title: ChIP-Seq analysis of H3K27ac in human rectal mucosa cells; DNA_Lib 1042

status: Public on Jul 18 2013

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1042
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14622
EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1112795_BI.Rectal_Mucosa.H3K27ac.29.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1042.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Rectal Mucosa H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Rectal Mucosa, Donor 29, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17251
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,768,755
FINDPEAKS_SCORE: 0.4492
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4813
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.997
IROC_PERCENTILE: 65
POISSON_SCORE: 0.522
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

ANALYSIS FILE NAME: GSM1112795_BI.Rectal_Mucosa.H3K27ac.29.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1042.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Rectal Mucosa, Donor 29, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17434
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: RM H3K27ac 29 42
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K27ac Donor 29 Library DNA_Lib 1042 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,768,755
FINDPEAKS_SCORE: 0.4492
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4813
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.997
IROC_PERCENTILE: 65
POISSON_SCORE: 0.522
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

source_name: Primary rectal mucosal tissue; DNA_Lib 1042

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample common name

value: Rectal Mucosa

tag: sra sample accession

value: surgery

value: normal mucosa

tag: disease

value: mucosa

value: white

value: Female

value: Primary Tissue

value: rectum

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac

value: Branson


title: WT_iPSC

status: Public on Sep 12 2013

type: RNA

city: Rehovot

first: Asaf

last: Zviran

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: MBD3+/+ mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming.

hyb_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.

data_processing: The data were analyzed with Matlab affyRMA command, with MoGene_1_0-st-v1.r3.cdf annotation file.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: WT iPSC

label_protocol: 250 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: N2B2715% KSR 2i/LIF mouse ESC media on mouse irradiated DR4 MEF cells.

extract_protocol: mRNA was extracted by TRIZOL reagent (Invitrogen) according to manufacturer's instructions.

treatment_protocol: Cells were washed with PBS and then harvested by trypsinization for RNA extraction.

tag: genotype/variation

value: MBD3+/+ transgenic for DOX inducible OSKM reprogramming

tag: cell type

value: Embryonic Fibroblast Cells (MEF)

tag: stage in reprogramming

value: iPSC


title: seq-Ab2621_H3K79me3_FEM2_AD_ChIP_Rep1

status: Public on Jul 26 2013

type: SRA

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: AB2621 H3K79me3:361576;target name: H3K79me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 tri methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2621;reference: http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab2621.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide tri-methylated at K79.;input DNA

library_source: genomic

data_processing: to be updated

molecule: genomic DNA

organism: Caenorhabditis elegans

growth_protocol: Worm_adult_growth_and_harvest_vHP2.  Synchronized cultures of worms were grown until gravid in 400 mL batches.  Gravid adults were isolated through sucrose floatation, and frozen into pellets in liquid nitrogen with EBS (250 mM HEPES (pH 7.5), 1180 mM NaCl, 480 mM KCl, 20 mM EDTA, 5 mM EGTA, sucrose (final 340 mM) and protease/phosphatase inhibitors.  The pellets were stored at -80°C.

extract_protocol:
Worm extract was made from adult worms.  Frozen worm popcorn was ground up in a mixer mill.  Samples were then fixed with 1% formaldehyde for 10 minutes. Chromatin was then sheared by sonication in the Bioruptor, and the soluble fraction was collected and stored at -80°C for future use.
Worm extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA.  Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay.
Worm_ChIP-seq_ DNA_Library_Preparation_vSS2. ChIP and 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated (concentrated T4 ligase) to annealed adaptors, size-selected, and amplified by PCR.Changes: Ligate O/N at 16C. Use adapters and primer cocktail from Illumina TruSeq kit. Use AMPure cleanup in the place of Qiagne cleanup. Use Pippin prep for size selection .
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

tag: strain

tag: developmental stage

value: Germline containing young adult

tag: genotype

tag: Sex

value: Hermaphrodite


title: EPN_319_2

status: Public on Aug 30 2013

city: Aurora

first: Lindsey

middle: M.

last: Hoffman

state: Colorado

address: 12800 East 19th Avenue

department: Pediatric Neuro-Oncology

country: USA

institute: University of Colorado Denver

description:
included_in_corresponding_manuscript:yes
Gene expression data from surgical tumor sample of ependymoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 17,664 genes.

label: biotin

organism: Homo sapiens

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

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: group

value: Recurrent

tag: tissue

value: brain tumor (ependymoma)


title: EPN_64_2


title: EPN_321_2


title: Affymetrix HG-U133 arrays of NIH Epigenomics Roadmap Cell Types; Primary rectal mucosal tissue; RNAPrp 26_632052

status: Public on Aug 07 2012

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Primary tissue from rectal mucosa was isolated from surgical samples; total RNA was isolated and subject to Affymetrix profiling
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13679
sample alias: 38

hyb_protocol: As recommended by Affymetrix

scan_protocol: As recommended by Affymetrix

data_processing: Processed data were not provided for this record

label_protocol: As recommended by Affymetrix

growth_protocol: Uncultured primary tissue

extract_protocol: Cells were lysed and RNA extracted using Qiagen Rneasy kit

treatment_protocol: untreated primary tissue

value: surgery

value: normal mucosa

value: mucosa

value: white

value: Female

value: Primary Tissue

value: rectum


title: orr_weaver_fat_body_rep2 extraction2_array1

status: Public on Jun 04 2012

type: genomic

hyb_protocol: The application of the isolated DNA samples to a specific set of 1 or more microarray slides, including the washing steps.

scan_protocol: This scanning protocol outputs raw images of intensity values resulting from the hybridization of the DNA sample to the microarray slide.  The raw tiffs are quantified and output in an Agilent text format.

data_processing: Normalization_and_smoothing_of_log2_ratios:DM:1 protocol. Two-color Agilent tiling arrays were processed by Bioconductor primarily with the Ringo package (Toedling et al., 2007, PMID: 17594472).  Briefly, each array was loess normalized and then probe log2 ratios were smoothed by running medians across windows of 10kb along the genome, requiring at least 3 probes within a window.

organism: Drosophila melanogaster

source_name: orr_weaver_fat_body_rep2 channel_1

label_protocol: Labeling of isolated DNA with cy5 or cy3

growth_protocol: Adult fat body:Newly hatched (0-24hours) female and male Oregon R flies from the modENCODE strain were dissected into an Eppendorf tube full of unsupplemented Grace?s media on ice.  Holding each fly by the thorax with forceps, the abdomen was opened with another pair of forceps, and the layer of fat cells permitted to stream into the tube.

