title: Brain_human_RE

status: Public on Apr 16 2010

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

description: RE Library.

data_processing:
Sequence reads were mapped to the human hg18 (March, 2006) genome sequence using the AB SOLiD mate-pair analysis pipeline.  Uniquely mapping DNAs were then filtered based on the existence of restriction sites on at least one end of the fragments.  The ratios of McrBC and RE fragments were normalized and fragments were overlapped with the locations of restriction sites in the genome.

The .qual files for the human brain RE library are not available. Quality value information was not used in the mapping algorithms used in the analysis.

source_name: Brain, RE library

growth_protocol: DNA was extracted from primary human brain (dorsolateral prefrontal cortex) tissues.

extract_protocol: Briefly, DNA was fractionated into methylated (RE) and unmethylated (McrBC) fractions using methylation-sensitive (AciI, BstUI,  HhaI, HpaII, HpyCh4IV) and -dependent (McrBC) enzymes, respectively.  After digestion, fragments were size-selected for everything 800bp and above. Mate-pair sequencing tags were isolated using AB’s mate-pair library protocol with slight modification. Libraries were prepared for sequencing by emulsion PCR and sequenced on an AB SOLiD sequencer per the manufacturer's instructions. For mapping purposes, size cutoffs from 0-15kb were set; 0 since some small fragments will comigrate with larger ones in the gel, and 15kb since very few fragments above that length survived the circularization process.

treatment_protocol: Untreated.

tag: tissue

value: brain

tag: methylation status

value: methylated


title: ChIP-Seq analysis of H3K27me3 in human pancreatic islets normal cells; 42LTMAAXX090725-1-S

status: Public on Apr 28 2010

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0000016
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-13149
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2245
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2244
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM537658_BI.Pancreatic_Islets.H3K27me3.pancreatic_islets_normal_3_27_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LTMAAXX090725-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of Pancreatic Islets Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.4742
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 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2062
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.2476
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.8866
IROC_PERCENTILE: 37
POISSON_SCORE: 0.4285
POISSON_PERCENTILE: 42

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

ANALYSIS FILE NAME: GSM537658_BI.Pancreatic_Islets.H3K27me3.pancreatic_islets_normal_3_27_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LTMAAXX090725-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.5016
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 2
BROWSER_TRACK_NAME: PI H3K27me3 27
BROWSER_TRACK_DESCRIPTION: BI Pancreatic Islets Histone H3K27me3 Donor pancreatic islets normal_3/27/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2062
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.2476
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.8866
IROC_PERCENTILE: 37
POISSON_SCORE: 0.4285
POISSON_PERCENTILE: 42

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

molecule: genomic DNA

organism: Homo sapiens

source_name: pancreatic islets from a normal donor; 42LTMAAXX090725-1-S

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

value: genomic DNA

tag: disease

value: Islet Cell Resource Center

value: Primary Cell

value: Pancreatic Islets

tag: markers

value: pancreatic islets normal_3/27/09

value: Male

value: not passaged

value: Histone H3K27me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Millipore


title: Exon arrays of Roadmap cell types; Fetal Heart primary tissue, day 101; DS12810-exon

status: Public on Oct 06 2010

type: RNA

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3494
sample alias: fHeart.H-22727d101
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2456

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

label: biotin

molecule: total RNA

label_protocol: A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.

growth_protocol: Followed vendor recommendations for growth protocol/media

extract_protocol: At cell harvest, a subset of cells was stored at -20 C in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: fetal heart

value: UW

value: fetal

value: 101 days

value: Unknown


title: ChIP-Seq analysis of H3K36me3 in human CD34 cells, 30EBJAAXX090206-7-S

status: Public on Jan 06 2010

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1618
Library name: Solexa-9988
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1619
****************
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: GSM486714_BI.CD34_Primary_Cells.H3K36me3.CD34_39811.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBJAAXX090206-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD34 Primary Cells, Donor CD34_39811 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.4744
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 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.3144
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.3251
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9627
IROC_PERCENTILE: 50
POISSON_SCORE: 0.595
POISSON_PERCENTILE: 72

