title: mix2 rep2 [technical replicate]

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

description: fmol of spiked oligos per 1mg of total RNA

hyb_protocol: Labeled RNA was hybridized with a 8X15 Human miRNA array rel 14 v2 (design number 29297) at 55°C and 20 rpm for 20 hours, and then washed according to the manufacturer’s instructions.

scan_protocol: Scanning was performed on an Agilent Scanner using 5uM resolution.

data_processing:
gProcessedSignals processed without batch correction.
The signal intensity was set to the maximum of either "TotalGeneSignal" or the "TotalGeneError" in the GeneView file. Batch correction was performed using the Partek software defaults. The signal intensities were log2 transformed and scaled by quantile normalization.

source_name: placenta

label_protocol: 100 ng RNA was labeled using  miRNA complete labeling and hyb kit (Agilent #5190-0456) with Cy3-pCp following diphosphorylation. Desalting done using micro-bio spin columns.

growth_protocol: RNA Purchased (see extract protocol).

extract_protocol: Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005.

treatment_protocol: Oligos representing mature, modified and precursor miRNA were artificially introduced to native RNA

tag: type of replicate

value: technical replicate of mix2 rep2

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p

tag: precursor spike-in hsa-mir-338-3p

tag: precursor spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-429


title: T-ETV1_Luminal cells-B

status: Public on Mar 01 2013

type: RNA

city: Boston

first: Esther

last: Baena

state: MA

address: 300 Longwood Avenue

department: Hematology/Oncology

country: USA

institute: Childrens Hospital Boston

description: Prostate cells FACS-sorted, GFP+ luminal cells (Lin-Sca1-CD49f+) population

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed by dchip and arrays were normalized against the baseline array that has the median brightness.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Primary prostate cells

label_protocol: Biotinulated cRNA were prepared according to the NuGEN protocol for Affumetrix arrays.

extract_protocol: Trizol extraction of total RNA was performed following the manufacturer's protocol, followed by NuGEN V2cDNA amplification

treatment_protocol: Prostate single cells were isolated from the prostate, and stained for FACS sorting. Sorted cells were resuspended in Trizol for RNA extraction.

tag: cell type

value: prostate luminal cells

tag: genotype/variation


title: 25DAF rep2

city: Saskatoon

first: Adrian

last: Cutler

address: 110 Gymnasium Place

country: Canada

institute: National Research Council of Canada

description: Biological replicate 2 of 6, 25DAF seeds

hyb_protocol: 5 µg fragmented Cy5-aRNAs were mixed with hybridization buffer (6xSSPE, 0.05% Tween-20, 20 mM EDTA, 25% deionized formamide, 0.1 mg/mL sheared salmon sperm DNA and 0.04% SDS) and hybridized to the Combimatrix Brassica 90K arrays at 45°C overnight in the dark. After hybridization, stringent washes were performed according to the manufacturer’s instructions, and the slides were immediately coated with an imaging solution (CombiMatrix) prior to scanning.

scan_protocol: Scanning on a GenePix 4000B scanner (Axon Instruments, CA, USA) using  PMT from 400-500, 5µm resolution and 100% laser power.

data_processing: The image analysis was performed using GenePix Pro version 6.0 software (Axon Instruments, CA, USA). After automatic alignment, feature indicators were manually moved, resized and fine-tuned. The local background corrected spot fluorescence intensities for the Cy5 channel were saved as GPR files.    The GPR files were loaded in GeneSpring GX 11.0 (Agilent Technologies Inc. and Strand Life Sciences Pvt. Ltd) with percentile shift normalization and baseline to median of all samples.  Signal intensity cut-off was set to 200. One way ANOVA analysis was carried out with the asymptotic p-value computation method.  Multiple testing correction method is Benjamini-Hochberg FDR. Corrected p-value (Benjamini-Hochberg FDR) cut-off set to 0.05 and fold change is more than 2.

organism: Brassica napus

source_name: Developing seeds, 25 days after flowering

label_protocol: RNA amplification was carried out using the MessageAmp aRNA kit (Ambion, Catalog# 1750) according to the supplied protocol. During the second round of in vitro transcription, aminoallyl-UTP was incorporated into the newly synthesized aRNA.Dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.

growth_protocol: Plants of Brassica napus L. cv.DH12075 were grown in 6-in pots containing soil mixture with a slow-release fertilizer 14-14-14 in a growth cabinet with a 16h/8h day/night photoperiod, light intensity of 250μmol m−2 s−1, and day/night temperatures of 22°C/18°C. Individual flowers were tagged with colored tapes on the day of flower opening.

extract_protocol: Total RNA was extracted using RNA aqueous kit (Ambion)

treatment_protocol: Seeds of 10, 15, 20, 25, 30, 35, 40 and 45  days after flowering (DAF) were dissected from siliques and immediately put in RNAlater (Ambion) and kept in 4 degree for a few days and stored in -20 degree

tag: tissue

value: Developing seeds

tag: days after flowering


title: 25DAF rep3

description: Biological replicate 3 of 6, 25DAF seeds


title: mix3 rep2 [technical replicate]

organism: Homo sapiens

tag: type of replicate

value: technical replicate of mix3 rep2


title: WT-Luminal cells-A

description: Prostate cells FACS-sorted, luminal cells (Lin-Sca1-CD49f+) population

value: wild type


title: 30DAF rep6

description: Biological replicate 6 of 6, 30DAF seeds

source_name: Developing seeds, 30 days after flowering


title: 25DAF rep5

description: Biological replicate 5 of 6, 25DAF seeds


title: 35DAF rep1

description: Biological replicate 1 of 6, 35DAF seeds

source_name: Developing seeds, 35 days after flowering


title: 20DAF rep6

description: Biological replicate 6 of 6, 20DAF seeds

source_name: Developing seeds, 20 days after flowering


title: mix2 rep1 [technical replicate]

value: technical replicate of mix2 rep1

tag: spike-in hsa-mir-147


title: CAY 1511 tdh3-wor1 3

city: Providence

first: Richard

middle: J

last: Bennett

state: RI

address: 171 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

description: Biological replicate 3 of 4, CAY1511 tdh3-wor1 cells

hyb_protocol: 300ng of Cy3 and Cy5 samples were mixed together in a total volume of 25uL ddH2O, heated to 95C for 3 min, and cooled to room temperature. 25uL GE hybridization buffer was added to samples, mixed, and spun down. 40uL of hybridization sample was loaded onto slide, slide sealed, and incubated at 65C rotating at 10rpm for ~17 hours. Slide washed using Agilent Wash Buffers and Drying and Stabilization Solution.

scan_protocol: Scanned using Axon 4000b scanner, pixel size = 5 um, Lines to average = 2, Focus position = 15. Scanned for count ratio = 1.

data_processing: Data normalized using Goulphar. Mnorm log2 values were averaged for each spot.

organism: Candida tropicalis

source_name: C. tropicalis wor1 overexpressing cells

label_protocol: cDNA synthesized with Oligo(dT)20 + pdN9, with aa-dUTP/dNTPs using Superscript RT III. RNA hydrolyzed with 0.2M NaOH/0.03M EDTA and neutralized with 0.3M HCl. Samples cleaned using Zymo Columns. Sample dye-coupled in 0.1 M Na Bicarbonate, pH 9.0 and adding 1.25uL Cy3 (reference) or Cy5 (experimental). Samples were incubated at room temperature for 1 hour in darkness and cleaned up using Zymo columns.

growth_protocol: Cells grown overnight in liquid Spider media, diluted to 0.2 OD600, and grown to 1.0 - 1.2. Cells spun down and flash frozen in an ethanol/dry ice bath.

extract_protocol: RNA extracted using Ribopure Yeast Kit.

tag: strain

source_name: Universal reference

value: Mixed white, opaque, Δ/Δwor1, tdh3-wor1 reference


title: CAY 1511 tdh3-wor1 4

description: Biological replicate 4 of 4, CAY1511 tdh3-wor1 cells


title: Fast_Adult_Muscle_rep2

city: Rennes

first: Pierre-Yves

last: Rescan

address: Campus de Beaulieu

department: Phase

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing

scan_protocol: Scanning with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (channels: Green, resolution: 3µm, TIFF: 20 bit).

data_processing: Data were then obtained with the Agilent Feature Extraction software (v10.7.1.1) according to the appropriate GE protocol (GE1_107_Sep09). Before analysis, saturated spot, non-uniform spots were flagged using the Agilent GeneSpring GX software (v.10.0.2) and data were subsequently normalized using the quantile method.

organism: Oncorhynchus mykiss

label_protocol: GE microarray was performed using One-Color Microarray-Based Gene Expression Analysis kit (Agilent v6.5) according to the manufacturer procedure. Briefly, for each sample, 100 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

extract_protocol: Total RNA of laser captured material was isolated using the PicoPureRNA isolation kit (Arcturus) and had an RNA integrity number of 7.5 (Agilent). Total RNA of muscle was isolated using Trizol reagent

treatment_protocol: Ten-micron- thick transverse frozen sections were cut using a cryostat  mounted onto uncoated glass slides, fixed at −20 °C in 70% ethanol for 1 min, washed briefly in 70% ethanol and sequentially dehydrated in 100% ethanol and xylene. The sections were then microdissected using a Veritas Laser Capture Microdissection system (LCM) (Arcturus). The infrared laser was used with the following parameters: spot diameter, 20 μm; pulse duration, 3500 ms; power, 90 mW. All areas were selected and collected within 30 min of the preparation of the slide. Laser-captured material from 20-30 sections was pooled for each RNA extraction.).

