value: embryo-derived cell-line


title: Psc.S2 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Psc;target name: Psc;host: Rabbit;antigen: GST-fusion of aa 819-926 of PSC protein;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Vincent Pirrotta;short description: Polyclonal rabbit antibody raised against recombinant PSC protein. Eight ug/ul (3ul total) was used for ChIP experiments.;

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: GSM624671_pirrota_499_S14_Input18.320.CEL

source_name: Psc.S2 extraction3_array1 channel_1

value: late embryonic stage


title: Control Day 5 of diff, rep 3

source_name: Control lentivirus transduced CD34 cells at day 5 of differentiation, replicate 3


title: shMYB Day 5 of diff, rep 3

source_name: shMYB lentivirus transduced CD34 cells at day 5 of differentiation, replicate 3


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: GSM624661_pirrota_1059_L3_6_Input.799.CEL

source_name: PIWI-Q2569.D.mel 3rd Instar Larvae Nuclei extraction1_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).

value: Oregon-R

value: 3rd Instar Larvae

value: wild type


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: GSM624663_pirrota_1058_L3_3_Input(20cyc).798.CEL

source_name: PIWI-Q2569.D.mel 3rd Instar Larvae Nuclei extraction3_array1 channel_1


title: PIWI-Q2569.Clone_8 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: GSM624659_pirrota_825_CL8-1_InputDNA(20cyc).596.CEL

value: dorsal mesothoracic disc

value: third instar larval stage


title: Psc.BG3 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: GSM624665_pirrota_621_B5_Input-18cycles.406.CEL

source_name: Psc.BG3 extraction1_array1 channel_1

value: CNS-derived cell-line

value: y v f mal

value: Unknown


title: Psc.BG3 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: GSM624667_pirrota_620_B3_Input-18cycles.405.CEL

source_name: Psc.BG3 extraction3_array1 channel_1


title: PIWI-Q2569.Clone_8 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: GSM624657_pirrota_826_CL8-2_Input_DNA(20cyc).597.CEL


title: Psc.S2 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: GSM624669_pirrota_298_S11_Input.143.CEL

source_name: Psc.S2 extraction1_array1 channel_1


title: MRG15_Q2481.S2 extraction3_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: MRG15 Q2481;target name: MRG15;host: Rabbit;antigen: Amino acid 100-174;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2481;short description: MRG15;

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: GSM624655_pirrota_1089_A20_Input.847.CEL


title: MRG15_Q2481.BG3 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: GSM624647_pirrota_1205_B5_Input.936.CEL


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9acS10P (new abcam 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: GSM624639_pirrota_1041_Kc5_Input(20cyc).815.CEL

source_name: H3K9acS10P (new abcam lot).Kc extraction3_array1 channel_1

value: se/e

value: Female


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: GSM624643_pirrota_826_CL8-2_Input_DNA(20cyc).597.CEL

source_name: H3K9acS10P (new lot).Clone_8 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: GSM624641_pirrota_825_CL8-1_InputDNA(20cyc).596.CEL

source_name: H3K9acS10P (new lot).Clone_8 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: GSM624637_pirrota_1040_Kc4_Input(20cyc).814.CEL

source_name: H3K9acS10P (new abcam lot).Kc extraction1_array1 channel_1


title: ASH1 Q4177.S2 extraction3_array1

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

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: GSM624631_pirrota_873_S15_Input-18cycles.644.CEL

source_name: ASH1 Q4177.S2 extraction3_array1 channel_1


title: MRG15_Q2481.BG3 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: GSM624645_pirrota_1204_B3_Input.935.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: GSM624633_pirrota_1058_L3_3_Input(20cyc).798.CEL

source_name: H3K9acS10P (new abcam lot).D.mel 3rd Instar Larvae Nuclei extraction1_array1 channel_1


title: ASH1 Q4177.S2 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: GSM624629_pirrota_915_A17_Input-18cycles.670.CEL

source_name: ASH1 Q4177.S2 extraction1_array1 channel_1


title: NA18870 replicate-2

data_processing: BeadStudio software

source_name: HapMap Yoruba lymphoblastoid cell line

value: HapMap Yoruba lymphoblastoid cell line


title: MRG15_Q2481.S2 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: GSM624653_pirrota_1088_A21_Input.846.CEL