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

ANALYSIS FILE NAME: GSM486714_BI.CD34_Primary_Cells.H3K36me3.CD34_39811.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBJAAXX090206-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD34 Primary Cells, Donor CD34_39811 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.5018
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 2
BROWSER_TRACK_NAME: CD34 H3K36me3 11
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells Histone H3K36me3 Donor CD34_39811 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.3144
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.3251
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9627
IROC_PERCENTILE: 50
POISSON_SCORE: 0.595
POISSON_PERCENTILE: 72

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

source_name: ChIP-Seq analysis ofH3K36me3 in human CD34 cells

value: genomic DNA

value: FHCRC

value: Primary Cell

value: CD34 Primary Cells

value: Histone H3K36me3

value: Abcam


title: ChIP_RNAPII_8WG16_KCl_b1

status: Public on Apr 15 2010

city: boston

first: jesse

middle: M

last: gray

address: 77 avenue louis pasteur, NRB 356

department: Genetics

institute: Harvard Medical School

description: ChIP

data_processing:
Corona lite read alignment to mm9; discard non-uniquely aligned reads; conversion of uniquely aligned reads (0-3 mismatches) into bigWig (.bw) file
For ChIP-Seq, the .bw file reflects extended 120bp fragments corresponding to each ChIP-Seq read
For RNA-Seq, the .bw files contain information only about the 5' most base of each read; there are separate bigWig files for + and - genomic strands
The .bedgraph files from which the .bw files were derived are also provided.

organism: Mus musculus

source_name: 7 DIV E16.5 mouse cortical neurons, before and after membrane depolarization induced by extracellular potassium

growth_protocol: 7 DIV E16.5 mouse cortical neurons grown in B27/NB on PO-coated plastic 15-cm plates

extract_protocol:
Whole Transcriptome sequencing (WT-Seq, RNA-Seq: sequencing of total RNA): WT-Seq was performed according to a protocol/kit now available from Life Technologies, with minor modifications that are included below.  Briefly, 5–10ug of RNA isolated from mouse cortical cultures was depleted of ribosomal RNAs using two rounds of Human/Mouse RiboMinus treatment (Life Technologies) with overnight ethanol precipitations for sample re-concentration.  The removal of ribosomal RNAs was confirmed on a Bioanalyzer Nano Chip (Agilent).  500–1000ng of riboRNA-depleted total RNA was fragmented with 10–18 minutes 37° RNAseIII treatment, and 10 minutes of RNAseIII inactivation at 65°.  Fragmentation was followed by size selection of ~50 to ~150bp fragments using the flashPAGE denaturing PAGE-fractionator (Life Technologies) and ethanol precipitation overnight.  The resulting RNA was directionally ligated, reverse-transcribed, and RNAseH treated. After trial PCR to assess library quality and quantity, 30ul cDNA was run on a native 6% PAGE gel.  The 90–120bp size window (corresponding to 50–80bp RNA insert size) was cut from the gel, shredded, and inserted directly into a 400ul PCR reaction using standard WT-Seq kit components and submitted to 11–15 cycles of PCR.  The PCR product was phenol-chloroform extracted, ethanol precipitated, and resuspended in 20ul WT-Seq gel loading buffer.  The resulting sample was run on a 6% native PAGE gel, and the 150–175bp size range (corresponding to 60–85bp) was cut from the gel, shredded, and extracted overnight in WT-Seq PAGE elution buffer.  The resulting library was filtered through 0.45um spin filters (Life Technologies) to remove gel pieces and ethanol precipitated. We note that WT-Seq can detect neither the 5'-most fragment from transcripts with 5'-modified ends (such as mRNA 5' 7-methyl-guanosine caps) nor the 3'-most fragment from transcripts with 3'-modified ends.  However, for transcripts long enough to produce multiple 50+ bp fragments, WT-Seq should detect the remaining fragments. Mouse cortical neuron WT-Seq data presented in this manuscript are from one specific biological replicate, but each result was confirmed in at least one additional replicate.
Chromatin immunoprecipitation-sequencing (ChIP-Seq): Forty million mouse cortical neurons cultured to in vitro day 7 were used for each ChIP-Seq library construction.  ChIP was performed as described2 using antibodies listed above.  The immuno-precipitated DNA fragments were repaired by the End-It DNA End Repair Kit (Epicentre Biotechnology) according to the manufacturer’s instructions.  The end-repaired ChIP DNA fragments were purified by MinElute Reaction Cleanup Kit (Qiagen) and eluted in 20 ul in EB buffer.  The resulting DNA fragments were ligated with P1 and P2 adaptors for SOLiD genome analyzer (adaptor sequences can be available upon request) for 20 minutes at room temperature using the Quick Ligase Kit (NEB), followed by purification using MinElute Reaction Cleanup Kit (Qiagen).  The purified, adaptor-ligated ChIP DNA fragments were subject to 6% native-PAGE for an in-gel PCR reaction.  A gel slice containing 175–200 bp adaptor-ligated ChIP DNA fragments (corresponding to 125–150bp genomic fragment sizes) was cut and shredded.  PCR Platinum Supermix (100–200 ul, Invitrogen), 50 pmoles of PCR primers (available upon request), 0.5 ul Taq DNA polymerase (NEB), and 0.15 ul Pfu Turbo DNA polymerase (Stratagene) were added into the shredded gel slice.  The adaptor-ligated ChIP DNA fragments were amplified by 15 cycles of in-Gel PCR.  After the PCR reaction, gel pieces were filtered out by 0.45 um filter spin column, and the amplified ChIP-Seq library was purified by MinElute PCR purification kit (Qiagen).  The library was purified by one more round of 6% PAGE.  A gel slice containing 200–250 bp PCR products (110–150bp fragment size) was cut and shredded, and the amplified library was extract out of the gel by passive elution in elution buffer (1.5M ammonium acetate in 1X TE).  Gel pieces were filtered out by filter spin column, and the resulting ChIP-Seq library was purified using the Qiaquick PCR purification kit (Qiagen).