extract_protocol: DNA isolation:All tissues were homogenized with a pestle in an Eppendorf  tube in 500ul SDS lysis buffer. 5ul RNAse was added to each sample and incubated for one hour at room temperature.5 ul proteinase K was added and samples were incubated at 50oC for two hours.The samples were phenol/chloroform extracted and ethanol precipitated.The pellets were washed 70% ethanol and air dried then dissolved in 1X NEB buffer 4.The DNA was digested with RsaII and AluI for two hours at 37oCLabeling was done according to the Invitrogen protocol.

value: Oregon-R Orr-Weaver(genotype :TBA outcross :TBA description :Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by :wt population )

value: Fatbody

value: cleavage stage

value: TBA

value: Unknown

source_name: orr_weaver_embryo_rep2 channel_2

growth_protocol: Oregon R (TO-W strain) embryos were collected from a population cage for one hour, dechorionated with 50% bleach, and washed three times in PBS with 0.1% triton.


title: orr_weaver_midgut_rep2 extraction2_array1

source_name: orr_weaver_midgut_rep2 channel_1

growth_protocol: Adult malpighian tubules and midguts:Females from the Oregon R modENCODE strain were fattened for two days on wet yeast.  Holding the fly by the thorax, the internal organs were released into unsupplemented Grace?s media by opening the bottom of the abdomen with another forcepts.  The malpighian tubules and midgut were dissected into separate tubes.

value: Midgut


title: orr_weaver_malpighian_tubule_rep2 extraction2_array1

value: Malpighian tubules


title: orr_weaver_fat_body_rep1 extraction1_array1

source_name: orr_weaver_fat_body_rep1 channel_1

source_name: orr_weaver_embryo_rep1 channel_2


title: orr_weaver_malpighian_tubule_rep1 extraction1_array1


title: GBM-B11

status: Public on Aug 25 2013

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description:
Gene expression data from surgical tumor sample of glioblastoma
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 21,050 genes.

source_name: brain tumor (glioblastoma)

extract_protocol: RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: disease state

value: brain tumor

value: glioblastoma


title: GBM-B12


title: GBM-B10


title: GBM-B56


title: GBM-B57


title: Procat mouse model, Stroma (CID) 5

status: Public on Jan 07 2014

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Mouse Genome arrays and rotating over night at 65 degC.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used. 'signal' a measure of the ratio of transcript abundance of the sample versus a universal RNA reference.

label: Alexa Fluor 647

source_name: Procat mouse model, prostate stroma

label_protocol: Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

growth_protocol: Generation and genotyping of transgenic mice has been previously described: JOCK1 (Freeman, Gangula, et al. 2003), Pro-Cat are assayed the same as Ubi-Cat mice (Shahi et al. 2012).

extract_protocol: Total RNA was isolated using the CapSure® Macro LCM caps (Applied Biosystems LCM0211) and amplified using Arcturus™ RiboAmp® PLUS (Applied Biosystems KIT0501. Amplified RNA was then labeled using the Invitrogen cDNA labeling system (L1015-06) and hybridized to the Agilent Whole Mouse Genome Oligo (4×44) Microarray (G4122) chip for analysis.

treatment_protocol: Mice were treated biweekly starting at 6 weeks of age by intraperitoneal injections of AP20187 (aka, a Chemical Inducer of Dimerization, or CID; Ariad Pharmaceuticals, Cambridge, MA) at 2 mg/kg in drug diluent (16.7% propanediol, 22.5% PEG400, 1.25% TWEEN 80). Note: JOCK1 mice data for 40 and 60 weeks were obtained from previous experiments where treatment began at 12 weeks of age.

tag: mouse model

value: Procat

value: Stroma

tag: treatment

value: CID at 2 mg/kg

label: Alexa Fluor 555

source_name: mouse, universal reference RNA

tag: sample type

value: Stratagene, Universal Mouse Reference RNA Catalog #740100


title: 2.WT_PS2_(MoGene-1_0-st-v1)

status: Public on Jan 04 2013

city: Cincinnati

first: Satoshi

last: Namekawa

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 2.5 micrograms of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 7% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 1 minute. Fill the probe array with 80 microliters of hybridization cocktail. Incubate at 45C for 17 hours in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007. All solutions for the Fluidics Stations including the Stain and Antibody solutions are made by Affymetrix and contained in the Genechip Hybridization Wash and Stain Kit.

scan_protocol: The Genechip 1.0 ST arrays are scanned using the Affymetrix GeneChip Scanner 3000 7G. The Scanning software is Affymetrix Genechip Command Console version 3.2.

data_processing: Expression console software (v.1.1): RMA algorism

source_name: pachytene_wild type

label_protocol: The Ambion(r) WT Expression Kit (Life Technologies) combined with the GeneChip(r) WT Terminal Labeling Kit (Affymetrix), is used to create biotin - labeled sense -strand cDNA targets for hybridization to the Gene 1.0 ST Arrays.

extract_protocol: total RNAs were purified pachytene spermatocytes or round spermatids.

tag: strain background

value: wild type

tag: tissue type

value: pachytene spermatocytes


title: GBM-B17


title: 3.MT_PS1_(MoGene-1_0-st-v1)


title: HNSCC_primary_6346676

status: Public on Oct 10 2012

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Background subtracted data for the Cy5 (reference) and Cy3 (sample) channel were obtained using Agilent Feature Extraction software (version 9.5) based on MedianSignal calls

label_protocol: Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf]  Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0  Last Updated: 2/2006 Number of Pages: 70

extract_protocol:
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
Sample_reference_protocol:  A reference sample was made by processing of the Universal Human Reference cell line (Stratagene) similarly as the test samples.