value: Muscle

tag: Stage

value: Fast Adult Muscle 500g

tag: sampling

value: Transverse slice of fast Muscle beneath dorsal fin


title: 25DAF rep4

description: Biological replicate 4 of 6, 25DAF seeds


title: Laser_Capture_Peripheral Domain_rep2

source_name: Laser_Capture_Peripheral Domain_rep2

value: embryonic myotome

value: 19 days post fertilization

value: Laser Capture microdissection peripheral domain


title: Laser_Capture_Peripheral Domain_rep3

source_name: Laser_Capture_Peripheral Domain_rep3


title: Laser_Capture_Deep Domain_rep3

source_name: Laser_Capture_Deep Domain_rep3

value: Laser Capture microdissection deep domain


title: Laser_Capture_Deep Domain_rep1

source_name: Laser_Capture_Deep Domain_rep1


title: 30DAF rep1

description: Biological replicate 1 of 6, 30DAF seeds


title: 20DAF rep5

description: Biological replicate 5 of 6, 20DAF seeds


title: CAY 1511 Δ/Δwor1 3

description: Biological replicate 3 of 4, CAY1511 Δ/Δwor1 cells

source_name: C. tropicalis wor1 mutant cells


title: Laser_Capture_Peripheral Domain_rep1

source_name: Laser_Capture_Peripheral Domain_rep1


title: mix7 rep2

value: biological replicate 2

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383


title: 20DAF rep3

description: Biological replicate 3 of 6, 20DAF seeds


title: mix5 rep2

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p


title: mix4 rep2

tag: precursor spike-in hsa-mir-338-3p

tag: precursor spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-429


title: CAY 1511 Δ/Δwor1 4

description: Biological replicate 4 of 4, CAY1511 Δ/Δwor1 cells


title: mix6 rep2

description: fmol of spiked oligos per 1mg of total RNA


title: 20DAF rep4

description: Biological replicate 4 of 6, 20DAF seeds

tag: tissue

tag: days after flowering


title: gDNA_Strain 11a5_rep3

type: genomic

city: Berkeley

first: Patrick

last: Lee

state: CA

address: 209 O'Brien Hall

department: Civil and Environmental Engineering

institute: University of California, Berkeley

description: Pure culture

hyb_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

data_processing: Data analysis was performed using Affymetrix GeneChip software and the MAS5 algorithm. Each microarray was normalized by scaling the signal intensities of the positive control spike-mix to a target signal intensity of 2500 to allow comparison between microarrays.

label: Biotin

molecule: genomic DNA

organism: Dehalococcoides

source_name: Dehalococcoides sp. 11a5

label_protocol: One µg of gDNA was prepared for each microarray according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

growth_protocol: Multiple 100 mL cultures were grown in parallel with chlorinated ethene, hydrogen and acetate in order to obtain enough biomass.

extract_protocol: gDNA was extracted using either the Qiagen (Valencia, CA) DNeasy Blood & Tissue kit according to the manufacturers’ recommendations.


title: 15DAF rep6

description: Biological replicate 6 of 6, 15DAF seeds

source_name: Developing seeds, 15 days after flowering


title: mix2 rep2

tag: type of replicate

tag: spike-in hsa-mir-147


title: CAY 1511 opaque 3

description: Biological replicate 3 of 4, CAY1511 opaque cells

source_name: C. tropicalis opaque cells

tag: strain

value: CAY1511 opaque (CAY4048)


title: CAY 1511 white 4

description: Biological replicate 4 of 4, CAY1511 white cells

source_name: C. tropicalis white cells

value: CAY1511 white (CAY4413)


title: 20DAF rep1

description: Biological replicate 1 of 6, 20DAF seeds


title: mix3 rep2

source_name: placenta


title: gDNA_Strain 11a5_rep2

description: Pure culture

scan_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).


title: CAY 1511 white 3

description: Biological replicate 3 of 4, CAY1511 white cells


title: CAY 1511 tdh3-wor1 2

description: Biological replicate 2 of 4, CAY1511 tdh3-wor1 cells


title: 15DAF rep5

description: Biological replicate 5 of 6, 15DAF seeds


title: gDNA_Strain 11a5_rep1

description: Pure culture


title: gDNA_Strain 11a_rep3

description: Pure culture

source_name: Dehalococcoides sp. 11a


title: 15DAF rep4

description: Biological replicate 4 of 6, 15DAF seeds


title: mix7 rep1

value: biological replicate 1


title: gDNA_Strain 11a_rep2

description: Pure culture


title: mix1 rep2


title: mix6 rep1


title: WT-Luminal cells-B

description: Prostate cells FACS-sorted, luminal cells (Lin-Sca1-CD49f+) population

source_name: Primary prostate cells

tag: cell type

value: prostate luminal cells

tag: genotype/variation


title: CAY 1511 tdh3-wor1 1

description: Biological replicate 1 of 4, CAY1511 tdh3-wor1 cells


title: 20DAF rep2

description: Biological replicate 2 of 6, 20DAF seeds

value: Developing seeds


title: mix5 rep1

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p


title: CAY 1511 Δ/Δwor1 2

description: Biological replicate 2 of 4, CAY1511 Δ/Δwor1 cells


title: CAY 1511 Δ/Δwor1 1

description: Biological replicate 1 of 4, CAY1511 Δ/Δwor1 cells


title: CAY 1511 white 2

description: Biological replicate 2 of 4, CAY1511 white cells


title: 15DAF rep3

description: Biological replicate 3 of 6, 15DAF seeds


title: CAY 1511 opaque 4

description: Biological replicate 4 of 4, CAY1511 opaque cells


title: CAY 1511 opaque 1

description: Biological replicate 1 of 4, CAY1511 opaque cells


title: CAY 1511 white 1

description: Biological replicate 1 of 4, CAY1511 white cells


title: mix4 rep1

description: fmol of spiked oligos per 1mg of total RNA

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383


title: mix1 rep1

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147


title: gDNA_Strain 11a_rep1

description: Pure culture


title: 10DAF rep6

description: Biological replicate 6 of 6, 10DAF seeds

source_name: Developing seeds, 10 days after flowering


title: mix3 rep1

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p


title: 15DAF rep1

description: Biological replicate 1 of 6, 15DAF seeds


title: 25DAF rep1

description: Biological replicate 1 of 6, 25DAF seeds

source_name: Developing seeds, 25 days after flowering


title: 15DAF rep2

description: Biological replicate 2 of 6, 15DAF seeds


title: mix2 rep1

tag: precursor spike-in hsa-mir-338-3p

tag: precursor spike-in hsa-mir-383


title: 10DAF rep4

description: Biological replicate 4 of 6, 10DAF seeds

tag: tissue


title: 10DAF rep2

description: Biological replicate 2 of 6, 10DAF seeds

tag: days after flowering


title: 10DAF rep3

description: Biological replicate 3 of 6, 10DAF seeds


title: 10DAF rep1

description: Biological replicate 1 of 6, 10DAF seeds


title: RNA PolII (abcam) Nuclear L3 POF D.melanogaster ChIP Rep2

status: Public on Feb 22 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

institute: Ontario Institute for Cancer Research

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

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

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

organism: Drosophila melanogaster

source_name: RNA PolII (abcam) Nuc. L3 POF ChIP expt.1354 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: POF mutant

tag: developmental stage

value: 3rd Instar Larvae

tag: genotype

tag: transgene

value: deletion


title: H3K9me3 abcam Nuclear L3 POF D.melanogaster ChIP Rep2

source_name: H3K9me3 abcam Nuc. L3 POF ChIP expt.1350 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.

tag: strain


title: HP1 wa191 Nuclear L3 HP1a D.melanogaster ChIP Rep2

source_name: HP1 wa191 Nuc. L3 HP1a ChIP expt.1429 channel_1

value: HP1a mutant


title: HP1 wa191 Nuclear L3 HP1a D.melanogaster Input Rep1

description: Served as Input for: 1428.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 HP1a Input expt.1426 channel_1


title: RNA PolII (abcam) Nuclear L3 POF D.melanogaster Input Rep2

description: Served as Input for: 1354.Mvalues.bedgraph

source_name: RNA PolII (abcam) Nuc. L3 POF Input expt.1338 channel_1


title: RNA PolII (abcam) Nuclear L3 POF D.melanogaster ChIP Rep1

source_name: RNA PolII (abcam) Nuc. L3 POF ChIP expt.1353 channel_1


title: RNA PolII (abcam) Nuclear L3 POF D.melanogaster Input Rep1

description: Served as Input for: 1353.Mvalues.bedgraph

source_name: RNA PolII (abcam) Nuc. L3 POF Input expt.1337 channel_1


title: 10DAF rep5

description: Biological replicate 5 of 6, 10DAF seeds


title: H3K9me3 abcam Nuclear L3 POF D.melanogaster ChIP Rep1

source_name: H3K9me3 abcam Nuc. L3 POF ChIP expt.1349 channel_1


title: H3K9me3 abcam Nuclear L3 POF D.melanogaster Input Rep2

description: Served as Input for: 1350.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 POF Input expt.1336 channel_1


title: HP1 wa191 Nuclear L3 HP1a D.melanogaster Input Rep2

description: Served as Input for: 1429.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 HP1a Input expt.1427 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 POF D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 POF ChIP expt.1348 channel_1


title: HP1 wa191 Nuclear L3 HP1a D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L3 HP1a ChIP expt.1428 channel_1


title: H3K9me3 abcam Nuclear L3 POF D.melanogaster Input Rep1

description: Served as Input for: 1349.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 POF Input expt.1335 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 POF D.melanogaster Input Rep1

description: Served as Input for: 1347.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 POF Input expt.1335 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 POF D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 POF ChIP expt.1347 channel_1


title: H3K9me2-Ab2 (new lot 3) Nuclear L3 piwi2 D.melanogaster Input Rep1

description: Served as Input for: 2173.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot 3) Nuc. L3 piwi2 Input expt.1979 channel_1

value: PIWI2 mutant


title: H3K9me2-Ab2 (new lot 3) Nuclear L3 piwi2 D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot 3) Nuc. L3 piwi2 ChIP expt.2173 channel_1


title: H3K79Me3 ML-DmBG3-c2 D.melanogaster ChIP Rep3

source_name: H3K79Me3 BG3 ChIP expt.2050 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: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

tag: Sex

value: Unknown


title: H3K9me2-Ab2 (new lot 3) Nuclear L3 piwi2 D.melanogaster Input Rep2

description: Served as Input for: 2174.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot 3) Nuc. L3 piwi2 Input expt.1980 channel_1


title: H3K79Me3 ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: H3K79Me3 BG3 ChIP expt.223 channel_1


title: H3K9me2-Ab2 (new lot 3) Nuclear L3 piwi2 D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot 3) Nuc. L3 piwi2 ChIP expt.2174 channel_1


title: H3K79Me3 ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: H3K79Me3 BG3 ChIP expt.214 channel_1


title: H3K79Me3 ML-DmBG3-c2 D.melanogaster Input Rep3

description: Served as Input for: 2050.Mvalues.bedgraph

source_name: H3K79Me3 BG3 Input expt.2041 channel_1


title: H3K79Me3 ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 223.Mvalues.bedgraph