treatment_protocol: 0, 1, 2, or 6 hours of 55mM KCl, with overnight quieting with TTX/APV

tag: protein immunoprecipitated

value: RNAPII

tag: antibody

value: 8WG16, Covance (MMS-126R)

tag: strain

tag: agent

value: KCL

tag: kcl treatment time (hours)

tag: developmental stage

tag: cell type

value: cortical neuron

tag: biological rep

tag: technical rep


title: ChIP-Seq analysis of H3K9me3 in human CD34 cells, 30EDEAAXX090127-5-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1592
Library name: Solexa-9772
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1593
****************
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: GSM486712_BI.CD34_Primary_Cells.H3K9me3.CD34_39811.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD34 Primary Cells, Donor CD34_39811 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.4825
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1514
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.2121
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.8202
IROC_PERCENTILE: 51
POISSON_SCORE: 0.4607
POISSON_PERCENTILE: 73

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

ANALYSIS FILE NAME: GSM486712_BI.CD34_Primary_Cells.H3K9me3.CD34_39811.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD34 Primary Cells, Donor CD34_39811 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.5099
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 2
BROWSER_TRACK_NAME: CD34 H3K9me3 11
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells Histone H3K9me3 Donor CD34_39811 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1514
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.2121
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.8202
IROC_PERCENTILE: 51
POISSON_SCORE: 0.4607
POISSON_PERCENTILE: 73

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

source_name: ChIP-Seq analysis ofH3K9me3 in human CD34 cells

value: Histone H3K9me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume


title: ChIP-Seq analysis of H3K9me3 in human CD34 cells, 30ELUAAXX090512-7-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1586
Library name: Solexa-11489
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1587
****************
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: GSM486710_BI.CD34_Primary_Cells.H3K9me3.CD34_39889.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30ELUAAXX090512-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD34 Primary Cells, Donor CD34_39889 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.4812
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.288
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.3378
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.943
IROC_PERCENTILE: 86
POISSON_SCORE: 0.4557
POISSON_PERCENTILE: 71