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: GSM624623_pirrota_262_E2_Input.107.CEL

source_name: H3K9me2-Ab2 (new lot).2-4 hr OR embryo extraction3_array1 channel_1

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

value: Embryo 2-4hr OR


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me2 antibody2;target name: H3K9me2;host: Mouse;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 di methylated at K9.;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab1220;reference: http://www.abcam.com/Histone-H3-di-methyl-K9-antibody-mAbcam-1220-ChIP-Grade-ab1220.html;short description: mouse monoclonal against a synthetic peptide derived from within residues 1-100 of human H3 di methylated at K9;

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

input: GSM624625_pirrota_377_LarvaeTrial_Input.193CEL

source_name: H3K9me2 antibody2.D.mel 3rd Instar Larvae Nuclei 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: GSM624627_pirrota_284_Input.137.CEL

source_name: H3K9me2 antibody2.D.mel 3rd Instar Larvae Nuclei extraction3_array1 channel_1


title: MRG15_Q2481.Kc 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: GSM624651_pirrota_1362_Kc-5_Input.1114.CEL


title: MRG15_Q2481.Kc 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: GSM624649_pirrota_1361_Kc-4_Input.1113.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: GSM624635_pirrota_1059_L3_6_Input.799.CEL

source_name: H3K9acS10P (new abcam lot).D.mel 3rd Instar Larvae Nuclei extraction3_array1 channel_1


title: 35A1-35A0_237367 extraction4_array1

hyb_protocol: This protocol is copied from Chapter 4, Hybridization & Washing, in NimbleGen Arrays User's Guide ChIP-chip Analysis (Version 3.1, 27 May 2008), which describes the NimbleGen protocol for sample hybridization and washing.

scan_protocol: Two-Color Array Scanning is copied from Chapter 5, Two-Color Array Scanning, in NimbleGen Arrays User's Guide ChIP-chip Analysis (Version 3.1, 27 May 2008), which describes the protocol for scanning two-color NimbleGen arrays with a GenePix 4000B Scanner and associated software

data_processing: NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is R5.27.

label: Cy5 dye

molecule: polyA RNA

label_protocol:
This is a modification of the NimbleGen protocol for ChIP-chip labeling (http://www.nimblegen.com/). It yields adequate amounts of end-labeled material without PCR amplification starting with ≥ 0.2 ug fragmented DNA.

1) In a 0.5 ml PCR tube, mix up to 20 uL ds DNA with 20 uL of either Cy3- or Cy5-labeled 9-mers in random primer buffer (Cy3 and Cy5 9-mer Wobble from TriLink are mixed according to the NimbleGen protocol, aliquoted and stored frozen). Use 0.2-3 ug input DNA, the more the better, and add water to 20 uL. Protect the dye-labeled material from direct light, especially Cy5, throughout the procedure.

2) Heat at 98oC x 10 min. Quick chill in ice-water (this is important).

3) While the samples are denaturing, make a master mix with Klenow exo- (NEB 50,000u/ml) and dNTPs. For example, for 10 samples mix 42 uL water, 10.5 uL Klenow, 52.5 uL 10mM dNTPs (aliquoted and stored frozen). While samples are still in the ice-water bath and chilled, add 10 uL master mix to each tube with 10 or more strokes of the Pipetteman tip.

4) Following a brief spin, transfer tubes to a 37oC cycler. Incubate overnight (16 hr).

5) Prepare 1.5 ml tubes with NaCl+EDTA (equivalent of 5 uL 0.5 M EDTA, 5.7 uL 5 M NaCl, which can be added together). Remove the tubes from the cycler and transfer contents from the cycler to these 1.5 ml tubes. Add 60 uL 2-propanol (the volume is important). Let sit in dark 10' at room temperature.