source_name: H3K79Me3 BG3 Input expt.208 channel_1


title: Su(var)3-9-Q2598 Nuclear L3 EGG D.melanogaster ChIP Rep2

source_name: Su(var)3-9-Q2598 Nuc. L3 EGG ChIP expt.1937 channel_1

value: EGG mutant


title: Su(var)3-9-Q2598 Nuclear L3 EGG D.melanogaster ChIP Rep1

source_name: Su(var)3-9-Q2598 Nuc. L3 EGG ChIP expt.1936 channel_1


title: Su(var)3-9-Q2598 Nuclear L3 EGG D.melanogaster Input Rep2

description: Served as Input for: 1937.Mvalues.bedgraph

source_name: Su(var)3-9-Q2598 Nuc. L3 EGG Input expt.1604 channel_1


title: Su(var)3-9-Q2598 Nuclear L3 EGG D.melanogaster Input Rep1

description: Served as Input for: 1936.Mvalues.bedgraph

source_name: Su(var)3-9-Q2598 Nuc. L3 EGG Input expt.1603 channel_1


title: RPD3-Q3451 ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: RPD3-Q3451 BG3 ChIP expt.1136 channel_1


title: RPD3-Q3451 ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: RPD3-Q3451 BG3 ChIP expt.1137 channel_1


title: RPD3-Q3451 ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 1136.Mvalues.bedgraph

source_name: RPD3-Q3451 BG3 Input expt.423 channel_1


title: Rhino-Q3450 S2-DRSC D.melanogaster ChIP Rep3

source_name: Rhino-Q3450 S2 ChIP expt.771 channel_1

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: Rhino-Q3450 S2-DRSC D.melanogaster ChIP Rep2

source_name: Rhino-Q3450 S2 ChIP expt.722 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 POF D.melanogaster Input Rep2

description: Served as Input for: 1348.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 POF Input expt.1336 channel_1


title: Rhino-Q3450 S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 722.Mvalues.bedgraph

source_name: Rhino-Q3450 S2 Input expt.728 channel_1


title: Rhino-Q3450 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 721.Mvalues.bedgraph

source_name: Rhino-Q3450 S2 Input expt.724 channel_1


title: Rhino-Q3450 S2-DRSC D.melanogaster ChIP Rep1

source_name: Rhino-Q3450 S2 ChIP expt.721 channel_1


title: H3K79Me3 ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 214.Mvalues.bedgraph

source_name: H3K79Me3 BG3 Input expt.207 channel_1


title: Rhino-Q3450 S2-DRSC D.melanogaster Input Rep3

description: Served as Input for: 771.Mvalues.bedgraph

source_name: Rhino-Q3450 S2 Input expt.774 channel_1


title: RPD3-Q3451 ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 1137.Mvalues.bedgraph

source_name: RPD3-Q3451 BG3 Input expt.391 channel_1


title: H3K9me1 (Diagenode) S2-DRSC D.melanogaster ChIP Rep2

source_name: H3K9me1 (Diagenode) S2 ChIP expt.367 channel_1


title: H3K9me3 clone 6F12-H4 S2-DRSC D.melanogaster ChIP Rep2

source_name: H3K9me3 clone 6F12-H4 S2 ChIP expt.737 channel_1


title: H3 antibody3 Kc167 D.melanogaster Input Rep1

description: Served as Input for: 948.Mvalues.bedgraph

source_name: H3 antibody3 Kc Input expt.812 channel_1

value: se/e

value: Female


title: HP4 Q4072 ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: HP4 Q4072 BG3 ChIP expt.1678 channel_1


title: H3K9me1 (Diagenode) S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 367.Mvalues.bedgraph

source_name: H3K9me1 (Diagenode) S2 Input expt.372 channel_1


title: H3 antibody3 Kc167 D.melanogaster ChIP Rep1

source_name: H3 antibody3 Kc ChIP expt.948 channel_1


title: H3K9me3 clone 6F12-H4 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 678.Mvalues.bedgraph

source_name: H3K9me3 clone 6F12-H4 S2 Input expt.373 channel_1


title: Blanks (CG10630) S2-DRSC D.melanogaster ChIP Rep2

source_name: Blanks (CG10630) S2 ChIP expt.1926 channel_1


title: H3K9me1 (Diagenode) S2-DRSC D.melanogaster Input Rep3

description: Served as Input for: 677.Mvalues.bedgraph

source_name: H3K9me1 (Diagenode) S2 Input expt.679 channel_1


title: HP4 Q4072 ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: HP4 Q4072 BG3 ChIP expt.1679 channel_1


title: H3 antibody3 Kc167 D.melanogaster ChIP Rep2

source_name: H3 antibody3 Kc ChIP expt.949 channel_1


title: HP4 Q4072 ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 1678.Mvalues.bedgraph

source_name: HP4 Q4072 BG3 Input expt.1542 channel_1


title: H3K9me1 (Diagenode) S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 366.Mvalues.bedgraph

source_name: H3K9me1 (Diagenode) S2 Input expt.85 channel_1


title: H3K9me1 (Diagenode) S2-DRSC D.melanogaster ChIP Rep3

source_name: H3K9me1 (Diagenode) S2 ChIP expt.677 channel_1


title: H3K9me1 (Diagenode) S2-DRSC D.melanogaster ChIP Rep1

source_name: H3K9me1 (Diagenode) S2 ChIP expt.366 channel_1


title: H3 antibody3 Kc167 D.melanogaster Input Rep2

description: Served as Input for: 949.Mvalues.bedgraph

source_name: H3 antibody3 Kc Input expt.813 channel_1


title: H3K9me3 clone 6F12-H4 S2-DRSC D.melanogaster ChIP Rep1

source_name: H3K9me3 clone 6F12-H4 S2 ChIP expt.678 channel_1


title: HP4 Q4072 ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 1679.Mvalues.bedgraph

source_name: HP4 Q4072 BG3 Input expt.1483 channel_1


title: H3K9me3 clone 6F12-H4 S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 737.Mvalues.bedgraph

source_name: H3K9me3 clone 6F12-H4 S2 Input expt.728 channel_1


title: H3K9me1 (Diagenode) S2-DRSC D.melanogaster ChIP Rep4

source_name: H3K9me1 (Diagenode) S2 ChIP expt.683 channel_1


title: H3K9me1 (Diagenode) S2-DRSC D.melanogaster Input Rep4

description: Served as Input for: 683.Mvalues.bedgraph

source_name: H3K9me1 (Diagenode) S2 Input expt.689 channel_1


title: Blanks (CG10630) S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 1925.Mvalues.bedgraph

source_name: Blanks (CG10630) S2 Input expt.1919 channel_1


title: Blanks (CG10630) S2-DRSC D.melanogaster ChIP Rep1

source_name: Blanks (CG10630) S2 ChIP expt.1925 channel_1


title: Blanks (CG10630) S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 1926.Mvalues.bedgraph

source_name: Blanks (CG10630) S2 Input expt.1920 channel_1


title: HP1b Q4113 Kc167 D.melanogaster Input Rep2

description: Served as Input for: 2115.Mvalues.bedgraph

source_name: HP1b Q4113 Kc Input expt.1704 channel_1


title: HP1b Q4113 Kc167 D.melanogaster Input Rep1

description: Served as Input for: 2114.Mvalues.bedgraph

source_name: HP1b Q4113 Kc Input expt.1703 channel_1


title: HP1b Q4113 Kc167 D.melanogaster ChIP Rep2

source_name: HP1b Q4113 Kc ChIP expt.2115 channel_1


title: CAY 1511 opaque 2

description: Biological replicate 2 of 4, CAY1511 opaque cells

source_name: C. tropicalis opaque cells

value: CAY1511 opaque (CAY4048)

source_name: Universal reference

value: Mixed white, opaque, Δ/Δwor1, tdh3-wor1 reference


title: HP1b Q4113 Kc167 D.melanogaster ChIP Rep1

source_name: HP1b Q4113 Kc ChIP expt.2114 channel_1


title: HP1a wa184 ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: HP1a wa184 BG3 ChIP expt.446 channel_1


title: HP1a wa184 ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 446.Mvalues.bedgraph

source_name: HP1a wa184 BG3 Input expt.391 channel_1


title: HP1a wa184 ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 445.Mvalues.bedgraph

source_name: HP1a wa184 BG3 Input expt.423 channel_1


title: HP1a wa184 ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: HP1a wa184 BG3 ChIP expt.445 channel_1


title: Su(var) 3-9 H3K9me1 (new lot 2) Nuclear L3 06_17 D.melanogaster ChIP Rep1

source_name: Su(var) 3-9 H3K9me1 (new lot 2) Nuc. L3 ChIP expt.2094 channel_1

value: Su(var) 3-9 06 17 mutant


title: Su(var) 3-9 H3K9me1 (new lot 2) Nuclear L3 06_17 D.melanogaster ChIP Rep2

source_name: Su(var) 3-9 H3K9me1 (new lot 2) Nuc. L3 ChIP expt.2095 channel_1

value: 3rd Instar Larvae


title: PIWI Q2569 Nuclear L3 piwi2 D.melanogaster Input Rep2

description: Served as Input for: 1982.Mvalues.bedgraph

source_name: PIWI Q2569 Nuc. L3 piwi2 Input expt.1980 channel_1


title: PIWI Q2569 Nuclear L3 piwi2 D.melanogaster Input Rep1

description: Served as Input for: 1981.Mvalues.bedgraph

source_name: PIWI Q2569 Nuc. L3 piwi2 Input expt.1979 channel_1


title: Su(var) 3-9 H3K9me1 (new lot 2) Nuclear L3 06_17 D.melanogaster Input Rep1

description: Served as Input for: 2094.Mvalues.bedgraph

source_name: Su(var) 3-9 H3K9me1 (new lot 2) Nuc. L3 Input expt.1388 channel_1


title: Su(var) 3-9 H3K9me1 (new lot 2) Nuclear L3 06_17 D.melanogaster Input Rep2

description: Served as Input for: 2095.Mvalues.bedgraph

source_name: Su(var) 3-9 H3K9me1 (new lot 2) Nuc. L3 Input expt.1389 channel_1


title: PIWI Q2569 Nuclear L3 piwi2 D.melanogaster ChIP Rep2

source_name: PIWI Q2569 Nuc. L3 piwi2 ChIP expt.1982 channel_1


title: HP4 Q4072 S2-DRSC D.melanogaster ChIP Rep1

source_name: HP4 Q4072 S2 ChIP expt.1410 channel_1


title: LSD1 Q3430 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 1452.Mvalues.bedgraph