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

ANALYSIS FILE NAME: GSM486710_BI.CD34_Primary_Cells.H3K9me3.CD34_39889.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30ELUAAXX090512-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD34 Primary Cells, Donor CD34_39889 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.5086
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 2
BROWSER_TRACK_NAME: CD34 H3K9me3 89
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells Histone H3K9me3 Donor CD34_39889 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.288
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.3378
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.943
IROC_PERCENTILE: 86
POISSON_SCORE: 0.4557
POISSON_PERCENTILE: 71

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

value: Unknown


title: ChIP-Seq analysis of WCE in human CD34 cells, 30CAVAAXX081115-2-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1562
Library name: Solexa-8322/Solexa-8324
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1563
****************
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: GSM486702_BI.CD34_Primary_Cells.Input.CD34_39661.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-2-S-30CAVAAXX081115-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD34 Primary Cells, Donor CD34_39661 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.4642
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 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0148
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.0832
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.3079
IROC_PERCENTILE: 23
POISSON_SCORE: 0.1244
POISSON_PERCENTILE: 4

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

ANALYSIS FILE NAME: GSM486702_BI.CD34_Primary_Cells.Input.CD34_39661.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-2-S-30CAVAAXX081115-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD34 Primary Cells, Donor CD34_39661 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.4916
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 2
BROWSER_TRACK_NAME: CD34 Input 61
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells ChIP-Seq Input Donor CD34_39661 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0148
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.0832
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.3079
IROC_PERCENTILE: 23
POISSON_SCORE: 0.1244
POISSON_PERCENTILE: 4

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

value: genomic DNA

value: ChIP-Seq Input

value: Input

value: standard


title: ChIP-Seq analysis of H3K27me3 in human CD34 cells, 30EBYAAXX090127-6-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1574
Library name: Solexa-9766
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1575
****************
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: GSM486706_BI.CD34_Primary_Cells.H3K27me3.CD34_39804.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBYAAXX090127-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD34 Primary Cells, Donor CD34_39804 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.4745
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 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1212
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.214
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.8549
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4196
POISSON_PERCENTILE: 37

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

ANALYSIS FILE NAME: GSM486706_BI.CD34_Primary_Cells.H3K27me3.CD34_39804.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBYAAXX090127-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD34 Primary Cells, Donor CD34_39804 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.5019
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 2
BROWSER_TRACK_NAME: CD34 H3K27me3 04
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells Histone H3K27me3 Donor CD34_39804 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1212
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.214
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.8549
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4196
POISSON_PERCENTILE: 37

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

source_name: ChIP-Seq analysis ofH3K27me3 in human CD34 cells

value: FHCRC

value: Primary Cell

value: CD34 Primary Cells

value: Histone H3K27me3

value: Upstate


title: Exon arrays of Roadmap cell types; flow sorted CD34+ cells, mobilized; DS14129-exon

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3481
sample alias: RO 01517
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3100

value: FHCRC HEIMFELD

value: year 43

value: Male

value: Caucasian


title: Exon arrays of Roadmap cell types; Fetal Adrenal Gland primary tissue, day 96; DS12528-exon

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3497
sample alias: fAdrenal.H-22662d96
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2443

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: fetal adrenal

value: UW

value: fetal

value: 96 days


title: ChIP-Seq analysis of H3K36me3 in human CD34 cells, 30CAVAAXX081115-8-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1571
Library name: Solexa-8325
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1572
****************
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: GSM486705_BI.CD34_Primary_Cells.H3K36me3.CD34_39661.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD34 Primary Cells, Donor CD34_39661 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.4653
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 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.4371
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.3891
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.972
IROC_PERCENTILE: 56
POISSON_SCORE: 0.7062
POISSON_PERCENTILE: 93

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

ANALYSIS FILE NAME: GSM486705_BI.CD34_Primary_Cells.H3K36me3.CD34_39661.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD34 Primary Cells, Donor CD34_39661 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.4927
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 2
BROWSER_TRACK_NAME: CD34 H3K36me3 61
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells Histone H3K36me3 Donor CD34_39661 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.4371
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.3891
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.972
IROC_PERCENTILE: 56
POISSON_SCORE: 0.7062
POISSON_PERCENTILE: 93