tag: gender

value: male

value: head-neck

tag: tumor type

value: HNSCC

tag: age

tag: location

value: oropharynx

tag: ct

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade

tag: hpv

source_name: UHR

value: Stratagene Universal human reference cell line (UHR)


title: DISN147_H4K20ME1_001_N2_EEMB extraction2_array1 channel_1

status: Public on Apr 24 2012

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: DISN147 H4K20me1:001;target name: H4K20me1;host: Mouse;antigen: H4K20me1;clonal: Monoclonal;purified: Crude;company: Other;catalog: SN-147;short description: A mouse monoclonal antibody to H4K20me1 obtained from Diagenode (Cat# SN-147 lot #001). Used for ChIP.;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing: ChIP-chip normalization standard MA2C:JL:2 protocol. ChIP-chip_normalization_standard_MA2C_v2. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means that the INPUT or IP values for any probes which have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In a single experiment, median within the sliding window defined by 2x bandwidth parameter is assigned as MA2C score at the center of each probe. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by 2x bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS190

label: Cy3 dye

growth_protocol: Worm_embryo_growth_and_harvest_vSS4. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.

tag: strain

tag: developmental stage

value: Early Embryo

tag: genotype

tag: Sex

value: mixed Male and Hermaphrodite population

label: Cy5 dye


title: JL00001_DPY27_N2_EEMB extraction2_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: JL00001 DPY27;target name: DPY-27;host: Mouse;antigen: 1-409;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: JL00001 DPY27;reference: PMID: 17293863;short description: *  recombinant proteins were cloned and expressed with Novagen's Pet30-EkLIC system
* rabbit polyclonal antibodies were produced at Covance Immunology Services
* DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.;

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.


title: SDQ2357_AMA1_N2_MXEMB extraction3_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ2357-AMA1;target name: AMA-1;host: Rabbit;antigen: DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2357;short description: An affinity purified rabbit polyclonal antibody to AMA-1 obtained from SDI (AMA1-Q2357);

scan_protocol: ChIP-chip_scanning_nimblegen_v2. Array scanning and raw data extraction were performed according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software v2.5 according to the NimbleScan User?s Guide.

data_processing: ChIP-chip_normalization_standard_MA2C:JL:1 protocol. ChIP-chip_normalization_standard_MA2C_v1. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means the INPUT or IP values for any probes who have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS190

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol:
Worm_embryo_extraction_v1. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 7 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

value: Mixed Embryo


title: DISN147_H4K20ME1_001_N2_EEMB extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: DISN147 H4K20me1:001;target name: H4K20me1;host: Mouse;antigen: H4K20me1;clonal: Monoclonal;purified: Crude;company: Other;catalog: SN-147;short description: A mouse monoclonal antibody to H4K20me1 obtained from Diagenode (Cat# SN-147 lot #001). Used for ChIP.;
channel ch2 is input DNA;

growth_protocol: Worm_embryo_growth_and_harvest_vSS5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.


title: 5.WT_RS1_(MoGene-1_0-st-v1)

source_name: round spermatids_wild type

tag: genotype/variation

value: round spermatids


title: JL00001_DPY27_N2_EEMB extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JL00001 DPY27;target name: DPY-27;host: Mouse;antigen: 1-409;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: JL00001 DPY27;reference: PMID: 17293863;short description: *  recombinant proteins were cloned and expressed with Novagen's Pet30-EkLIC system
* rabbit polyclonal antibodies were produced at Covance Immunology Services
* DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.;
channel ch2 is input DNA;


title: HK00001_H3K36ME3_13C9_N2_YA_s7 extraction1_array1 channel_1

status: Public on Apr 23 2012

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura. Used for ChIP. Alternative name: CMA333;

growth_protocol: Worm_growth_and_harvest_vVR1. Worms were grown to the desired stage and cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos or worms were then washed twice with M9 Buffer, once with 100mM Tris-HCl pH 7.5  and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol:
Worm_extraction_vVR1.Embryos or worms were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was sonicated 15 times on ice at the following settings: 10 sec; 40% power output. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4?C and taking the supernatant.  Protein concentration was determined, and extracts were aliquoted and stored at -80?C.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.

value: Germline containing young adult

value: Hermaphrodite


title: SDQ3517_ZFP1_N2_MXEMB extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ3517 ZFP1;target name: ZFP-1;host: Rabbit;antigen: EGEWFCAKCTKASAMMPGSINEATFCCQLCPFDYGALKKTDRNGWAHVICALYIPEVRFGNVHSMEPVILNDVPTDKFNKLCYICNEERPNDAKKGACMS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3517 ZFP1;short description: An affinity purified rabbit polyclonal antibody to ZFP-1 obtained from Strategic Diagnostics Inc. (SDI). Raised against amino acids 46-145 of WP:CE25003.;
channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

data_processing: ChIP-chip normalization standard MA2C:JL:1 protocol. ChIP-chip_normalization_standard_MA2C_v1. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means the INPUT or IP values for any probes who have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS190

label: Cy5-monofunctional dye(1-)

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vMBJ1. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody (12.5 ug) was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 25 ul (packed volume) of protein A sepharose (GE Healthcare), and washed with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9. Amplification was carried out using 25-30 cycles.

label: Cy3-monofunctional dye(1-)


title: HNSCC_primary_6300028

hyb_protocol: Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0  Last Updated: 2/2006 Number of Pages: 70

value: female

tag: tissue

value: oral cavity

tag: sample type


title: SDQ3517_ZFP1_N2_MXEMB extraction2_array1 channel_1

label_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vMBJ5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody (10 ug) was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 25 ul packed volume of protein A sepharose (GE Healthcare), and washed with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9. Amplification was carried out using 25-30 cycles.


title: HNSCC_primary_3381597

tag: gender


title: 7.MT_RS1_(MoGene-1_0-st-v1)

source_name: round spermatids_RNF8-KO

tag: strain background

tag: tissue type


title: HNSCC_primary_7104117

tag: tumor type

tag: age

tag: location


title: orr_weaver_midgut_rep1 extraction1_array1

source_name: orr_weaver_midgut_rep1 channel_1

value: Oregon-R Orr-Weaver(genotype :TBA outcross :TBA description :Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by :wt population )

value: Midgut

value: cleavage stage

value: TBA

value: Female

value: Unknown


title: HNSCC_primary_6101764

value: head-neck

value: HNSCC

tag: ct

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt


title: HNSCC_primary_96331

value: oropharynx

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade

tag: hpv

value: Stratagene Universal human reference cell line (UHR)


title: HNSCC_primary_8089659


title: HNSCC_primary_8189540

value: male


title: 8.MT_RS2_(MoGene-1_0-st-v1)