source_name: LSD1 Q3430 S2 Input expt.1453 channel_1


title: MRG15 Q2482 S2-DRSC D.melanogaster ChIP Rep2

source_name: MGR15 Q2482 S2 ChIP expt.837 channel_1


title: MRG15 Q2482 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 836.Mvalues.bedgraph

source_name: MGR15 Q2482 S2 Input expt.846 channel_1


title: MRG15 Q2482 S2-DRSC D.melanogaster ChIP Rep1

source_name: MGR15 Q2482 S2 ChIP expt.836 channel_1


title: HP4 Q4072 S2-DRSC D.melanogaster ChIP Rep2

source_name: HP4 Q4072 S2 ChIP expt.1411 channel_1


title: LSD1 Q3430 S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 1946.Mvalues.bedgraph

source_name: LSD1 Q3430 S2 Input expt.1837 channel_1


title: LSD1 Q3430 S2-DRSC D.melanogaster ChIP Rep2

source_name: LSD1 Q3430 S2 ChIP expt.1946 channel_1


title: MRG15 Q2482 S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 837.Mvalues.bedgraph

source_name: MGR15 Q2482 S2 Input expt.847 channel_1


title: LSD1 Q3430 S2-DRSC D.melanogaster ChIP Rep1

source_name: LSD1 Q3430 S2 ChIP expt.1452 channel_1


title: HP4 Q4072 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 1410.Mvalues.bedgraph

source_name: HP4 Q4072 S2 Input expt.1386 channel_1


title: PIWI Q2569 Nuclear L3 piwi2 D.melanogaster ChIP Rep1

source_name: PIWI Q2569 Nuc. L3 piwi2 ChIP expt.1981 channel_1


title: HP4 Q4072 S2-DRSC D.melanogaster Input Rep2,3

description: Served as Input for: 1528.Mvalues.bedgraph, 1411.Mvalues.bedgraph

source_name: HP4 Q4072 S2 Input expt.1387 channel_1


title: dmTopo II (DAJ) S2-DRSC D.melanogaster ChIP Rep2

source_name: dmTopo II (DAJ) S2 ChIP expt.1425 channel_1


title: dmTopo II (DAJ) S2-DRSC D.melanogaster ChIP Rep1

source_name: dmTopo II (DAJ) S2 ChIP expt.1424 channel_1


title: dmTopo II (DAJ) S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 1424.Mvalues.bedgraph

source_name: dmTopo II (DAJ) S2 Input expt.847 channel_1


title: dmTopo II (DAJ) S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 1425.Mvalues.bedgraph

source_name: dmTopo II (DAJ) S2 Input expt.846 channel_1


title: HP2 (Ab2-90) 2-4 hr OR embryo D.melanogaster ChIP Rep3

source_name: HP2 (Ab2-90) 2-4 hr OR Em. ChIP expt.2013 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: Oregon-R

value: Embryo 2-4hr OR

value: wild type


title: HP4 Q4072 S2-DRSC D.melanogaster ChIP Rep3

source_name: HP4 Q4072 S2 ChIP expt.1528 channel_1


title: HP2 (Ab2-90) 2-4 hr OR embryo D.melanogaster ChIP Rep2

source_name: HP2 (Ab2-90) 2-4 hr OR Em. ChIP expt.955 channel_1


title: HP2 (Ab2-90) 2-4 hr OR embryo D.melanogaster Input Rep2

description: Served as Input for: 955.Mvalues.bedgraph

source_name: HP2 (Ab2-90) 2-4 hr OR Em. Input expt.800 channel_1


title: HP2 (Ab2-90) 2-4 hr OR embryo D.melanogaster Input Rep1

description: Served as Input for: 954.Mvalues.bedgraph

source_name: HP2 (Ab2-90) 2-4 hr OR Em. Input expt.690 channel_1


title: H3K27me1 S2-DRSC D.melanogaster ChIP Rep1

source_name: H3K27me1 S2 ChIP expt.778 channel_1


title: H3K27me1 S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 2042.Mvalues.bedgraph

source_name: H3K27me1 S2 Input expt.1883 channel_1


title: H3K27me1 S2-DRSC D.melanogaster Input Rep3

description: Served as Input for: 2043.Mvalues.bedgraph

source_name: H3K27me1 S2 Input expt.2040 channel_1


title: H3K27me1 S2-DRSC D.melanogaster ChIP Rep2

source_name: H3K27me1 S2 ChIP expt.2042 channel_1


title: H3K27me1 S2-DRSC D.melanogaster ChIP Rep3

source_name: H3K27me1 S2 ChIP expt.2043 channel_1


title: H3K27me1 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 778.Mvalues.bedgraph

source_name: H3K27me1 S2 Input expt.644 channel_1


title: POF (MO 459) Nuclear L3 HP1a D.melanogaster Input Rep2

description: Served as Input for: 1439.Mvalues.bedgraph

source_name: POF (MO 459) Nuc. L3 HP1a Input expt.1427 channel_1

value: HP1a mutant


title: POF (MO 459) Nuclear L3 HP1a D.melanogaster ChIP Rep2

source_name: POF (MO 459) Nuc. L3 HP1a ChIP expt.1439 channel_1


title: HP2 (Ab2-90) 2-4 hr OR embryo D.melanogaster ChIP Rep1

source_name: HP2 (Ab2-90) 2-4 hr OR Em. ChIP expt.954 channel_1


title: HP2 (Ab2-90) 2-4 hr OR embryo D.melanogaster Input Rep3

description: Served as Input for: 2013.Mvalues.bedgraph

source_name: HP2 (Ab2-90) 2-4 hr OR Em. Input expt.1996 channel_1


title: POF (MO 459) 14-16 hr OR embryo D.melanogaster ChIP Rep1

source_name: POF (MO 459) 14-16 hr OR Em. ChIP expt.1475 channel_1

value: Embryo 14-16hr OR


title: POF (MO 459) 14-16 hr OR embryo D.melanogaster Input Rep2

description: Served as Input for: 1476.Mvalues.bedgraph

source_name: POF (MO 459) 14-16 hr OR Em. Input expt.975 channel_1


title: POF (MO 459) Nuclear L3 HP1a D.melanogaster Input Rep1

description: Served as Input for: 1438.Mvalues.bedgraph

source_name: POF (MO 459) Nuc. L3 HP1a Input expt.1426 channel_1


title: POF (MO 459) 14-16 hr OR embryo D.melanogaster ChIP Rep2

source_name: POF (MO 459) 14-16 hr OR Em. ChIP expt.1476 channel_1


title: POF (MO 459) Nuclear L3 HP1a D.melanogaster ChIP Rep1

source_name: POF (MO 459) Nuc. L3 HP1a ChIP expt.1438 channel_1


title: POF (MO 459) 14-16 hr OR embryo D.melanogaster Input Rep1

description: Served as Input for: 1475.Mvalues.bedgraph

source_name: POF (MO 459) 14-16 hr OR Em. Input expt.974 channel_1


title: HP1 wa191 Nuclear L3 Su(var) 3-9 06_17 D.melanogaster Input Rep1

description: Served as Input for: 1412.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 Su(var) Input expt.1388 channel_1


title: HP1 wa191 Nuclear L3 Su(var) 3-9 06_17 D.melanogaster Input Rep2

description: Served as Input for: 1413.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 Su(var) Input expt.1389 channel_1


title: HP1 wa191 Nuclear L3 Su(var) 3-9 06_17 D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L3 Su(var) ChIP expt.1412 channel_1


title: HP1 wa191 Nuclear L3 Su(var) 3-9 06_17 D.melanogaster ChIP Rep2

source_name: HP1 wa191 Nuc. L3 Su(var) ChIP expt.1413 channel_1


title: H3K9me3 abcam Nuclear L3 Su(var) 3-9 06_17 D.melanogaster ChIP Rep1

source_name: H3K9me3 abcam Nuc. L3 Su(var) ChIP expt.1444 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Su(var) 3-9 06_17 D.melanogaster Input Rep2

description: Served as Input for: 1443.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 Su(var) Input expt.1389 channel_1


title: H3K36me3 abcam Nuclear L3 Su(var) 3-9 06_17 D.melanogaster ChIP Rep1

source_name: H3K36me3 abcam Nuclear L3 Su(var) ChIP expt.1468 channel_1


title: H3K36me3 abcam Nuclear L3 Su(var) 3-9 06_17 D.melanogaster Input Rep1

description: Served as Input for: 1468.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuclear L3 Su(var) Input expt.1388 channel_1


title: H3K9me3 abcam Nuclear L3 Su(var) 3-9 06_17 D.melanogaster Input Rep2

description: Served as Input for: 1445.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 Su(var) Input expt.1389 channel_1


title: H3K9me3 abcam Nuclear L3 Su(var) 3-9 06_17 D.melanogaster ChIP Rep2

source_name: H3K9me3 abcam Nuc. L3 Su(var) ChIP expt.1445 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Su(var) 3-9 06_17 D.melanogaster Input Rep1

description: Served as Input for: 1442.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 Su(var) Input expt.1388 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Su(var) 3-9 06_17 D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 Su(var) ChIP expt.1443 channel_1


title: H3K9me3 abcam Nuclear L3 Su(var) 3-9 06_17 D.melanogaster Input Rep1

description: Served as Input for: 1444.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 Su(var) Input expt.1388 channel_1


title: H3K36me3 abcam Nuclear L3 Su(var) 3-9 06_17 D.melanogaster Input Rep2

description: Served as Input for: 1469.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuclear L3 Su(var) Input expt.1389 channel_1


title: H3K36me3 abcam Nuclear L3 Su(var) 3-9 06_17 D.melanogaster ChIP Rep2

source_name: H3K36me3 abcam Nuclear L3 Su(var) ChIP expt.1469 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Su(var) 3-9 06_17 D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 Su(var) ChIP expt.1442 channel_1


title: H3K18Ac 14-16h OR embryos mixedABlot D.melanogaster ChIP Rep2

source_name: H3K18Ac 14-16h OR Em. ChIP expt.698 channel_1


title: H3K18Ac 14-16h OR embryos mixedABlot D.melanogaster ChIP Rep1

source_name: H3K18Ac 14-16h OR Em. ChIP expt.246 channel_1


title: H3K18Ac 14-16h OR embryos mixedABlot D.melanogaster Input Rep2

description: Served as Input for: 698.Mvalues.bedgraph

source_name: H3K18Ac 14-16h OR Em. Input expt.651 channel_1


title: H3K18Ac 14-16h OR embryos mixedABlot D.melanogaster Input Rep1

description: Served as Input for: 246.Mvalues.bedgraph

source_name: H3K18Ac 14-16h OR Em. Input expt.242 channel_1


title: Su(var) 3-9 Q2598 OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1867.Mvalues.bedgraph