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

value: genomic DNA

value: Unknown

value: Histone H3K36me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume


title: Exon arrays of Roadmap cell types; flow sorted CD34+ cells from cord blood; DS12771-exon

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3486
sample alias: RO 01480
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2407

value: FHCRC HEIMFELD

value: Primary Cell

value: CD34 Primary Cells

value: 27 years

value: Female


title: Exon arrays of Roadmap cell types; flow sorted CD34+ cells from cord blood; DS12774-exon

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3485
sample alias: RO 01492
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2412

value: 39 years

value: Male

value: Caucasian


title: Exon arrays of Roadmap cell types; Fetal Brain primary tissue, day 117; DS14464-exon

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3496
sample alias: fBrain.H-22911d117
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3143

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: fetal brain

value: UW

value: fetal

value: day 117


title: Exp8_3_2005091305high

status: Public on Dec 01 2007

type: genomic

city: Leuven

first: Joke

last: Allemeersch

address: Herestraat 49

country: Belgium

institute: VIB MicroArray Facility

description: Nine loop designs comapring 27 patients with mental retardation (MR) and multiple congenital anomalies (MCA).

hyb_protocol: The probe was placed on the slide under a glass cover slip (24x24 mm). The slides were incubated for 42-72 hours at 37 degrees Celsius  under humified conditions. Post hybridization washing was performed by soaking in 1xPBS for 10 minutes and followed by a stringency wash on 42 degrees Celsius for 30 minutes in 50% formamide 2x SSC solution and 10 minutes in 1x PBS at room temperature. To finalize, the slides were dried by centrifugation for at least 1 minute.  See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.

scan_protocol: A two colour scan was performed with an axon laser scanner GenePix 4000B (Molecular Devices, Union City, CA) at 532 nm and 635 nm using genepixpro 6.0 program.

data_processing: The median spot intensities were corrected with the local median background, and only those spots with a signal above background (i.e., the foreground intensity is larger than the local background intensity plus twice the local standard deviation of the background) were retained for the analysis.  The ratios of the Cy5 to the Cy3 intensities were computed for each target and base 2 log transformed.  The log ratios are normalized using a 2D spatial loess normalization, in which one applies a loess regression to fit the base 2 log-ratios (M-values) on the coordinates on the slide as predictor variables.

label_protocol: 150 ng of patient DNA was labeled by a random prime labeling system (BioPrime Array CGH Genomic Labeling System, Invitrogen) using Cy5-dCTPs (Amersham Biosciences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.

extract_protocol: Genomic DNA was isolated from blood lymphocytes of 27 individuals according to standard procedures.

tag: Normal individual

label_protocol: 150 ng of patient DNA was labeled by a random prime labeling system (BioPrime Array CGH Genomic Labeling System, Invitrogen) using Cy3-dCTPs (Amersham Biosciences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.


title: Exp9_3_2005101351a

tag: Patient with duplication on chromosome 21 and deletion on chromosome 21

tag: Patient with deletion of chromosome X


title: Exp9_2_2005101351b

tag: Patient with duplication on chromosome 7 and deletion on chromosome 7


title: Exp9_1_2005101359b


title: Exon arrays of Roadmap cell types; IMR90 Cell Line; DS11764-exon

status: Public on May 05 2010

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2589
sample alias: IMR90
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632

source_name: IMR90 Cell Line; DS11764-exon

value: ATCC

value: Cell Line

tag: line

tag: lineage

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Eagle's Minimum Essential Medium, Catalog No. 30-2003.

tag: Sex

tag: batch


title: Exp6_3_2005121311a

tag: Patient with deletion on chromosome 12


title: Exp1_2_2004112552

tag: Patient with deletion on chromosome 13, confirmed by karyotyping


title: Exp6_2_2005121310b

tag: Patient with deletion on chromosome 9


title: Exp7_3_2005092712low

description: Nine loop designs comparing 27 patients with mental retardation (MR) and multiple congenital anomalies (MCA).