6) Spin at 13.2k rpm for 10 min at room temperature. Carefully decant the supernatant from the deeply colored pellet with a P200 Pipetteman. Add 500 uL ice-cold 80% ethanol and spin briefly in the cold. Carefully pour or pull off the ethanol - large pellets tend to dislodge. Quick spin and pull off the excess ethanol. Let air dry (~10 min at room temperature).

7) Add 20 uL water to dissolve. Note that the deepness of the red (Cy3) or blue (Cy5) is a good measure of the yield. For samples in which there was little starting material, and/or the DNA was small, there will not be enough for an array, and the color will be faint. For samples with deep color, add an additional 30 uL water. Measure OD260 and calculate yield. Store at 4oC for brief periods or at -20oC longer term in dark.

8) For samples with less than 30 ug/array, do another round of labeling, using 20 uL of the labeled DNA from the first round prep. The second round is much more efficient than the first round and consistently yields ≥ 60 ug.

9) Check sizes on a 1.5% gel without ethidium. Cy3 fluoresces well enough to see 1 ug, but Cy5 is much fainter and might not be visible. DNA should be about the same average size as the starting material. Follow with ethidium staining: DNA typically smears up towards the top of the gel, but this material is evidently low in molar amount of label and does not appear to cause a problem.

10) For each 2.1 M array, mix 30 ug Cy3-labeled DNA with 30 ug Cy5-labeled DNA and speed-vac dry on low or medium. If Cy3 is input DNA then Cy5 is pull-down DNA and vice versa.

11) Reduce volume by speedvac on low to 12.3 uL, or lyophilize samples for hybridization to NimbleGen arrays using standard NimbleGen hybridization protocol.

growth_protocol: Basic protocol for growth of Drosophila tissue culture cell lines.

extract_protocol: Drosophila tissue culture cells are lysed in TRIzol, extracted with CHCl3, and total cellular RNA is precipitated with isopropanol. Total RNA was used as a template to synthesize oligo(dT)-primed first-strand cDNA.

label: Cy3 dye


title: 1_41A0A1_271532-5 extraction6_array1


title: 29A1-29A0_237370 extraction1_array1


title: AC_56C0C1_353355-5 extraction2_array1

growth_protocol: RNAi and induction:1. Grow cells in SFM+FCS up to 20 days to mid-late log phase (0.6 - 1.5 x 107 cells/ml).2. Collect cells in 50 ml tube and resuspend in SFM at 2 x 106 cells/ml (4 x 106 cells/ml for 3d RNAi samples). Put 5 ml of suspended cells in each 10 cm plate and add dsRNA to a final concentration of 15 ug/ml.3. Incubate 30 min, and then add an additional 10 ml of SFM+FCS. (0.67 or 1.3 x 106 cells/ml x 15 ml/plate; 6 - 10 plates per sample)4. Monitor cell number and cell viability daily.5. On day 5 harvest the cells.Cells can be used to purify chromatin, or RNA, or protein.


title: Kc_600_mM_Salt_Extracted_Chromatin_Pellet extraction1_array1

data_processing: NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is R5.27.

extract_protocol: Salt fractionation protocol


title: Kc_H2Av_Knockdown_600_mM_Salt_Extracted_Chromatin_Pellet extraction2_array1

extract_protocol: Salt fractionation of chromatin from RNAi-treated tissue culture cells.


title: Kc_H2Av_Knockdown_600_mM_Salt_Extracted_Chromatin extraction1_array1


title: X_56A0A1_353629-4 extraction1_array1


title: Kc_H2Av_Knockdown_600_mM_Salt_Extracted_Chromatin extraction2_array1


title: Kc_600_mM_Salt_Extracted_Chromatin_Pellet extraction2_array1


title: P_57C0C1_383370-2 extraction4_array1


title: Kc_600_mM_Salt_Extracted_Chromatin extraction2_array1


title: Fly_wing_disc_150_mM_Salt_Extracted_Chromatin extraction1_array1


title: Kc_H2Av_Knockdown_600_mM_Salt_Extracted_Chromatin_Pellet extraction1_array1