source_name: Su(var) 3-9 Q2598 OR Input expt.1790 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: Su(var) 3-9 Q2598 OR Head Nuclear D.melanogaster ChIP Rep2

source_name: Su(var) 3-9 Q2598 OR ChIP expt.1867 channel_1


title: Su(var) 3-9 Q2598 OR Head Nuclear D.melanogaster ChIP Rep1

source_name: Su(var) 3-9 Q2598 OR ChIP expt.1866 channel_1


title: RNA Pol II (abcam) Nuclear L3 HP1a D.melanogaster ChIP Rep3

source_name: RNA Pol II (abcam) Nuc. L3 Hp1a ChIP expt.1798 channel_1


title: Su(var) 3-9 Q2598 OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1866.Mvalues.bedgraph

source_name: Su(var) 3-9 Q2598 OR Input expt.1789 channel_1


title: RNA Pol II (abcam) Nuclear L3 HP1a D.melanogaster ChIP Rep2

source_name: RNA Pol II (abcam) Nuc. L3 Hp1a ChIP expt.1435 channel_1


title: RNA Pol II (abcam) Nuclear L3 HP1a D.melanogaster Input Rep2

description: Served as Input for: 1435.Mvalues.bedgraph

source_name: RNA Pol II (abcam) Nuc. L3 Hp1a Input expt.1427 channel_1


title: RNA Pol II (abcam) Nuclear L3 HP1a D.melanogaster ChIP Rep1

source_name: RNA Pol II (abcam) Nuc. L3 Hp1a ChIP expt.1434 channel_1


title: RNA Pol II (abcam) Nuclear L3 HP1a D.melanogaster Input Rep1

description: Served as Input for: 1434.Mvalues.bedgraph

source_name: RNA Pol II (abcam) Nuc. L3 Hp1a Input expt.1426 channel_1


title: POF (MO 459) OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1862.Mvalues.bedgraph

source_name: POF (MO 459) OR Head Nuc. Input expt.1789 channel_1


title: POF (MO 459) OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1863.Mvalues.bedgraph

source_name: POF (MO 459) OR Head Nuc. Input expt.1790 channel_1


title: POF (MO 459) OR Head Nuclear D.melanogaster ChIP Rep1

source_name: POF (MO 459) OR Head Nuc. ChIP expt.1862 channel_1


title: POF (MO 459) Nuclear L3 POF D.melanogaster ChIP Rep1

source_name: POF (MO 459) Nuc. L3 POF ChIP expt.1351 channel_1

value: POF mutant

value: deletion


title: POF (MO 459) Nuclear L3 POF D.melanogaster ChIP Rep2

source_name: POF (MO 459) Nuc. L3 POF ChIP expt.1352 channel_1


title: RNA Pol II (abcam) Nuclear L3 HP1a D.melanogaster Input Rep3

description: Served as Input for: 1798.Mvalues.bedgraph

source_name: RNA Pol II (abcam) Nuc. L3 Hp1a Input expt.1786 channel_1


title: POF (MO 459) Nuclear L3 POF D.melanogaster Input Rep2

description: Served as Input for: 1352.Mvalues.bedgraph

source_name: POF (MO 459) Nuc. L3 POF Input expt.1338 channel_1


title: HP2 (Ab2-90) OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1860.Mvalues.bedgraph

source_name: HP2 (Ab2-90) OR Head Nuc. Input expt.1789 channel_1


title: POF (MO 459) Nuclear L3 EGG D.melanogaster ChIP Rep1

source_name: POF (MO 459) Nuc. L3 EGG ChIP expt.1597 channel_1

value: EGG mutant


title: POF (MO 459) Nuclear L3 EGG D.melanogaster ChIP Rep3

source_name: POF (MO 459) Nuc. L3 EGG ChIP expt.1797 channel_1


title: POF (MO 459) Nuclear L3 EGG D.melanogaster ChIP Rep2

source_name: POF (MO 459) Nuc. L3 EGG ChIP expt.1598 channel_1


title: HP2 (Ab2-90) OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1861.Mvalues.bedgraph

source_name: HP2 (Ab2-90) OR Head Nuc. Input expt.1790 channel_1


title: HP1 wa191 Nuclear L3 POF D.melanogaster ChIP Rep2

source_name: HP1 wa191 Nuc. L3 POF ChIP expt.1346 channel_1


title: HP2 (Ab2-90) OR Head Nuclear D.melanogaster ChIP Rep2

source_name: HP2 (Ab2-90) OR Head Nuc. ChIP expt.1861 channel_1


title: HP1 wa191 Nuclear L3 POF D.melanogaster ChIP Rep3

source_name: HP1 wa191 Nuc. L3 POF ChIP expt.1801 channel_1


title: POF (MO 459) Nuclear L3 EGG D.melanogaster Input Rep2,3

description: Served as Input for: 1797.Mvalues.bedgraph, 1598.Mvalues.bedgraph

source_name: POF (MO 459) Nuc. L3 EGG Input expt.1604 channel_1


title: HP1 wa191 Nuclear L3 POF D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L3 POF ChIP expt.1345 channel_1


title: POF (MO 459) Nuclear L3 EGG D.melanogaster Input Rep1

description: Served as Input for: 1597.Mvalues.bedgraph

source_name: POF (MO 459) Nuc. L3 EGG Input expt.1603 channel_1


title: POF (MO 459) Nuclear L3 POF D.melanogaster Input Rep1

description: Served as Input for: 1351.Mvalues.bedgraph

source_name: POF (MO 459) Nuc. L3 POF Input expt.1337 channel_1


title: HP1 wa191 Nuclear L3 POF D.melanogaster Input Rep2,3

description: Served as Input for: 1346.Mvalues.bedgraph, 1801.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 POF Input expt.1338 channel_1


title: HP1c (MO 462) OR Head Nuclear D.melanogaster ChIP Rep2

source_name: HP1c (MO 462) OR Head Nuc. ChIP expt.1859 channel_1


title: HP1c (MO 462) OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1858.Mvalues.bedgraph

source_name: HP1c (MO 462) OR Head Nuc. Input expt.1789 channel_1


title: HP1c (MO 462) OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1859.Mvalues.bedgraph

source_name: HP1c (MO 462) OR Head Nuc. Input expt.1790 channel_1


title: HP1b Q4114 OR Head Nuclear D.melanogaster ChIP Rep2

source_name: HP1b Q4114 OR Head Nuc. ChIP expt.1857 channel_1


title: HP1b Q4114 OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1857.Mvalues.bedgraph

source_name: HP1b Q4114 OR Head Nuc. Input expt.1790 channel_1


title: HP1c (MO 462) OR Head Nuclear D.melanogaster ChIP Rep1

source_name: HP1c (MO 462) OR Head Nuc. ChIP expt.1858 channel_1


title: HP2 (Ab2-90) OR Head Nuclear D.melanogaster ChIP Rep1

source_name: HP2 (Ab2-90) OR Head Nuc. ChIP expt.1860 channel_1


title: POF (MO 459) OR Head Nuclear D.melanogaster ChIP Rep2

source_name: POF (MO 459) OR Head Nuc. ChIP expt.1863 channel_1


title: HP1 wa191 Nuclear L3 POF D.melanogaster Input Rep1

description: Served as Input for: 1345.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 POF Input expt.1337 channel_1


title: HP1b Q4114 OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1856.Mvalues.bedgraph

source_name: HP1b Q4114 OR Head Nuc. Input expt.1789 channel_1


title: H3K9me3 abcam Nuclear L3 HP1a D.melanogaster Input Rep3

description: Served as Input for: 1799.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 HP1a Input expt.1786 channel_1


title: H3K9me3 abcam Nuclear L3 HP1a D.melanogaster ChIP Rep1

source_name: H3K9me3 abcam Nuc. L3 HP1a ChIP expt.1432 channel_1


title: H3K9me3 abcam Nuclear L3 HP1a D.melanogaster ChIP Rep3

source_name: H3K9me3 abcam Nuc. L3 HP1a ChIP expt.1799 channel_1


title: H3K9me3 abcam Nuclear L3 HP1a D.melanogaster Input Rep1

description: Served as Input for: 1432.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 HP1a Input expt.1426 channel_1


title: H3K9me3 abcam Nuclear L3 HP1a D.melanogaster Input Rep2

description: Served as Input for: 1433.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 HP1a Input expt.1427 channel_1


title: H3K9me3 abcam Nuclear L3 EGG D.melanogaster ChIP Rep2

source_name: H3K9me3 abcam Nuc. L3 EGG ChIP expt.1596 channel_1


title: HP1b Q4114 OR Head Nuclear D.melanogaster ChIP Rep1

source_name: HP1b Q4114 OR Head Nuc. ChIP expt.1856 channel_1


title: H3K9me2-Ab2 (new lot) OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1810.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) OR Head Nuc. Input expt.1790 channel_1


title: H3K9me3 abcam Nuclear L3 EGG D.melanogaster ChIP Rep1

source_name: H3K9me3 abcam Nuc. L3 EGG ChIP expt.1595 channel_1


title: H3K9me2-Ab2 (new lot) OR Head Nuclear D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot) OR Head Nuc. ChIP expt.1809 channel_1


title: H3K9me2-Ab2 (new lot) OR Head Nuclear D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot) OR Head Nuc. ChIP expt.1810 channel_1


title: H3K9acS10P (new lot) OR Head Nuclear D.melanogaster ChIP Rep1

source_name: H3K9acS10P (new lot) OR Head Nuc. ChIP expt.1807 channel_1


title: H3K9me3 abcam Nuclear L3 EGG D.melanogaster Input Rep1

description: Served as Input for: 1595.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 EGG Input expt.1603 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 HP1a D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 HP1a ChIP expt.1431 channel_1


title: H3K9acS10P (new lot) OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1808.Mvalues.bedgraph

source_name: H3K9acS10P (new lot) OR Head Nuc. Input expt.1790 channel_1


title: H3K9me2-Ab2 (new lot) OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1809.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) OR Head Nuc. Input expt.1789 channel_1