title: HK00001_H3K36ME3_13C9_N2_L3_s5 extraction1_array1 channel_1

tag: strain

tag: developmental stage

value: L3 Larva

tag: genotype

value: wild type

value: mixed Male and Hermaphrodite population


title: HK00001_H3K36ME3_13C9_N2_L2_s4 extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura. Used for ChIP. Alternative name: CMA333;
channel ch2 is input DNA;

value: L2 Larva

tag: Sex


title: HK00001_H3K36ME3_13C9_N2_L4_s6 extraction1_array1 channel_1

value: L4 Larva


title: 4.MT_PS2_(MoGene-1_0-st-v1)

tag: genotype/variation

value: pachytene spermatocytes


title: HK00001_H3K36ME3_13C9_N2_EEMB_s1 extraction1_array1 channel_1

value: Early Embryo


title: WA30534819_H3K4ME3_N2_YA_s7 extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: WA305-34819 H3K4me3;target name: H3K4me3;host: Mouse;antigen: ART(me3-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA305-34819;short description: A protein G purified mouse monoclonal antibody to H3K3me3 (cat #305-34819) obtained from Waco. Used for ChIP.;
channel ch2 is input DNA;

value: Germline containing young adult

value: Hermaphrodite


title: HK00001_H3K36ME3_13C9_N2_LTEMB_s2 extraction1_array1 channel_1

value: Late Embryos


title: WA30534819_H3K4ME3_N2_L2_s4 extraction1_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: WA305-34819 H3K4me3;target name: H3K4me3;host: Mouse;antigen: ART(me3-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA305-34819;short description: A protein G purified mouse monoclonal antibody to H3K3me3 (cat #305-34819) obtained from Waco. Used for ChIP.;


title: WA30534819_H3K4ME3_N2_L1_s3 extraction1_array1 channel_1

value: L1 Larva


title: WA30534819_H3K4ME3_N2_L4_s6 extraction1_array1 channel_1


title: WA30534819_H3K4ME3_N2_EEMB_s1 extraction1_array1 channel_1


title: WA30534819_H3K4ME3_N2_LTEMB_s2 extraction1_array1 channel_1


title: 1.WT_PS1_(MoGene-1_0-st-v1)


title: 6.WT_RS2_(MoGene-1_0-st-v1)

value: round spermatids


title: ABAB817_8WG16_N2_LTEMB extraction3_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ABAB817 8WG16:346588;target name: RNA polII CTD domain unphosophorylated;host: Mouse;antigen: Native RNA Polymerase II purified from wheat germ;clonal: Monoclonal;purified: Size;company: Abcam;catalog: ab817;short description: A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) was used for ChIP.;
channel ch2 is input DNA;

growth_protocol: Worm_embryo_growth_and_harvest_vRG1. Synchronized worm cultures were grown at 20 °C in batches of 500 ml using 2.8-L Fernbach flasks shaking at 230 rpm. Gravid adults were separated from debris by sucrose floating. Embryos were isolated by bleaching and fixed after chitinase treatment with 1 % formaldehyde for 10 min on ice. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vRG1. Fixed embryos were suspended in 5 volumes of ChIP buffer (50 mM Hepes-KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) and sonicated on ice with a Branson sonifier microtip (30 % power setting for 3 min; 40 % power setting for 1 min).  Debris were pelleted at 10 000 g for 20 min and the supernatant was made 10 % in glycerol.  The extract was snap frozen in liquid nitrogen aliquots containing 3 mg of protein and stored at ? 80 °C.
Worm_chromatin_immunoprecipitation_vRG1. For each ChIP reaction, 3 mg of protein extract was diluted with ChIP buffer (50 mM Hepes KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) to 900 ?l.  Then 35 ?l 30 % sarcosyl (1 % final) and 20 ?l 5 % Na-deoxycholate (0.1 % final) were added.  50 ?l of the diluted extract were removed (input sample), mixed with Elution buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 250 mM NaCl, 1 % SDS) and processed as described for ChIP samples.  100 ?l antibody/bead suspension (5?g antibody pre-bound to 50 ?l Dynabeads, suspended in ChIP buffer) was added and the mixture and rotated over night at 4 °C.  Beads were washed with 2 × 1 ml FA Buffer (50 mM Hepes-KOH pH 7.6, 150 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 5 min each; with 1 ml FA-1000 buffer (50 mM Hepes-KOH pH 7.6, 1 M NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml FA-500 buffer (50 mM Hepes-KOH pH 7.6, 500 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% NP-40, 1% Na-deoxycholate) for 10 min; and briefly with 1 ml TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA).  Immunocomplexes were eluted with 50 ?l Elution buffer for 15 min at 67 °C.  Eluates were incubated over night at 65 °C to reverse cross-links, then treated with proteinase K (0.44 mg/ml) at 37 °C for 2 h.  Nucleic acids were recovered by phenol/chloroform extraction and ethanol precipitation.  After digestion with RNAse A (0.33 mg/ml) for 2h at 37 °C, DNA was purified using the Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_vRG1. ChIP and input DNA was blunt ended with T4 polymerase for 20 min at 12 °C and purified by phenol/chloroform extraction and EtOH precipitation. Annealed oligonucleotide linkers (oligo 1: gcggtgacccgggagatctgaattc; oligo 2: gaattcagatc) were ligated to the DNA fragments over night at 16 °C. The ligated DNA was precipitated with EtOH, disolved in 10 mM Tris-HCl pH 8, and amplified with a Taq/Pfu polymerase mix using oligo 1. For a detailed protocol see http://www.modencode.org/.


title: ABAB817_8WG16_N2_LTEMB extraction1_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ABAB817 8WG16:346588;target name: RNA polII CTD domain unphosophorylated;host: Mouse;antigen: Native RNA Polymerase II purified from wheat germ;clonal: Monoclonal;purified: Size;company: Abcam;catalog: ab817;short description: A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) was used for ChIP.;


title: ABAB817_8WG16_N2_EEMB extraction3_array1 channel_1


title: ABAB817_8WG16_N2_LTEMB extraction2_array1 channel_1


title: DISN147_H4K20ME1_001_N2_L3 extraction2_array1 channel_1

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
Worm_LM-PCR_Amplification_for_ChIP-chip_vIL1. 1/3 of ChIP and 10ng of input are blunted (T4 polymerase), ligated (concentrated T4 ligase) to annealed linkers and amplified by PCR using longer oligonucleotide as a primer. Generally two rounds of amplification are used to get the amount needed for microarray. Amplified DNA is tested by q-PCR and DNA gel is run to ensure small size and lack of degradation.