title: Fly_wing_disc_600_mM_Salt_Extracted_Chromatin_Pellet extraction2_array1


title: Fly_wing_disc_80_mM_Salt_Extracted_Chromatin extraction2_array1


title: Fly_wing_disc_600_mM_Salt_Extracted_Chromatin_Pellet extraction1_array1


title: Kc_600_mM_Salt_Extracted_Chromatin extraction1_array1


title: Fly_wing_disc_600_mM_Salt_Extracted_Chromatin extraction2_array1


title: Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin_Pellet extraction3_array1

extract_protocol: Staged Drosophila embryos are harvested.  Nuclei are isolated and gently digested with micrococcal nuclease to yield nucleosomes.  The DNA is purified for labelling, and the proteins are analyzed by gel electrophoresis.

value: B3(made_by :Paul Talbert description :A strain that expresses a conditionally expressed biotin-tagged histone H3.3.  The strain also contains the E. coli BirA gene that is expressed under the control of a GAL4 UAS. tags :Transposon transgene :Histone H3.3::biotin-recognition-peptide outcross :New Line genotype :y w; A5C-GAL4/cyO; B3 official name :B3 )

value: y w; A5C-GAL4/cyO; B3

tag: transgene


title: Fly_wing_disc_80_mM_Salt_Extracted_Chromatin 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: GSM624621_pirrota_454_E4_Input.276.CEL

source_name: H3K9me2-Ab2 (new lot).2-4 hr OR embryo extraction1_array1 channel_1


title: Fly_wing_disc_600_mM_Salt_Extracted_Chromatin extraction1_array1


title: NA18501 replicate-2

value: Male


title: O_57A0A1_353281-4 extraction2_array1

value: embryo-derived cell-line


title: Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin extraction2_array1


title: Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin_Pellet extraction1_array1


title: Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin extraction1_array1


title: Fly_embryos_4-6_hr_150_mM_Salt_Extracted_Chromatin extraction1_array1


title: Fly_wing_disc_150_mM_Salt_Extracted_Chromatin extraction2_array1


title: Fly_embryos_1-3_hr_600_mM_Salt_Extracted_Chromatin_Pellet extraction2_array1


title: Fly_embryos_4-6_hr_150_mM_Salt_Extracted_Chromatin extraction2_array1


title: Fly_embryos_1-3_hr_600_mM_Salt_Extracted_Chromatin_Pellet extraction1_array1


title: Fly_embryos_1-3_hr_600_mM_Salt_Extracted_Chromatin extraction2_array1


title: Fly_embryos_1-3_hr_600_mM_Salt_Extracted_Chromatin extraction1_array1


title: Fly_embryos_1-3_hr_150_mM_Salt_Extracted_Chromatin extraction3_array1


title: embryo_AVE_neurons_tiling_array extraction2_array1

hyb_protocol: Array hybridization and processing was performed at the Vanderbilt Shared Microarray Resource (VMSR) http://array.mc.vanderbilt.edu/. Briefly, targets in Hyb cocktail were received in the VMSR for hybridization services. Affymetrix targets in hyb cocktail were heat denatured at 99C for 5', and then held at 45C for at least 5 minutes. Targets were loaded on the Affymetrix Tiling arrays and the arrays were hybridized for 16 h at 45C in a rotisserie oven. After hybridization, arrays were washed using the Affymetrix fluidics station and the Affymetrix HWS kit (cat#900720), which provides pre-made stains (SAPE and antibody) as well as final holding buffer, including wash buffers A and B.  All steps were completed according to the Affymetrix technical manual. Washed arrays were scanned on an Affymetrix GeneChip Scanner 3000.  Cel files were posted to the investigator.

data_processing: Tiling_Array_Signal_Extraction protocol. Mismatch (MM) probe values are subtracted from their corresponding perfect match (PM) probes.  Processed data are obtained using following parameters: BPMap is BPmap:GPL5634:RW:1&oldid=22907

label: Biotin

organism: Caenorhabditis elegans

label_protocol: The NuGEN WT Pico RNA amplification kit was used to generate amplified single stranded cDNA from RNA samples. Starting material is 10 ng of RNA for mRNA tagging experiments and 1-5 ng of RNA for embryonic cells isolated by FACS.  The NuGEN WT-Ovation Exon Module was used to synthesize double stranded cDNA from the amplified single stranded cDNA template.   This was followed by fragmentation and labeling with the NuGEN FL-Ovation cDNA Biotin Module.