title: H3K9acS10P (new lot) OR Head Nuclear D.melanogaster ChIP Rep2

source_name: H3K9acS10P (new lot) OR Head Nuc. ChIP expt.1808 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 HP1a D.melanogaster Input Rep1

description: Served as Input for: 1430.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 HP1a Input expt.1426 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 HP1a D.melanogaster Input Rep2

description: Served as Input for: 1431.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 HP1a Input expt.1427 channel_1


title: H3K9me3 abcam Nuclear L3 EGG D.melanogaster Input Rep2

description: Served as Input for: 1596.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 EGG Input expt.1604 channel_1


title: H3K9acS10P (new lot) OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1807.Mvalues.bedgraph

source_name: H3K9acS10P (new lot) OR Head Nuc. Input expt.1789 channel_1


title: H3K9ac OR Head Nuclear D.melanogaster ChIP Rep1

source_name: H3K9ac OR Head Nuc. ChIP expt.1805 channel_1


title: H3K9ac OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1806.Mvalues.bedgraph

source_name: H3K9ac OR Head Nuc. Input expt.1790 channel_1


title: H3K9ac OR Head Nuclear D.melanogaster ChIP Rep2

source_name: H3K9ac OR Head Nuc. ChIP expt.1806 channel_1


title: H3K9ac OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1805.Mvalues.bedgraph

source_name: H3K9ac OR Head Nuc. Input expt.1789 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 HP1a D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 HP1a ChIP expt.1430 channel_1


title: H3K9ac 14-16 hr OR Embryo D.melanogaster ChIP Rep3

source_name: H3K9ac 14-16 hr OR Em. ChIP expt.1803 channel_1


title: H3K9ac 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K9ac 14-16 hr OR Em. ChIP expt.1060 channel_1


title: H3K9ac 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1060.Mvalues.bedgraph

source_name: H3K9ac 14-16 hr OR Em. Input expt.1065 channel_1


title: H3K9ac 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1059.Mvalues.bedgraph

source_name: H3K9ac 14-16 hr OR Em. Input expt.1064 channel_1


title: H3K36me3 abcam Nuclear L3 HP1a D.melanogaster ChIP Rep2

source_name: H3K36me3 abcam Nuc. L3 HP1a ChIP expt.1465 channel_1


title: H3K9ac 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K9ac 14-16 hr OR Em. ChIP expt.1059 channel_1


title: H3K36me3 abcam Nuclear L3 HP1a D.melanogaster ChIP Rep3

source_name: H3K36me3 abcam Nuc. L3 HP1a ChIP expt.1800 channel_1


title: H3K9ac 14-16 hr OR Embryo D.melanogaster Input Rep3

description: Served as Input for: 1803.Mvalues.bedgraph

source_name: H3K9ac 14-16 hr OR Em. Input expt.1791 channel_1


title: H3K36me3 abcam Nuclear L3 HP1a D.melanogaster ChIP Rep1

source_name: H3K36me3 abcam Nuc. L3 HP1a ChIP expt.1464 channel_1


title: H3K36me3 abcam Nuclear L3 HP1a D.melanogaster Input Rep3

description: Served as Input for: 1800.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 HP1a Input expt.1786 channel_1


title: H3K18Ac (new lot) 14-16 hr OR Embryo D.melanogaster ChIP Rep3

source_name: H3K18Ac (new lot) 14-16 hr OR Em. ChIP expt.1129 channel_1


title: H3K23ac Head Nuclear OR D.melanogaster Input Rep2

description: Served as Input for: 1814.Mvalues.bedgraph

source_name: H3K23ac Head Nuc. OR Input expt.1790 channel_1


title: H3K23ac Head Nuclear OR D.melanogaster ChIP Rep2

source_name: H3K23ac Head Nuc. OR ChIP expt.1814 channel_1


title: H3K36me3 abcam Nuclear L3 HP1a D.melanogaster Input Rep1

description: Served as Input for: 1464.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 HP1a Input expt.1426 channel_1


title: H3K36me3 abcam Nuclear L3 HP1a D.melanogaster Input Rep2

description: Served as Input for: 1465.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 HP1a Input expt.1427 channel_1


title: H3K23ac Head Nuclear OR D.melanogaster ChIP Rep1

source_name: H3K23ac Head Nuc. OR ChIP expt.1813 channel_1


title: H3K23ac Head Nuclear OR D.melanogaster Input Rep1

description: Served as Input for: 1813.Mvalues.bedgraph

source_name: H3K23ac Head Nuc. OR Input expt.1789 channel_1


title: H3K18Ac (new lot) 14-16 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K18Ac (new lot) 14-16 hr OR Em. ChIP expt.698 channel_1


title: H3K18Ac (new lot) 14-16 hr OR Embryo D.melanogaster Input Rep3

description: Served as Input for: 1129.Mvalues.bedgraph

source_name: H3K18Ac (new lot) 14-16 hr OR Em. Input expt.1065 channel_1


title: Chro (Chriz) WR 14-16 hr OR embryo D.melanogaster ChIP Rep2

source_name: Chro (Chriz) WR 14-16 hr OR Em. ChIP expt.168 channel_1


title: Chro (Chriz) WR 14-16 hr OR embryo D.melanogaster Input Rep1

description: Served as Input for: 166.Mvalues.bedgraph

source_name: Chro (Chriz) WR 14-16 hr OR Em. Input expt.172 channel_1


title: Chro (Chriz) WR 14-16 hr OR embryo D.melanogaster ChIP Rep1

source_name: Chro (Chriz) WR 14-16 hr OR Em. ChIP expt.166 channel_1


title: Chro (Chriz) WR 14-16 hr OR embryo D.melanogaster Input Rep2

description: Served as Input for: 168.Mvalues.bedgraph

source_name: Chro (Chriz) WR 14-16 hr OR Em. Input expt.173 channel_1


title: RNA Pol II (abcam) Nuclear L3 HP1c D.melanogaster ChIP Rep1

source_name: RNA Pol II (abcam) Nuc. L3 HP1c ChIP expt.1400 channel_1

value: HP1c mutant

value: PBac insertion


title: RNA Pol II (abcam) Nuclear L3 HP1c D.melanogaster Input Rep2

description: Served as Input for: 1401.Mvalues.bedgraph

source_name: RNA Pol II (abcam) Nuc. L3 HP1c Input expt.1214 channel_1


title: RNA Pol II (abcam) Nuclear L3 HP1c D.melanogaster ChIP Rep2

source_name: RNA Pol II (abcam) Nuc. L3 HP1c ChIP expt.1401 channel_1


title: RNA Pol II (abcam) Nuclear L3 HP1c D.melanogaster Input Rep1

description: Served as Input for: 1400.Mvalues.bedgraph

source_name: RNA Pol II (abcam) Nuc. L3 HP1c Input expt.1213 channel_1


title: HP1 wa191 Nuclear L3 Su(var) 3-9 D.melanogaster ChIP Rep2

source_name: HP1 wa191 Nuc. L3 Su(var) ChIP expt.959 channel_1

value: Su(var)3-9 mutant


title: H3K18Ac (new lot) 14-16 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 769.Mvalues.bedgraph

source_name: H3K18Ac (new lot) 14-16 hr OR Em. Input expt.772 channel_1


title: HP1 wa191 Nuclear L3 Su(var) 3-9 D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L3 Su(var) ChIP expt.958 channel_1


title: HP1 wa191 Nuclear L3 Su(var) 3-9 D.melanogaster Input Rep2

description: Served as Input for: 959.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 Su(var) Input expt.963 channel_1


title: H3K18Ac (new lot) 14-16 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 698.Mvalues.bedgraph

source_name: H3K18Ac (new lot) 14-16 hr OR Em. Input expt.651 channel_1


title: HP1 wa191 Nuclear L3 mt2 D.melanogaster ChIP Rep2

source_name: HP1 wa191 Nuc. L3 mt2 ChIP expt.1451 channel_1

value: mt2 mutant


title: HP1 wa191 Nuclear L3 Su(var) 3-9 D.melanogaster Input Rep1

description: Served as Input for: 958.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 Su(var) Input expt.962 channel_1


title: H3K18Ac (new lot) 14-16 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K18Ac (new lot) 14-16 hr OR Em. ChIP expt.769 channel_1


title: HP1 wa191 Nuclear L3 mt2 D.melanogaster Input Rep1

description: Served as Input for: 1450.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 mt2 Input expt.1488 channel_1


title: HP1 wa191 Nuclear L3 mt2 D.melanogaster Input Rep2

description: Served as Input for: 1451.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 mt2 Input expt.1489 channel_1


title: HP1 wa191 Nuclear L3 EGG D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L3 EGG ChIP expt.1605 channel_1


title: HP1 wa191 Nuclear L3 EGG D.melanogaster Input Rep2

description: Served as Input for: 1606.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 EGG Input expt.1604 channel_1


title: HP1 wa191 Nuclear L3 EGG D.melanogaster ChIP Rep2

source_name: HP1 wa191 Nuc. L3 EGG ChIP expt.1606 channel_1


title: HP1c (MO 462) Nuclear L3 HP1a D.melanogaster Input Rep1

description: Served as Input for: 1436.Mvalues.bedgraph

source_name: HP1c (MO 462) Nuc. L3 HP1a Input expt.1426 channel_1


title: HP1c (MO 462) Nuclear L3 HP1a D.melanogaster Input Rep2

description: Served as Input for: 1437.Mvalues.bedgraph

source_name: HP1c (MO 462) Nuc. L3 HP1a Input expt.1427 channel_1


title: HP1c (MO 462) Nuclear L3 HP1a D.melanogaster ChIP Rep2

source_name: HP1c (MO 462) Nuc. L3 HP1a ChIP expt.1437 channel_1


title: H4K16ac(M) 14-16 hr OR embryo D.melanogaster ChIP Rep1

source_name: H4K16ac(M) 14-16 hr OR Em. ChIP expt.163 channel_1


title: H4K16ac(M) 14-16 hr OR embryo D.melanogaster ChIP Rep2

source_name: H4K16ac(M) 14-16 hr OR Em. ChIP expt.165 channel_1


title: H4K16ac(M) 14-16 hr OR embryo D.melanogaster Input Rep1

description: Served as Input for: 163.Mvalues.bedgraph

source_name: H4K16ac(M) 14-16 hr OR Em. Input expt.172 channel_1


title: H4K16ac(L) 14-16 hr OR embryo D.melanogaster ChIP Rep1

source_name: H4K16ac(L) 14-16 hr OR Em. ChIP expt.162 channel_1


title: H4K16ac(L) 14-16 hr OR embryo D.melanogaster ChIP Rep2

source_name: H4K16ac(L) 14-16 hr OR Em. ChIP expt.164 channel_1


title: H4K16ac(L) 14-16 hr OR embryo D.melanogaster Input Rep1

description: Served as Input for: 162.Mvalues.bedgraph

source_name: H4K16ac(L) 14-16 hr OR Em. Input expt.172 channel_1


title: HP1 wa191 Nuclear L3 mt2 D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L3 mt2 ChIP expt.1450 channel_1