tag: Patient with duplication on chromosome 5 and deletion on chromosome 18


title: Exp8_1_2005091304low

tag: Patient with duplication on chromosome 13 and deletion on chromosome 13


title: Exp4_3_2005121953a

tag: Patient with deletion on chromosome 4


title: Exp1_1_2004112551


title: Exp7_2_2005092713low


title: Exp5_3_2005121329a


title: LCL Concordant for Epilepsy twin pair 1 (CCE1.2)(TP22)

status: Public on Feb 28 2008

city: Brisbane

first: Nicholas

last: Matigian

state: Queensland

address: 170 Kessels Rd, Nathan

country: Australia

institute: National Adult Stem Cell Centre

hyb_protocol: Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.

data_processing: Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared

label: Biotin

source_name: Concordant for Epilepsy twin pair 1 (Affected patient of MZ twin pair CCE1)

growth_protocol: LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22  LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture.  RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions.  RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value.  All samples had an RIN of 9.9 or 10, which designates very high quality RNA

extract_protocol: LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software

tag: Sample ID

tag: Twin Pair ID

tag: Clinical Status

value: Childhood Absence Epilepsy + Febrile Seizures

tag: Age of Onset:-5

tag: Age at interview & blood sampling

tag: Current Age (2007):25

value: FEMALE

tag: Medication at blood sampling


title: BM-MSC culture rep 2

status: Public on Dec 15 2007

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

country: Germany

institute: Charité

description:
Gene expression data of human bone marrow derived mesenchymal stem cells.
BM-MSC of a male 72-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2 for 1 passage.

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database (www.bioretis.de).

source_name: bone marrow MSC in culture from normal donor 2

label_protocol: 2µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)

growth_protocol: Human BM cells obtained from iliac crest aspirates were amplified by cultivation in alpha-MEM with 10 % fetal calf serum (FCS), 1 ng/mL fibroblast growth factor 2 (FGF2), 20 µmol/L L-glutamine and 100 units/mL penicillin G

extract_protocol: RNA was collected using the RNeasy mini kit (Qiagen)

treatment_protocol: None.

tag: cell type

value: bone marrow-derived mesenchymal stem cells

tag: gender

value: male

tag: age

value: 72 years

tag: treatment


title: Exp8_2_2005091304high

tag: Normal individual


title: Exp5_2_2005121329b

tag: Patient with deletion on chromosome 12


title: Exp6_1_2005121310a

tag: Patient with deletion on chromosome 9


title: Exp1_3_2004112553


title: Exp7_1_2005092713high


title: Exp5_1_2005121328b


title: Exp4_2_2005121953b


title: BM-MSC culture rep 1

description:
Gene expression data of human bone marrow derived mesenchymal stem cells.
BM-MSC of a male 67-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2 for 1 passage.

source_name: bone marrow MSC in culture from normal donor 1

value: 67 years


title: Exon arrays of Roadmap cell types; flow sorted CD34+ cells from cord blood; DS12339-exon

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2587
sample alias: RO 01536
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2397

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

value: CD34 Primary Cells

tag: markers

value: 27 years

value: Female

value: Hispanic


title: Exon arrays of Roadmap cell types; flow sorted CD34+ cells from cord blood; DS12274-exon

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2586
sample alias: RO 01535
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1659

value: Unknown


title: Endosperm DNA methylation IP/total DNA (MGE_220242)

status: Public on Jun 12 2009

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Methylated endosperm DNA and endosperm gDNA (200-300 bp) were prepared for Illumina GA sequencing, labeled with Cy3 and Cy5, and hybridized to arrays