growth_protocol:
Animals were synchronized by treating a mixed stage hermaphrodite population with bleach to collect embryos.   The embryos surviving bleach treatment were incubated without food, causing the larvae to arrest at the L1 stage upon hatching.  Starved L1 larvae were plated in the presence of food and raised at 20 degrees Celsius (or indicated temperature) to desired stage.
For embryonic assays, embryonic cells were obtained using methods previously described [Christensen et al, 2002). Briefly, embryos were isolated from gravid adults following lysis in a hypochlorite solution. Intact embryos were separated from debris by flotation on 30% sucrose. For later stages, the embryos were incubated without food, causing the larvae to arrest at the L1 stage upon hatching. Starved L1 larvae were plated on standard NGM plates in the presence of food (OP50) and raised at 20 degrees Celsius. Staging was determined by examining a subset of animals under Nomarski optics at intervals for postdeirid, vulval and germline development. Animals were collected at the mid-L2, late L3-mid L4 and young adult (pre-gravid) stages and washed in M9 buffer. mid-L2 worms were collected when postdeirid divisions complete. L3/L4 animals were collected when a majority of animals diplayed a bilaterally symmetrical "christmas tree" vulval anatomy (See view at 40 hr, Fig 18, Sulston and Horvitz, Dev. Biol. 56, 110-156, 1977) Young Adult  were collected when vulvae fully formed and oocytes present in gonad, but no embryos. The worms were centrifuged on a sucrose cushion to remove debris and recovered in several washes of M9 buffer.
Embryonic cells were obtained using methods previously described [Christensen et al, 2002). Briefly, embryos were isolated from gravid adults following lysis in a hypochlorite solution. Intact embryos were separated from debris by flotation on 30% sucrose. Eggshells were removed by incubation in 0.5 ml chitinase (0.5 U/ml in egg buffer) for 45 minutes. Following resuspension in L-15 medium supplemented with 10% FBS (L15-10) and antibiotics, the embryos were dissociated by passage through a 5?m syringe filter (Durapore). Cells were plated on poly-L-lysine (0.01%, Sigma) coated single-well chambered coverglasses (Nalgene Nunc International) at a density of ~10 million cells/ml and maintained in L15-10 media. Cells were incubated at 25°C in a humidified chamber. Wildtype (N2) cells were isolated and treated similarly.FACSSorting experiments were performed on a FACStar Plus flow cytometer equipped with a 488 nm argon laser or on a FACS Aria (488nm, 633 nm lasers) (Becton Dickinson, San Jose, CA). Emission filters were 530 ± 30 nm for GFP fluorescence and 585 ± 22 nm for PI fluorescence. The machine was flushed with egg buffer [6] prior to sorting to enhance viability. 2 um fluorescent beads were used to calibrate light scattering parameters for the relatively small size of C. elegans embryonic cells. Cells were sorted at a rate of 4000-5000 cells per second through a 70 um nozzle. Immediately prior to sorting, supernatant from the 24 hour cultures was removed and discarded. 1 ml of egg buffer was added to the chamber coverglass. Cells are loosely adherent to poly-L-lysine and can be easily dislodged with gentle pipetting. 3 ml of egg buffer + cells were drawn into a 3 cc syringe and the suspension filtered with a 5 ?m Durapore  syringe filter. Propidium Iodide (PI) was added to the cell suspension at a final concentration of 5 ug/ml prior to sorting. Autofluorescence levels were established by flow cytometry of cells isolated from wildtype (i.e. non-GFP) embryos (See Fig 2A). Next, wildtype cells stained with PI were used to define the sorting gate for damaged cells. GFP+ cells containing no PI were sorted to establish the intensity range of GFP fluorescence. Finally, unc-4::GFP cells stained with PI were gated (Fig 2B) using the parameters established above. The sorting gate for size and granularity (Fig 2C) was empirically adjusted to exclude cell clumps and debris and to achieve ~90% enrichment for GFP-labeled cells. unc-4::GFP cells were collected in a 15 ml conical tube containing 1 ml of L15-10 media. Cells were pelleted using low-speed cenrifugation (300 × g) and either plated on peanut lectincoated slides for visualization [6] or used for RNA isolation (see below). Reference cells were obtained from 1 day old cultures of embryonic blastomeres isolated from the non-GFP wildtype strain (N2). In this case, all viable cells (i.e. non-PI stained) were collected by FACS for RNA isolation.(from Fox et al.,2005)