title: H4K16ac(M) 14-16 hr OR embryo D.melanogaster Input Rep2

description: Served as Input for: 165.Mvalues.bedgraph

source_name: H4K16ac(M) 14-16 hr OR Em. Input expt.173 channel_1


title: H4K16ac(L) 14-16 hr OR embryo D.melanogaster Input Rep2

description: Served as Input for: 164.Mvalues.bedgraph

source_name: H4K16ac(L) 14-16 hr OR Em. Input expt.173 channel_1


title: H3K9me3 abcam Nuclear L3 Su(var) 3-9 D.melanogaster Input Rep2

description: Served as Input for: 1122.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 Su(var) Input expt.1170 channel_1


title: H3K9me3 abcam Nuclear L3 Su(var) 3-9 D.melanogaster ChIP Rep2

source_name: H3K9me3 abcam Nuc. L3 Su(var) ChIP expt.1122 channel_1


title: H3K9me3 abcam Nuclear L3 Su(var) 3-9 D.melanogaster Input Rep1

description: Served as Input for: 1121.Mvalues.bedgraph

source_name: H3K9me3 abcam Nuc. L3 Su(var) Input expt.1169 channel_1


title: H3K9me3 abcam Nuclear L3 Su(var) 3-9 D.melanogaster ChIP Rep1

source_name: H3K9me3 abcam Nuc. L3 Su(var) ChIP expt.1121 channel_1


title: HP1 wa191 Nuclear L3 EGG D.melanogaster Input Rep1

description: Served as Input for: 1605.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 EGG Input expt.1603 channel_1


title: HP1c (MO 462) Nuclear L3 HP1a D.melanogaster ChIP Rep1

source_name: HP1c (MO 462) Nuc. L3 HP1a ChIP expt.1436 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 mt2 D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 mt2 ChIP expt.1358 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Su(var) 3-9 D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 Su(var) ChIP expt.983 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 mt2 D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 mt2 ChIP expt.1357 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Su(var) 3-9 D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 Su(var) ChIP expt.984 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 mt2 D.melanogaster Input Rep1

description: Served as Input for: 1357.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 mt2 Input expt.1339 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Su(var) 3-9 D.melanogaster Input Rep1

description: Served as Input for: 983.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 Su(var) Input expt.962 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Su(var) 3-9 D.melanogaster Input Rep2

description: Served as Input for: 984.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 Su(var) Input expt.963 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 EGG D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 EGG ChIP expt.1593 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 EGG D.melanogaster Input Rep2

description: Served as Input for: 1594.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 EGG Input expt.1604 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 EGG D.melanogaster Input Rep1

description: Served as Input for: 1593.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 EGG Input expt.1603 channel_1


title: H3K4me2 JBC 1360331 Nuclear L3 Su(var) 3-9 D.melanogaster ChIP Rep2

source_name: H3K4me2 JBC 1360331 Nuc. L3 Su(var) ChIP expt.1120 channel_1


title: H3K4me2 JBC 1360331 Nuclear L3 Su(var) 3-9 D.melanogaster Input Rep2

description: Served as Input for: 1120.Mvalues.bedgraph

source_name: H3K4me2 JBC 1360331 Nuc. L3 Su(var) Input expt.1170 channel_1


title: H3K4me2 JBC 1360331 Nuclear L3 Su(var) 3-9 D.melanogaster ChIP Rep1

source_name: H3K4me2 JBC 1360331 Nuc. L3 Su(var) ChIP expt.1119 channel_1


title: H3K4me2 JBC 1360331 Nuclear L3 Su(var) 3-9 D.melanogaster Input Rep1

description: Served as Input for: 1119.Mvalues.bedgraph

source_name: H3K4me2 JBC 1360331 Nuc. L3 Su(var) Input expt.1169 channel_1


title: H3K36me3 abcam Nuclear L3 POF D.melanogaster Input Rep2

description: Served as Input for: 1467.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 POF Input expt.1338 channel_1


title: H3K36me3 abcam Nuclear L3 EGG D.melanogaster ChIP Rep2

source_name: H3K36me3 abcam Nuc. L3 EGG ChIP expt.1624 channel_1


title: H3K36me3 abcam Nuclear L3 POF D.melanogaster Input Rep1

description: Served as Input for: 1466.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 POF Input expt.1337 channel_1


title: H3K36me3 abcam Nuclear L3 POF D.melanogaster ChIP Rep1

source_name: H3K36me3 abcam Nuc. L3 POF ChIP expt.1466 channel_1


title: H3K36me3 abcam Nuclear L3 POF D.melanogaster ChIP Rep2

source_name: H3K36me3 abcam Nuc. L3 POF ChIP expt.1467 channel_1


title: H3K36me3 abcam Nuclear L3 EGG D.melanogaster Input Rep2

description: Served as Input for: 1624.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 EGG Input expt.1604 channel_1


title: H3K36me3 abcam Nuclear L3 EGG D.melanogaster ChIP Rep1

source_name: H3K36me3 abcam Nuc. L3 EGG ChIP expt.1623 channel_1


title: H3K36me3 abcam Nuclear L3 EGG D.melanogaster Input Rep1

description: Served as Input for: 1623.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 EGG Input expt.1603 channel_1


title: H3 antibody2 S2-DRSC D.melanogaster ChIP Rep5

source_name: H3 antibody2 S2 ChIP expt.786 channel_1

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: H3 antibody2 S2-DRSC D.melanogaster ChIP Rep6

source_name: H3 antibody2 S2 ChIP expt.649 channel_1


title: H3 antibody2 S2-DRSC D.melanogaster ChIP Rep4

source_name: H3 antibody2 S2 ChIP expt.785 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 EGG D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 EGG ChIP expt.1594 channel_1

value: 3rd Instar Larvae


title: H3 antibody2 S2-DRSC D.melanogaster ChIP Rep3

source_name: H3 antibody2 S2 ChIP expt.199 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 mt2 D.melanogaster Input Rep2

description: Served as Input for: 1358.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 mt2 Input expt.1340 channel_1


title: Su(var)3-7 Q3448 Nuclear L3 OR D.melanogaster ChIP Rep2

source_name: Su(var)3-7 Q3448 Nuc. L3 OR ChIP expt.970 channel_1

value: Oregon-R


title: H3 antibody2 S2-DRSC D.melanogaster Input Rep6

description: Served as Input for: 649.Mvalues.bedgraph

source_name: H3 antibody2 S2 Input expt.609 channel_1


title: H3 antibody2 S2-DRSC D.melanogaster Input Rep7

description: Served as Input for: 682.Mvalues.bedgraph

source_name: H3 antibody2 S2 Input expt.689 channel_1


title: H3 antibody2 S2-DRSC D.melanogaster Input Rep2,3

description: Served as Input for: 88.Mvalues.bedgraph, 199.Mvalues.bedgraph

source_name: H3 antibody2 S2 Input expt.85 channel_1


title: H3 antibody2 S2-DRSC D.melanogaster Input Rep4

description: Served as Input for: 785.Mvalues.bedgraph

source_name: H3 antibody2 S2 Input expt.788 channel_1


title: H3 antibody2 S2-DRSC D.melanogaster ChIP Rep2

source_name: H3 antibody2 S2 ChIP expt.88 channel_1


title: H3 antibody2 S2-DRSC D.melanogaster Input Rep5

description: Served as Input for: 786.Mvalues.bedgraph

source_name: H3 antibody2 S2 Input expt.789 channel_1


title: Su(var)3-7 Q3448 Nuclear L3 OR D.melanogaster Input Rep2

description: Served as Input for: 970.Mvalues.bedgraph

source_name: Su(var)3-7 Q3448 Nuc. L3 OR Input expt.1004 channel_1


title: H3 antibody2 S2-DRSC D.melanogaster ChIP Rep1

source_name: H3 antibody2 S2 ChIP expt.47 channel_1


title: Su(var)3-7 Q3448 Nuclear L3 OR D.melanogaster Input Rep1

description: Served as Input for: 969.Mvalues.bedgraph

source_name: Su(var)3-7 Q3448 Nuc. L3 OR Input expt.1003 channel_1


title: Su(var)3-7 Q3448 Nuclear L3 OR D.melanogaster ChIP Rep1

source_name: Su(var)3-7 Q3448 Nuc. L3 OR ChIP expt.969 channel_1


title: HP1b (Henikoff) Nuclear L3 OR D.melanogaster ChIP Rep2

source_name: HP1b (Henikoff) Nuc. L3 OR ChIP expt.875 channel_1


title: H3 antibody2 S2-DRSC D.melanogaster ChIP Rep7

source_name: H3 antibody2 S2 ChIP expt.682 channel_1


title: HP1b (Henikoff) Nuclear L3 OR D.melanogaster ChIP Rep1

source_name: HP1b (Henikoff) Nuc. L3 OR ChIP expt.874 channel_1


title: H3 antibody2 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 47.Mvalues.bedgraph

source_name: H3 antibody2 S2 Input expt.48 channel_1


title: HP1b (Henikoff) Nuclear L3 OR D.melanogaster Input Rep2

description: Served as Input for: 875.Mvalues.bedgraph

source_name: HP1b (Henikoff) Nuc. L3 OR Input expt.799 channel_1


title: HP1b (Henikoff) ML-DmBG3-c2 D.melanogaster ChIP Rep4

source_name: HP1b (Henikoff) BG3 ChIP expt.1044 channel_1

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: HP1b (Henikoff) Nuclear L3 OR D.melanogaster Input Rep1

description: Served as Input for: 874.Mvalues.bedgraph

source_name: HP1b (Henikoff) Nuc. L3 OR Input expt.798 channel_1

value: wild type


title: HP1b (Henikoff) ML-DmBG3-c2 D.melanogaster Input Rep2,3

description: Served as Input for: 591.Mvalues.bedgraph, 868.Mvalues.bedgraph

source_name: HP1b (Henikoff) BG3 Input expt.391 channel_1


title: HP1b (Henikoff) ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: HP1b (Henikoff) BG3 ChIP expt.591 channel_1


title: HP1b (Henikoff) ML-DmBG3-c2 D.melanogaster ChIP Rep3

source_name: HP1b (Henikoff) BG3 ChIP expt.868 channel_1


title: HP1b (Henikoff) ML-DmBG3-c2 D.melanogaster Input Rep1,4

description: Served as Input for: 590.Mvalues.bedgraph, 1044.Mvalues.bedgraph

source_name: HP1b (Henikoff) BG3 Input expt.423 channel_1


title: HP1b (Henikoff) ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: HP1b (Henikoff) BG3 ChIP expt.590 channel_1


title: H3K9me3 abcam Nuclear L3 HP1a D.melanogaster ChIP Rep2

source_name: H3K9me3 abcam Nuc. L3 HP1a ChIP expt.1433 channel_1

value: HP1a mutant


title: 128454 PVTT

status: Public on Jan 19 2013

city: shanghai

first: WEIXING

last: GUO

address: CHANGHAI ROAD

country: China

institute: ehbh

description: PVTT is known to be an extension of liver parenchyma tumor (PT) into the main portal trunk and its branches.