title: ABAB817_8WG16_N2_EEMB extraction1_array1 channel_1


title: HK00001_H3K36ME3_13C9_N2_L1_s3 extraction1_array1 channel_1


title: SDQ2330_LIN15B_N2_LTEMB extraction2_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ2330-LIN15B;target name: LIN-15B;host: Rabbit;antigen: PMRAALRLPNSEQKSGAPSSINGKVQRDDFKLEPLDDFNGEPDYDNLIGAQRLMYSDNLNDASAEDAFARHRVTMEFQKRRACNRRCAVCGHLEIHERLK;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: 3861.00.02;short description: An affinity purified rabbit polyclonal antibody to LIN-15B obtained from SDI (SDQ2330-LIN15B).;

growth_protocol: Worm_embryo_growth_and_harvest_vSS7. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Embryos were incubated for 3.5 hours in M9 then frozen in liquid nitrogen.

extract_protocol:
Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later,washed pellets are resuspended in FA buffer and subjected to sonication in a DiagenodeBioruptor (40 pulses of 30 seconds with 1 minute rests in between at full power). Extractsare then spun down and the soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.


title: HNSCC_primary_1273330

tag: gender

tag: tissue

value: head-neck

tag: sample type


title: SDQ2330_LIN15B_N2_LTEMB extraction1_array1 channel_1


title: ABAB817_8WG16_N2_EEMB extraction2_array1 channel_1


title: SDQ2324_HPL2_N2_LTEMB extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ2324-HPL2;target name: HPL-2;host: Rabbit;antigen: EDPKDNVFMVEKVLDKRTGKAGRDEFLIQWQGFPESDSSWEPRENLQCVEMLDEFEREFSKREKPIRKRHSQKPEPSEDQADPEEDKDEKKETNQNDKFS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: 3863.00.02;short description: An affinity purified rabbit polyclonal antibody to HPL-2 obtained from SDI (HPL2-Q2324);
channel ch2 is input DNA;


title: V6.5 ESC Utx WT

status: Public on May 30 2012

first: Noa

last: Novershtern

address: Weizmann Institute

description: Gene expression data of the indicated cell line

hyb_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

data_processing: The data were analyzed with Affy Expression Console software, using RMA method. Probes were further filtered to include only probes that have at least one call > 6 (in log2-scale)

source_name: V6.5 ESC Utx +/Y

growth_protocol: N2B27 2i/LIF mouse ESC media

extract_protocol: mRNA was extracted byTRIZOL reagent (invitogene) according to manufacturer's instructions

treatment_protocol: Cells were washed with PBS and then harvested by trypsinization for RNA extraction

tag: cell type

value: Mouse Embryonic Stem Cell (ESC)

value: UTX+/Y (WT)


title: SDQ2324_HPL2_N2_LTEMB extraction2_array1 channel_1


title: DISN147_H4K20ME1_001_N2_L3 extraction1_array1 channel_1


title: MP07030_H3K4ME2DAM1570816_N2_EEMB extraction2_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MP07030 H3K4me2:DAM157816;target name: H3K4me2;host: Rabbit;antigen: KLH conjugated synthetic peptide (ARTME2KQTAR-GC) corresponding to amino acis 1-8 of human histone H3;clonal: Polyclonal;purified: Crude;company: Upstate/Millipore;catalog: 07-030;short description: Rabbit serum to H3K4me2 from Millipore (07-030 lot # DAM1570816). Used for ChIP.;
channel ch2 is input DNA;


title: SDQ2357_AMA1_N2_MXEMB extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ2357-AMA1;target name: AMA-1;host: Rabbit;antigen: DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2357;short description: An affinity purified rabbit polyclonal antibody to AMA-1 obtained from SDI (AMA1-Q2357);
channel ch2 is input DNA;

value: Mixed Embryo


title: SDQ2357_AMA1_N2_MXEMB extraction2_array1 channel_1


title: MP07030_H3K4ME2DAM1570816_N2_EEMB extraction1_array1 channel_1

growth_protocol: Worm_embryo_growth_and_harvest_vSS3. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85 % formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.


title: TJ00001_H3K27ME18835_N2_EEMB extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: TJ00001 H3K27me1:8835;target name: H3K27me1;host: Rabbit;antigen: peptide including monomethyl-lysine 27 of histone H3;clonal: Polyclonal;purified: Crude;company: Lab;catalog: TJ00001;short description: Rabbit serum to H3K27me1 (rabbit 8835) obtained from Thomas Jenuwein. Used for ChIP.;
channel ch2 is input DNA;


title: WA30834809_H3K4ME2_N2_EEMB extraction2_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: WA308-34809 H3K4me2;target name: H3K4me2;host: Mouse;antigen: ART(me2-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA308-34809;short description: A protein G purified mouse monoclonal antibody to H3K4me2 (cat #308-34809) obtained from Waco. Used for ChIP.;
channel ch2 is input DNA;


title: TJ00001_H3K27ME18835_N2_EEMB extraction2_array1 channel_1


title: WA30834809_H3K4ME2_N2_EEMB extraction1_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: WA308-34809 H3K4me2;target name: H3K4me2;host: Mouse;antigen: ART(me2-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA308-34809;short description: A protein G purified mouse monoclonal antibody to H3K4me2 (cat #308-34809) obtained from Waco. Used for ChIP.;


title: SDQ4129_Y39G10AR18_N2_MXEMB extraction2_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: SDQ4129 Y39G10AR18;target name: Y39G10AR.18;host: Rabbit;antigen: TDVTELLAGSKQIVTQHKGLTNTVAQMENSVAVEEQKLRLIGGPDAVRYFDEAMSHPNVDIAKLTDLVITTRPPNFVAQILLPDDSPTASIDSKVSPSSS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4129 Y39G10AR18;short description: An affinity purified rabbit polyclonal antibody to Y39G10AR.18 obtained from Strategic Diagnostics Inc. (SDIX). Raised against amino acids 763-862  of WP:CE38003.;
channel ch2 is input DNA;

extract_protocol:
Worm_embryo_extraction_v3. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vMBJ5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody (10 ug) was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 25 ul packed volume of protein A sepharose (GE Healthcare), and washed with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9. Amplification was carried out using 25-30 cycles.