extract_protocol: Add cells lysate/Trizol (from FACS) to Phase Lock Gel Heavy tubes, extract with phenol/chloroform and precipitate RNA with isopropanol. Wash pellet with 75% ethanol and dissolve pellet in DEPC dwater for purification and concentration with ZYMO DNA-free RNA kit(Detailed protocol: MAPCeL_RNA_isolation.doc)

value: NC1750 (engineered, target gene opt-3 tagged by GFP)

value: embryo-AVE

value: Mixed stage of embryos 20dC

value: KM173 (opt-3::GFP[pRF4]); hdIs32 (glr-1::DsRed2)

value: Hermaphrodite


title: Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin_Pellet extraction2_array1


title: embryo_0hr_reference_tiling_array extraction3_array1

scan_protocol: Washed arrays were scanned on an Affymetrix GeneChip Scanner 3000.  Cel files were posted to the investigator.

value: reference (early embryo)

value: wild type


title: embryo_AVE_neurons_tiling_array extraction3_array1


title: embryo_PVC_neurons_tiling_array extraction2_array1

value: NC2015 (engineered, target gene glr-1 tagged by dsRed)

value: PVC neurons (embryonic)


title: embryo_0hr_reference_tiling_array extraction1_array1


title: embryo_PVC_neurons_tiling_array extraction1_array1


title: embryo_BAG_neurons_tiling_array extraction3_array1

status: Public on Aug 24 2010

scan_protocol: Array hybridization and processing was performed at the Vanderbilt Shared Microarray Resource (VMSR) http://array.mc.vanderbilt.edu/. Briefly, targets in Hyb cocktail were received in the VMSR for hybridization services. Affymetrix targets in hyb cocktail were heat denatured at 99C for 5', and then held at 45C for at least 5 minutes. Targets were loaded on the Affymetrix Tiling arrays and the arrays were hybridized for 16 h at 45C in a rotisserie oven. After hybridization, arrays were washed using the Affymetrix fluidics station and the Affymetrix HWS kit (cat#900720), which provides pre-made stains (SAPE and antibody) as well as final holding buffer, including wash buffers A and B.  All steps were completed according to the Affymetrix technical manual. Washed arrays were scanned on an Affymetrix GeneChip Scanner 3000.  Cel files were posted to the investigator.

value: MT17370 (engineered, target gene gcy-33 tagged by GFP)

value: BAG neurons (embryonic)

tag: sex


title: embryo_pharyngeal_muscle_tiling_array extraction3_array1

value: NC1293 (engineered, target gene myo-2 tagged by GFP)

value: pharyngeal muscle


title: embryo_0hr_reference_tiling_array extraction2_array1


title: embryo_BAG_neurons_tiling_array extraction2_array1


title: embryo_pharyngeal_muscle_tiling_array extraction1_array1


title: embryo_PVC_neurons_tiling_array extraction3_array1


status: Public on Aug 10 2010

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

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

input: GSM575517_pirrota_499_S14_Input18.320.CEL

source_name: Cell Line S2-DRSC;Antibody mod2.2-VC (target is MOD(MDG4)67.2) extraction3_array1 channel_1

value: late embryonic stage


title: SOH11C3_26_vs_SOH11C5_25_247384 extraction1_array1

data_processing: NimbleGen Scaling protocol. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS190.