hyb_protocol: Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit.

scan_protocol: Array scanning using the Agilent Scanner G2505C. Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: portal vein tumor thrombus tissue

label_protocol: Total RNA of each sample was used for labeling as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step.

value: portal vein tumor thrombus

tag: patient id

tag: disease state

value: hapatocellular carcinoma


title: ESC UNDIFF LINE WA01 PASSAGE 52

status: Public on Oct 31 2012

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: ESC UNDIFF LINE WA01 PASSAGE 52

hyb_protocol: Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.

scan_protocol: Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.

data_processing: The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.

source_name: ESC UNDIFF LINE WA01 PASSAGE 52

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.

extract_protocol: RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.

tag: class

value: ESC

tag: condition

value: UNDIFF

tag: passage

tag: gender

value: MALE


title: UniRef Processing Control 1

description: UniRef Processing Control

source_name: UniRef Processing Control

value: UniRef


title: ESC UNDIFF LINE WA01 PASSAGE 56

description: ESC UNDIFF LINE WA01 PASSAGE 56

source_name: ESC UNDIFF LINE WA01 PASSAGE 56


title: 128454 T

source_name: primary tumor tissue

value: liver parenchyma tumor nodules


title: ESC UNDIFF LINE UC01 PASSAGE 60

description: ESC UNDIFF LINE UC01 PASSAGE 60

source_name: ESC UNDIFF LINE UC01 PASSAGE 60

value: FEMALE


title: ESC UNDIFF LINE UC01 PASSAGE 56

description: ESC UNDIFF LINE UC01 PASSAGE 56

source_name: ESC UNDIFF LINE UC01 PASSAGE 56


title: 128625 T


title: 128360T


title: ESC UNDIFF LINE ES02 PASSAGE 45

description: ESC UNDIFF LINE ES02 PASSAGE 45

source_name: ESC UNDIFF LINE ES02 PASSAGE 45


title: ESC UNDIFF LINE TE03 PASSAGE 66

description: ESC UNDIFF LINE TE03 PASSAGE 66

source_name: ESC UNDIFF LINE TE03 PASSAGE 66


title: ESC UNDIFF LINE TE03 PASSAGE 70

description: ESC UNDIFF LINE TE03 PASSAGE 70

source_name: ESC UNDIFF LINE TE03 PASSAGE 70


title: UniRef Processing Control 2

description: UniRef Processing Control


title: ESC UNDIFF LINE BG02 PASSAGE 54

description: ESC UNDIFF LINE BG02 PASSAGE 54

source_name: ESC UNDIFF LINE BG02 PASSAGE 54


title: 128360 PVTT


title: IFNAR-/- CD11b DC, MCMV, replicate 2

status: Public on Oct 17 2012

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

description:
Sample name: MDD_C39
IFNAR-KO spleen CD11b+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.2(pos)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430.2 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v5 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were RMA normalized in R and Bioconductor, using the limma package.

label_protocol: Except for sample A7 where only 8 ng was available, 50 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from between 5x10E4 and 3x10E6 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.

treatment_protocol: Mice were infected intraperitoneally with salivary gland-murine cytomegalovirus (5x10e4 pfu/mouse). Spleens were harvested at 36 hours post-infection and digested with collagenase (Liberase CI), erythrocytes were lysed with NH(4)Cl, and leukocytes were resuspended in PBS EDTA 5mM before sorting by flow cytometry

tag: chimera description

tag: genotype/variation

value: IFNAR-KO

tag: cell type

value: CD11b+ dendritic cells (DC)

tag: infection

value: murine cytomegalovirus


title: 128625 PVTT

tag: tissue


title: ESC UNDIFF LINE ES02 PASSAGE 49

description: ESC UNDIFF LINE ES02 PASSAGE 49

source_name: ESC UNDIFF LINE ES02 PASSAGE 49


title: ESC UNDIFF LINE BG02 PASSAGE 50

description: ESC UNDIFF LINE BG02 PASSAGE 50

source_name: ESC UNDIFF LINE BG02 PASSAGE 50


title: WT NK, MCMV, replicate 2

description:
Sample name: MDD_C40
WT spleen natural killer (NK) cells from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.1(pos)

value: WT

value: natural killer (NK) cells


title: WT CD11b DC, steady-state, replicate 2

description:
Sample name: MDD_A9
WT spleen CD11b+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.1(pos)


title: IFNAR-/- CD11b DC, steady-state, replicate 2

description:
Sample name: MDD_B23
IFNAR-KO spleen CD11b+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.2(pos)


title: WT CD11b DC, MCMV, replicate 1

description:
Sample name: MDD_C32
WT spleen CD11b+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.1(pos)


title: IFNAR-/- CD11b DC, MCMV, replicate 1

description:
Sample name: MDD_A6
IFNAR-KO spleen CD11b+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.2(pos)


title: IFNAR-/- CD11b DC, steady-state, replicate 1

description:
Sample name: MDD_C29
IFNAR-KO spleen CD11b+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.2(pos)


title: WT NK, steady-state, replicate 2

description:
Sample name: MDD_B24
WT spleen natural killer (NK) cells from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.1(pos)


title: WT NK, MCMV, replicate 1

description:
Sample name: MDD_A7
WT spleen natural killer (NK) cells from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.1(pos)


title: WT CD11b DC, MCMV, replicate 2

description:
Sample name: MDD_B26
WT spleen CD11b+ dendritic cells (DC) from d1.5 MCMV-infected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.1(pos)


title: WT CD11b DC, steady-state, replicate 1

description:
Sample name: MDD_B16
WT spleen CD11b+ dendritic cells (DC) from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(neg), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD11c(high), CD8a(neg), CD45.1(pos)


title: WT NK, steady-state, replicate 1

description:
Sample name: MDD_C30
WT spleen natural killer (NK) cells from uninfected [CD45.1 WT / CD45.2 IFNAR-KO] mixed bone marow chimera mice, FACS sorted as: live, NKp46(pos), CD19(neg), TCRbeta(neg), 120G8(neg/low), CD45.1(pos)


title: US_BM_40_K014

status: Public on Sep 05 2012

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

description:
PBMC gene expression data
US_BM_40_K014.CEL

hyb_protocol: 25 ng/ul fragmented and labeled DNA target was hybridized according to the protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Images were processed using the Affymetrix Microarray Suite 5.0, cel files were normalized with RMA and further analyzed using Bioconductor software based on R language.

source_name: healthy control_peripheral blood

label_protocol: 100 ng Total RNA Labeling protocol, whole transcript sense target labeling assay

growth_protocol: RNA was extracted from whole blood of bacterial meningitis patients and healthy controls.

extract_protocol: Tempus blood extraction

treatment_protocol: Samples are from bactreial meningitis patients and healthy controls.

tag: sample group

value: healthy control

value: whole blood

tag: bacteria

tag: outcome

value: normal


title: US_BM_33_K009

description:
PBMC gene expression data
US_BM_33_K009.CEL


title: US_BM_21_K011

description:
PBMC gene expression data
US_BM_21_K011.CEL


title: US_BM_36_K020

description:
PBMC gene expression data
US_BM_36_K020.CEL


title: US_BM_14_K005

description:
PBMC gene expression data
US_BM_14_K005.CEL


title: US_BM_30_K018

description:
PBMC gene expression data
US_BM_30_K018.CEL


title: US_BM_38_K015

description:
PBMC gene expression data
US_BM_38_K015.CEL


title: US_BM_12_K004

description:
PBMC gene expression data
US_BM_12_K004.CEL


title: US_BM_31_K008

description:
PBMC gene expression data
US_BM_31_K008.CEL


title: US_BM_28_K007

description:
PBMC gene expression data
US_BM_28_K007.CEL


title: US_BM_17_K006

description:
PBMC gene expression data
US_BM_17_K006.CEL

value: good


title: US_BM_11_K010

description:
PBMC gene expression data
US_BM_11_K010.CEL


title: US_BM_39_K013

description:
PBMC gene expression data
US_BM_39_K013.CEL


title: US_BM_10_K012

description:
PBMC gene expression data
US_BM_10_K012.CEL


title: US_BM_07_K024

description:
PBMC gene expression data
US_BM_07_K024.CEL


title: US_BM_03_K027

description:
PBMC gene expression data
US_BM_03_K027.CEL


title: US_BM_06_K016

description:
PBMC gene expression data
US_BM_06_K016.CEL


title: US_BM_02_K003

description:
PBMC gene expression data
US_BM_02_K003.CEL


title: Primary_SMOOTHMUSCLE_HSkMC268_pUNK_208.561.1.1

status: Public on Sep 18 2012

city: La Jolla

first: Rathi

middle: D

last: Thiagarajan

address: 2880 Torrey Pines Scenic Drive

department: Reproductive Medicine

institute: UCSD

description: SAMPLE 18

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HD Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using IScan using standard recommended Illumina scanner setting

data_processing: Genome Studio software v2010.3

label: Cy5 and Cy3

source_name: Primary human skeletal smooth muscle cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: UNKNOWN

tag: passage number

value: Unknown

tag: loring pipeline sample id

value: primary human skeletal smooth muscle cells