title: ChIP-Seq analysis of H3K4me1; rectal sm musc cls; Lib:XZ:20100827:10--ChIP:XZ:20100824:10:rectal smooth muscle:H3K4Me1

status: Public on Mar 31 2011

description:
sample_term_id: NTR_0001404
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100827:10--ChIP:XZ:20100824:10:rectal smooth muscle:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5705
EDACC Genboree Sample Page:

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669964_BI.Rectal_Smooth_Muscle.H3K4me1.30.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:10--ChIP:XZ:20100824:10:rectal smooth muscle:H3K4Me1-Lib:XZ:20100423:26--ChIP:XZ:70100407:15:rectal mucosa:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Rectal Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Rectal Mucosa, Donor 30 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6560
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.1086
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.2008
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.935
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3341
POISSON_PERCENTILE: 7

**********************************************************************

ANALYSIS FILE NAME: GSM669964_BI.Rectal_Smooth_Muscle.H3K4me1.30.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:10--ChIP:XZ:20100824:10:rectal smooth muscle:H3K4Me1-Lib:XZ:20100423:26--ChIP:XZ:70100407:15:rectal mucosa:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Rectal Mucosa, Donor 30 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6770
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: RM H3K4me1 30
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K4me1 Donor 30 Library Lib:XZ:20100827:10--ChIP:XZ:20100824:10:rectal smooth muscle:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.1086
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.2008
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.935
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3341
POISSON_PERCENTILE: 7

**********************************************************************

source_name: Primary rectal smooth muscle tissue; Lib:XZ:20100827:10--ChIP:XZ:20100824:10:rectal smooth muscle:H3K4Me1

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Rectal Smooth Muscle

value: surgery

value: normal smooth muscle

tag: molecule

value: genomic DNA

tag: disease

value: smooth muscle

value: white

value: Female

value: Primary Tissue

value: rectum

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: seq-NA_N2_MXemb_5_EE6 [input DNA]

status: Public on May 02 2011

city: Chapel Hill

first: Tristan

last: De Buysscher

state: NC

address: CB# 3280, Coker Hall

department: Biology

institute: University of North Carolina at Chapel Hill

description:
C. elegans N2 L3 input control.

Input lanes for ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus.

Contributors: Jason Lieb, Morten Jensen.

data_processing:
BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/. It runs as DEFAULT for both bwa aln and bwa samse.
Processed data file build: ce6

source_name: Control sample from mixed embryo N2 worms, whole body

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: Libraries were prepared according to Illumina's instructions for "Preparing Samples for ChIP Sequencing of DNA", with some variation. DNA was end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 DNA polymerase.  A's were then added to the 3' ends of the fragments using Kelow fragment (3'  5' exo minus). Paired-end adapters were then ligated onto the ends of the fragments.  DNA library was size selected by gel purification, fragments of 250-500 bp were band isolated from an agarose gel. DNA was PCR amplified for 18 cycles. The Bioanalyzer was used to verify fragment purification and quantify DNA.

treatment_protocol: Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.

value: whole body

tag: Stage

value: mixed stages


title: AB2886_H3K79ME1_361912_N2_L3 extraction1_array1 channel_1

status: Public on Mar 09 2011

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: AB2886 H3K79me1:361912;target name: H3K79me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 mono methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2886;reference: http://www.abcam.com/histone-h3-mono-methyl-k79-antibody-chip-grade-ab2886.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide mono-methylated at K79.;

data_processing: ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS190

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vMBJ6. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody (3 ug) was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9. Amplification was carried out using 25-30 cycles.

value: L3 Larva

value: wild type

value: mixed Male and Hermaphrodite population

tag: Strain

tag: Developmental Stage

tag: Genotype


title: DISN147_H4K20ME1001_N2_LTEMB extraction2_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: DISN147 H4K20me1:001;target name: H4K20me1;host: Mouse;antigen: H4K20me1;clonal: Monoclonal;purified: Crude;company: Other;catalog: SN-147;short description: A mouse monoclonal antibody to H4K20me1 obtained from Diagenode (Cat# SN-147 lot #001). Used for ChIP.;

tag: strain

value: Late Embryos

value: Hermaphrodite


title: AB3594_H3K79ME2346021_N2_MXEMB extraction2_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: AB3594 H3K79me2:346021;target name: H3K79me2;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 di methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab3594;reference: http://www.abcam.com/Histone-H3-di-methyl-K79-antibody-ChIP-Grade-ab3594.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide di-methylated at K79.;
channel ch2 is input DNA;

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vMBJ6. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody (3 ug) was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9. Amplification was carried out using 25-30 cycles.

tag: developmental stage

value: Mixed Embryo


title: AB3594_H3K79ME2346021_N2_MXEMB extraction1_array1 channel_1

tag: genotype


title: AB2621_H3K79ME3361576_N2_MXEMB extraction2_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: AB2621 H3K79me3:361576;target name: H3K79me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 tri methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2621;reference: http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab2621.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide tri-methylated at K79.;

tag: Sex


title: DISN147_H4K20ME1001_N2_LTEMB extraction1_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: DISN147 H4K20me1:001;target name: H4K20me1;host: Mouse;antigen: H4K20me1;clonal: Monoclonal;purified: Crude;company: Other;catalog: SN-147;short description: A mouse monoclonal antibody to H4K20me1 obtained from Diagenode (Cat# SN-147 lot #001). Used for ChIP.;
channel ch2 is input DNA;


title: AB2621_H3K79ME3361576_N2_MXEMB extraction1_array1 channel_1


title: WA30534819_H3K4ME3_N2_L3_s5 extraction1_array1

status: Public on Jul 19 2011

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: WA305-34819 H3K4me3;target name: H3K4me3;host: Mouse;antigen: ART(me3-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA305-34819;short description: A protein G purified mouse monoclonal antibody to H3K3me3 (cat #305-34819) obtained from Waco. Used for ChIP.;
channel ch2 is input DNA;


title: Hyb3 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JL00006 ZFP1;target name: ZFP-1;host: Rabbit;antigen: ISQNGTSSTS QSNRLNLPSF MEQLLERQWD QGSSLLMANA HFDVAQLLSC LFQLKSENFR LEENLSGLRK RRDHLFALNS RLAEVNTLDV SKRQRSDGLL LQQQIAHHLD PTSIVPKAEV HKQEPLSAPT SVPLPANHSS SLFEDIKAPK ATYSRKTPSN IPLTVPLSTA ATALTTTTAA SSGAPVNSNI QNHRATPSTA GAPMAATPIM TAVTSANELA ALSPERAQAL LNMYRMPLDA NVAAQLSMIT NFPGQVNPSL FSRLLAVNMM NGGLQPNGQP LSALPPPTSA TPNGK; clonal: Polyclonal;purified: Affinity;company: Covance;catalog: Jason Lieb lab;short description: A rabbit polyclonal antibody raised against amino acids 573-867 of AAK26137/WP:CE25003/F54F2.2a. Antibody was affinity purified against the same region of ZFP-1 as used for immunization.;
channel ch2 is input DNA;