growth_protocol: Large cultures of transgenic worm strains were grown on enriched plates and embryos were isolated from gravid adult hermaphrodites by treatment with alkaline hypochlorite.  The eggshells were removed by chitinase digestion, yielding embryonic blastomeres.

extract_protocol: C. elegans embryos are lysed in Trizol, extracted with CHCl3, and total cellular RNA is precipitated with isopropanol. Total RNA was used as a template to synthesize oligo(dT)-primed first-strand cDNA.

value: N2(official name :N2 genotype :wild type genotype :DR subclone of DB original (Tc1 pattern I) )

value: Young Adult


title: embryo_pharyngeal_muscle_tiling_array extraction2_array1


title: embryo_BAG_neurons_tiling_array 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: GSM575515_pirrota_873_S15_Input-18cycles.644.CEL

source_name: Cell Line S2-DRSC;Antibody mod2.2-VC (target is MOD(MDG4)67.2) extraction1_array1 channel_1

value: embryo-derived cell-line

value: Male


title: Fly_embryos_1-3_hr_150_mM_Salt_Extracted_Chromatin extraction1_array1

value: B3(made_by :Paul Talbert description :A strain that expresses a conditionally expressed biotin-tagged histone H3.3.  The strain also contains the E. coli BirA gene that is expressed under the control of a GAL4 UAS. tags :Transposon transgene :Histone H3.3::biotin-recognition-peptide outcross :New Line genotype :y w; A5C-GAL4/cyO; B3 official name :B3 )

value: y w; A5C-GAL4/cyO; B3


title: Fly_embryos_1-3_hr_150_mM_Salt_Extracted_Chromatin extraction2_array1


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: GSM575511_pirrota_243_S12_Input_20_cycles.86.CEL

source_name: Cell Line S2-DRSC;Antibody Su(var)3-9 (target is Su(var)3-9) 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: GSM575509_pirrota_506_A12_Input_20cyc.328.CEL

source_name: Cell Line S2-DRSC;Antibody Su(var)3-9 (target is Su(var)3-9) extraction1_array1 channel_1


title: embryo_AVE_neurons_tiling_array extraction1_array1

value: NC1750 (engineered, target gene opt-3 tagged by GFP)

value: embryo-AVE

value: Mixed stage of embryos 20dC

value: KM173 (opt-3::GFP[pRF4]); hdIs32 (glr-1::DsRed2)


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

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: GSM575507_pirrota_683_A11_Input.452.CEL

source_name: Cell Line S2-DRSC;Antibody Su(var)3-7-Q3448 (target is Su(var)3-7) 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: GSM575513_pirrota_584_A14_Input_20cycles.373.CEL

source_name: Cell Line S2-DRSC;Antibody Su(var)3-9 (target is Su(var)3-9) extraction5_array1 channel_1


title: SOH10C3_24_vs_SOH10C5_23_247382-2 extraction2_array1

value: wild type

value: Hermaphrodite


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: GSM575499_pirrota_600_Kc1_Input_20cycles.389.CEL

source_name: Cell Line Kc167;Antibody HP1c (MO 462) (target is HP1c) 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: GSM575497_pirrota_647_Kc2_Input_20cycles.424.CEL

source_name: Cell Line Kc167;Antibody HP1c (MO 462) (target is HP1c) 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: GSM575501_pirrota_646_B3_Input2_20cycles.423.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody Su(var)3-7-Q3448 (target is Su(var)3-7) extraction1_array1 channel_1

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: GSM575503_pirrota_602_B5_Input_20cycles.391.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody Su(var)3-7-Q3448 (target is Su(var)3-7) extraction3_array1 channel_1


description: channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1a wa184; target name: HP1a; host: Rabbit; antigen: entire HP1a protein; clonal: Unknown; purified: Affinity; 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: GSM575489_pirrota_584_A14_Input_20cycles.373.CEL

source_name: Cell Line S2-DRSC;Antibody HP1a wa184 (target is HP1a) extraction1_array1 channel_1

value: late embryonic stage


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: GSM575491_pirrota_243_S12_Input_20_cycles.86.CEL

source_name: Cell Line S2-DRSC;Antibody HP1a wa184 (target is HP1a) extraction3_array1 channel_1