hyb_protocol: Standard NimbleGen hybridization protocol (http://www.nimblegen.com/products/chip/index.html) performed by the Fred Hutchinson Cancer Research Center Genomics Facility. Set MAUI hybridization unit to 42 deg C and allow time for the temperature to stabilize. Based on the A_260 measurement, combine 13 micrograms each of the Test and Reference Samples into a single 1.5 ml microcentrifuge tube. Protect tube from light during handling to prevent photobleaching of the light-sensitive Cy dyes. Dry the combined contents in a Speed-Vac on low heat. Resuspend the sample in 10.9microliter VWR water and vortex to completely dissolve the sample. Spin the tube down briefly to collect the contents in the bottom. Using the NimbleGen Array Reuse Kit, add the following to the resuspended sample: 19.5 microliter 2X Hybridization Buffer, 7.8 microliter Hybridization Component A, 0.4 microliter Cy3 CPK6 50mer Oligo (50nM), 0.4 microliter Cy5 CPK6 50mer Oligo (100nM). CPK6 oligos are included in the hybridization as controls that hybridize to alignment features on the NimbleGen arrays. They are required for proper extraction of array data from the scanned image. Mix the tube briefly then spin down to collect the contents in the bottom and place at 95 deg C for 5 minutes. Immediately transfer the tube to the MAUI 42 deg C sample block and hold at this temperature until you are are ready for sample loading. Place the MAUI Mixer SL Hybridization Chamber on the array using the provided assembly/disassembly jig and carefully follow MAUI setup instructions. Use the braying tool to remove all air bubbles from the adhesive gasket around the outside of the hybridization chamber. Put the array and hybridization chamber on the MAUI and allow 30 seconds for the chips to come up to temperature. Load the sample using the pipet supplied with the MAUI Station and following manufacturer instructions. During the loading, a small amount (3-7 microliter) of the sample may flow out of the outlet port. Confirm that there are no bubbles in the chamber. If there are, very gently massage any bubbles to either of the ends, away from the center of the array. Avoid applying too much pressure since this will force liquid out of the ports. Place the loaded array into one of the four MAUI bays and let equilibrate for 30 seconds. Wipe off any sample leakage at the ports with a Kim-Wipe, and adhere MAUI stickers to both ports. Close the bay clamp and select mix mode B. Hold down the mix button to start mixing. Confirm that the mixing is in progress before closing the cover. Hybridize the sample 16-20 hours. Prior to removing the array from the MAUI Hybridization Station, prepare the following solutions. You will need two 250ml dishes of Wash I, and one each for Wash II and Wash III. One dish for Wash I should be shallow and be wide enough to accomodate the array and mixer loaded in the MAUI assembly/dissassembly jig. The lid from a 1000 microliter pipet tip box works well. Also, the buffer in the first Wash I dish should be heated to 42 deg C to help soften the adhesive on the hybridization chamber; this will help prevent braking the array. Place the remaining three wash solutions in 300 microliter Tissue-Tek slide staining dishes. Wash I: 225 ml VWR Water, 25ml 10X Wash Buffer I, 25microliter 1M DTT. Wash II: 225ml VWR Water, 25ml 10X Wash Buffer II, 25microliter 1M DTT. Wash III: 225ml VWR Water, 25microliter 10X Wash Buffer III, 25microliter 1M DTT. Remove chip from MAUI Hybridization Station, load it back into the MAUI assembly/disassembly jig, and immerse in the shallow 250ml Wash I at 42 deg C. Peel the hybridization chamber off very slowly to prevent the slide from cracking. Do not let the surface of the slide dry out at any point during washing. While the chip is submerged, carefully peel off the mixer. Gently agitate the chip in Wash I for 10-15 seconds. Transfer the slide into a slide rack in the second dish of Wash I and incubate 2 minutes with agitation. Transfer to Wash II and incubate 1 minute with agitation. Rock the disk to move the wash over the tops of the arrays. Transfer to Wash III and incubate for 15 sec with agitation. Remove array and spin dry in array-drying unit for 1 minute. Store the dried array in a dark desiccator.