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vMBJ9. 4.4 mg extract was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was pre-bound to protein A-sepharose beads (GE Healthcare) and added to each IP sample and incubated for 1 hr at 4oC. Beads were then washed with 1 mL of each of the following solutions: Twice with FA (50 mM HEPES/KOH, pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl), FA Buffer with 1 M NaCl, FA Buffer with 500 mM NaCl, ChIP Wash Buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and twice with TE (10 mM Tris-HCl, pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 uL elution buffer for 15 minutes at 65oC. Samples were treated with proteinase K at 55oC for 1-2 hrs then transfer to 65oC overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9. Amplification was carried out using 25-30 cycles.


title: Hyb1 extraction1_array1

growth_protocol: Worm_embryo_growth_and_harvest_v3. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.


title: SDQ4129_Y39G10AR18_N2_MXEMB extraction1_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ4129 Y39G10AR18;target name: Y39G10AR.18;host: Rabbit;antigen: TDVTELLAGSKQIVTQHKGLTNTVAQMENSVAVEEQKLRLIGGPDAVRYFDEAMSHPNVDIAKLTDLVITTRPPNFVAQILLPDDSPTASIDSKVSPSSS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4129 Y39G10AR18;short description: An affinity purified rabbit polyclonal antibody to Y39G10AR.18 obtained from Strategic Diagnostics Inc. (SDIX). Raised against amino acids 763-862  of WP:CE38003.;


title: Hyb2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: JL00006 ZFP1;target name: ZFP-1;host: Rabbit;antigen: ISQNGTSSTS QSNRLNLPSF MEQLLERQWD QGSSLLMANA HFDVAQLLSC LFQLKSENFR LEENLSGLRK RRDHLFALNS RLAEVNTLDV SKRQRSDGLL LQQQIAHHLD PTSIVPKAEV HKQEPLSAPT SVPLPANHSS SLFEDIKAPK ATYSRKTPSN IPLTVPLSTA ATALTTTTAA SSGAPVNSNI QNHRATPSTA GAPMAATPIM TAVTSANELA ALSPERAQAL LNMYRMPLDA NVAAQLSMIT NFPGQVNPSL FSRLLAVNMM NGGLQPNQPL SALPPPTSAT PNGK; clonal: Polyclonal;purified: Affinity;company: Covance;catalog: Jason Lieb lab;short description: A rabbit polyclonal antibody raised against amino acids 573-867 of AAK26137/WP:CE25003/F54F2.2a. Antibody was affinity purified against the same region of ZFP-1 as used for immunization.;

growth_protocol: Worm_embryo_growth_and_harvest_v1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C.

extract_protocol:
Worm_embryo_extraction_v1. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 7 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vMBJ1. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody (12.5 ug) was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 25 ul (packed volume) of protein A sepharose (GE Healthcare), and washed with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9. Amplification was carried out using 25-30 cycles.


title: V19-OSKM MEF Utx WT + DOX

description: Gene expression data of the indicated cell line

source_name: V19-OSKM MEF Utx +/Y (++ DOX)

value: Mouse Embryonic Fibroblast Cells (MEFs)

tag: genotype/variation

value: UTX+/Y (WT)

tag: dox induction

value: yes


title: AB2621_H3K79ME3_361576_N2_L3 extraction2_array1 channel_1

status: Public on Jan 17 2011

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: AB2621 H3K79me3:361576;target name: H3K79me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 tri methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2621;reference: http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab2621.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide tri-methylated at K79.;
channel ch2 is input DNA;

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
Worm_LM-PCR_Amplification_for_ChIP-chip_vIL1. 1/3 of ChIP and 10ng of input are blunted (T4 polymerase), ligated (concentrated T4 ligase) to annealed linkers and amplified by PCR using longer oligonucleotide as a primer. Generally two rounds of amplification are used to get the amount needed for microarray. Amplified DNA is tested by q-PCR and DNA gel is run to ensure small size and lack of degradation.


title: HTH_Haltere

status: Public on Jan 21 2011

city: Duluth

first: Matthew

last: Slattery

state: MINNESOTA

address: 1035 University Drive, SMed 219

institute: University of Minnesota Medical School

description: Hth haltere disc ChIP, replicates 1-3

hyb_protocol: Hybridization Cocktail (for 1 reaction): DNA (around 60 ul); Control Oligo B2 (3.3 ul); 2X Hybridization Buffer (110 ul); DMSO (15.4 ul); Water (31.3 ul), for a total of 220 ul volume per sample.  Boil 5 min at 99 C Cool to room temperature.  Hybridizations are done in the core facility as per the Affy protocol.

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing:
ChIP-chip data were generated using Affymetrix Drosophila tiling array 2.0 and are subjected to the analysis using TAS (Tiling Analysis Software, Affymetrix) and MAT (model based analysis of tiling arrays; Johnson et al, 2006). In MAT, all Control and IP samples corresponding to the same experiment are analyzed together.  We specified the MAT parameters Bandwidth, MaxGap and Minprobe parameters to be 200, 100 and 10 respectively. We used non-redundant dm3 BPMAP file and self generated Repeat Library files available for download at http://liulab.dfci.harvard.edu/MAT/Download.htm.  Peaks were called at 5% FDR.
Processed files descriptions: All .bar files were generated by Affymetrix TAS software.  signal.bar files contain log2(IP/Input) fold changes for each probe. pvalue.bar files contain p-value for each probe. Ubx_Haltere_MAT-FDR5.bed, Ubx_Leg_MAT-FDR5.bed, Hth_Haltere_MAT-FDR5.bed, Hth_Leg_MAT-FDR5.bed contain peaks called by MAT software (Johnson et al, PNAS, 2006)  at 5% FDR.  Ubx_Haltere_TAS-Top5.bed, Ubx_Leg_TAS-Top5.bed, Hth_Haltere_TAS-Top5.bed, Hth_Leg_TAS-Top5.bed contain the top 5% of peaks, based on p-value, as calculated by TAS.