value: embryo-derived cell-line


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: GSM575484_pirrota_825_CL8-1_InputDNA_20cyc.596.CEL

source_name: Cell Line CME-W1-Cl.8+;Antibody HP1 wa191 (target is HP1a) extraction3_array1 channel_1

value: dorsal mesothoracic disc

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: GSM575493_pirrota_826_CL8-2_Input_DNA_20cyc.597.CEL

source_name: Cell Line CME-W1-Cl.8+;Antibody HP1c (MO 462) (target is HP1c) extraction1_array1 channel_1


source_name: Cell Line CME-W1-Cl.8+;Antibody HP1 wa191 (target is HP1a) 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: GSM575487_pirrota_826_CL8-2_Input_DNA_20cyc.597.CEL

source_name: Cell Line CME-W1-Cl.8+;Antibody HP1 wa191 (target is HP1a) extraction4_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: GSM575482_pirrota_425_B2_Input.251.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody HP1 wa191 (target is HP1a) extraction5_array1 channel_1


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

input: GSM575495_pirrota_825_CL8-1_InputDNA_20cyc.596.CEL

source_name: Cell Line CME-W1-Cl.8+;Antibody HP1c (MO 462) (target is HP1c) 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: GSM575478_pirrota_646_B3_Input2_20cycles.423.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody HP1 wa191 (target is HP1a) extraction1_array1 channel_1


title: HP1_wa191.2-4_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: GSM575476_pirrota_879_E_early_1_Input.650.CEL

value: Oregon-R

value: Embryo 2-4hr OR


title: HP1_wa191.2-4_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: GSM575474_pirrota_935_Eearly2_Input_20cyc.690.CEL


title: expt.478 extraction3_array1

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: GSM575472_pirrota_724_OR_Head_prep4_Input_14cyc.488.CEL

source_name: expt.478 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


title: expt.477 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: GSM575470_pirrota_723_OR_Head_Prep3_Input_14cyc.487.CEL

source_name: expt.477 extraction1_array1 channel_1


title: H3K9me3_(new_lot).14-16_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: GSM575465_pirrota_721_E10_Input_14cyc.487.CEL

value: Embryo 14-16hr OR


title: H3K9me3_(new_lot).14-16_hr_OR_embryo extraction3_array1


title: H3K9me3_(new_lot).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: GSM575463_pirrota_722_E11_Input_14cyc.486.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: GSM575505_pirrota_684_A15_Input.453.CEL

source_name: Cell Line S2-DRSC;Antibody Su(var)3-7-Q3448 (target is Su(var)3-7) 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: GSM575480_pirrota_424_B1_Input.250.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody HP1 wa191 (target is HP1a) extraction3_array1 channel_1


title: H3K9me2-Ab2_(new_lot).2-4_hr_OR_embryo extraction3_array1

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

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: GSM575457_pirrota_454_E4_Input.276.CEL


title: H3K9me2-Ab2_(new_lot).2-4_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: GSM575459_pirrota_262_E2_Input.107.CEL


title: H3K9me2-Ab2_(new_lot).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: GSM575451_pirrota_263_E3_Input.108.CEL


title: H3K9me2-Ab2_(new_lot).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: GSM575449_pirrota_835_E_late1_Input_DNA_14cyc.606.CEL


title: H3K9me2-Ab2_(new_lot).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: GSM575453_pirrota_880_E_late_2_Input.651.CEL


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: GSM575447_pirrota_684_A15_Input.453.CEL

source_name: Cell Line S2-DRSC;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) extraction5_array1 channel_1


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

input: GSM575445_pirrota_584_A14_Input_20cycles.373.CEL

source_name: Cell Line S2-DRSC;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) 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: GSM575443_pirrota_967_A18_Input_20cyc.728.CEL

source_name: Cell Line S2-DRSC;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) 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: GSM575438_pirrota_602_B5_Input_20cycles.391.CEL

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) extraction1_array1 channel_1


source_name: Cell Line ML-DmBG3-c2;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) extraction5_array1 channel_1