source_name: Haltere imaginal disc ChIP; yw strain; Hth antibody

label_protocol: ChIP and Input DNA amplified using Sigma Whole Genome Amplifcation kit (WGA4).  After amplification, labeling proceeds as follows: Use the Bioprime DNA labeling Kit from Invitrogen, 20 ul of DNA (around 300ng/ul of PCR-purified DNA) 20 ul of 2.5X Random Primers solution.  Boil at 95C for 5 min, return to ice.  Add 5ul of 10X dnTP+U and 3ul of water, flick mix, spin.  Add 2ul of Klenow.  Incubate 2.5 hours at 37C, then add 5ul of stop buffer.  Purify using PCR purification kit, elute in 30 ul of buffer.  Quantify the amount of DNA using the Nanodrop spectrophotometer, and use 7.5 ug of DNA for susequent reaction. Use the Affymetrix double-stranded DNAlabeling kit to label DNA.  Prepare labeling mix -- 10X cDNA fragmentation buffer UDG, 10 U/ul APE1, 100 U/ul Nuclease-free H2O up to 48ul.  Incubate 1 hour at 37 C.  Boil at 93C for 2 min, let stand on ice for at least 2 min.  Label the fragmented double-stranded DNA with 5X TdT buffer (12ul) TdT (2ul) 5mM DNA labeling reagent (1ul).  Add the 15ul Mix to the DNA samples.  Incubate 60 min at 37C, 10 min at 70C and at least 2min on ice.

growth_protocol: Wandering 3rd instar larvae were manually removed from Drosophila culture. Larvae were inverted in PBS to expose imaginal discs. Imaginal discs dissected off after fixation.

extract_protocol: Third instar larvae were dissected in PBS and fixed for 20 minutes at room temperature in 1.8% formaldehyde, 50mM HEPES, 1mM EDTA, 0.5mM EGTA, 100mM NaCl. After quenching (0.125M Glycine, 1xPBS, 0.01% Triton) the fixed tissue was washed first in Buffer A (10mM HEPES, 10mM EDTA, 0.5mM EGTA, 0.25% Triton, 1mM PMSF), then in Buffer B (10mM HEPES, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.01% Triton, 1mM PMSF), for 10 minutes at 4C.  Imaginal discs were then dissected off the cuticles in Buffer B.  Discs were sonicated in Buffer C (10mM HEPES, 1mM EDTA, 0.5mM EGTA, 1mM PMSF, plus complete protease inhibitor cocktail (Roche)) on ice/EtOH.  Soluble chromatin was transferred to new tubes after centrifugation.  Fresh chromatin, precleared with protein G sepharose beads (Roche), was incubated overnight at 4C with antibody in RIPA buffer (140mM NaCl, 10mM HEPES, 1mM EDTA, 1% Glycerol, 1% Triton X-100, 0.1% DOC, 1mM PMSF).  Antibody-chromatin complexes were pulled down with protein G sepharose beads for 3 hours at 4C.  Bound beads were washed 4-times in RIPA buffer (as above plus 0.1mg/mL ssDNA) and once in TE.  Chromatin was eluted twice in Elution Buffer (1% SDS, 0.1M NaHCO3).  20ug Proteinase K was added, and samples were incubated for 3 hours at 55C, then 65C overnight.  DNA was purified via phenol-chloroform extraction and ethanol precipitation.

value: yw

tag: tissue

value: haltere imaginal disc

tag: chip antibody

value: anti-Hth

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody catalog number

tag: chip antibody lot number

source_name: Haltere imaginal disc ChIP; yw strain [input DNA]


title: UBX_Haltere

description: Ubx haltere disc ChIP, replicates 1-3

source_name: Haltere imaginal disc ChIP; yw strain; Ubx antibody

value: anti-Ubx

tag: chip antibody provider

value: Kevin White lab


title: HTH_Leg

description: Hth leg disc ChIP, replicates 1-3

source_name: Leg (T3) imaginal disc ChIP; yw strain; Hth antibody

value: T3 leg imaginal disc

source_name: Leg (T3) imaginal disc ChIP; yw strain [input DNA]


title: AB3594_H3K79ME2_346021_N2_L3 extraction2_array1 channel_1


title: UP07448_H3K27ME124439_N2_EEMB extraction1_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: UP07448 H3K27me1:24439;target name: H3K27me1;host: Rabbit;antigen: peptide including monomethyl-lysine 27 of histone H3;clonal: Polyclonal;purified: Affinity;company: Upstate/Millipore;catalog: 07-448;short description: A rabbit polyclonal antibody to H3K27me1 obtained from Upstate (07-448 lot #24439). Used for ChIP.;

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.

value: Early Embryo


title: UP07448_H3K27ME124439_N2_EEMB extraction2_array1 channel_1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: UP07448 H3K27me1:24439;target name: H3K27me1;host: Rabbit;antigen: peptide including monomethyl-lysine 27 of histone H3;clonal: Polyclonal;purified: Affinity;company: Upstate/Millipore;catalog: 07-448;short description: A rabbit polyclonal antibody to H3K27me1 obtained from Upstate (07-448 lot #24439). Used for ChIP.;
channel ch2 is input DNA;


title: AB2886_H3K79ME1_361912_N2_L3 extraction2_array1 channel_1

value: L3 Larva


title: AB3594_H3K79ME2_346021_N2_L3 extraction1_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: AB3594 H3K79me2:346021;target name: H3K79me2;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 di methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab3594;reference: http://www.abcam.com/Histone-H3-di-methyl-K79-antibody-ChIP-Grade-ab3594.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide di-methylated at K79.;

value: wild type


title: UBX_Leg

description: Ubx leg disc ChIP, replicates 1-3

source_name: Leg (T3) imaginal disc ChIP; yw strain; Ubx antibody


title: AB2621_H3K79ME3_361576_N2_L3 extraction1_array1 channel_1

value: mixed Male and Hermaphrodite population