scan_protocol: Standard NimbleGen scan procedure (http://www.nimblegen.com/products/chip/index.html) performed by the Fred Hutchinson Cancer Research Center Genomics Facility. Axon Scanner (model 4000B). Turn on the power of the scanner. The switch is on the back right hand side. Launch GenePix Software 10 minutes before scanning to allow lasers to warm. Open the scanner door and open the side carriage. Place chip in carriage so that array is face down and barcode end is closest to you. Move the black lever on the left side of the carriage left until the array is lying flat in the carriage. Release the lever so that the arry is pushed over gently to the right side of the carriage and held firmly. Close the carriage (you should hear a click) and slide the scanner door shut. Open the hardware settings. Select the following settings for scanning: Wavelength (532=Cy3, 635=Cy5). Set the 532 laser PMT Gain to 650 and the 635 laser PMT Gain to 750. Power=100%. Pixel Size=5m. Lines to average=1. Focus position=0micrometer. Select Image/Ratio to view both channels simultaneously. Perform a preview scan by clicking on the fast-forward icon. Stop scan once the full arry is in view by pressing the stop icon. Switch to zoom mode by clicking on the array image and pressing Z. Click and drag the mouse on the area in which you want to zoom. Center the image of the entire array area within the viewing window. Under Tools on the left side of the screen, click the Scan Area icon. Click and drag to define a box that bounds the visibile array area. The box dimensions should be stretched to create a box just slightly larger than the array area. It is critical to include all of the corner probes within the scan image. Scan chip by clicking the play icon. While scanning, set the zoom level to view the whole image and adjust the brightness and contrast of the displayed image to eliminate visible saturation. Based on the appearance of the array features, adjust the PMT setting as appropriate. The features should be mostly yellow. If your features are mostly green, either decrease the 532 PMT or raise the 635 PMT. If the features are mostly red or orange, either raise the 532 PMT or decrease the 635 PMT. Zoom the view to a region scanned under the most recent PMT settings and click on the Histogram tab at the top of the left side of the screen to check global intensity of the features. On the top left side of the screen make sure you have the 532 and 635 wavelength boxes checked so both wavelength histograms are displayed. Make sure the Log Axis box is checked. You want the red and green curves to be as close as possible to one another. If the red curve is above the green, lower the red PMT setting or raise the green PMT setting. You want the curve to have 1e-5 normalized counts at the 65,000 intensity level (saturation). This means that you have about 1% of the features saturated. The position of the two curves on top of each other is more important than hitting the 1% saturation mark.  The histogram only graphs the area of the image that is viewable in the screen on the image tab. If the histogram is no longer changing then either the chip is done scanning or the area that you can see on the image screen has been scanned. After the PMT settings are properly adjusted, stop the current scan, do not save this image. Restart the scan under the new settings and wait until the scan has completed. Save the images. Make sure you save both the 532nm and 635nm images as separate single image tif files.

data_processing: Log base 2 ratios were bi-weight mean centered by NimbleGen, then converted to standard deviates.

organism: Arabidopsis thaliana

source_name: Methylated DNA isolated from endosperm total genomic DNA

label_protocol: Standard NimbleGen label protocol (http://www.nimblegen.com/products/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

extract_protocol:
embryo DNA isolated with 5-methylcytosine antibody IP and prepared for Illumina GA sequencing
Methods are described in Gehring et al (submitted)

tag: Ecotype

value: Columbia-glabrous Age:Torpedo-stage seeds Tissue:Endosperm

source_name: endosperm total genomic DNA

label_protocol: Standard NimbleGen labeling protocol.

extract_protocol:
total genomic DNA prepared for Illumina GA sequencing
Methods are described in Gehring et al (submitted)


title: Exp2_3_2005121948high


title: Exp2_1_2005121947low

tag: Patient with trisomy 18,  confirmed by karyotyping and FISH


title: dme-2 endosperm DNA methylation IP/total DNA (MGd_220241)

description: Methylated dme-2 endosperm DNA and dme-2 endosperm gDNA (200-300 bp) were prepared for Illumina GA sequencing, labeled with Cy3 and Cy5, and hybridized to arrays

source_name: Methylated DNA isolated from dme-2 endosperm total genomic DNA

extract_protocol:
dme-2 endosperm DNA isolated with 5-methylcytosine antibody IP and prepared for Illumina GA sequencing
Methods are described in Gehring et al (submitted)

value: Columbia-glabrous Mutant:dme-2 Age:Seeds arrested at heart stage Tissue:Endosperm

source_name: dme-2 endosperm total genomic DNA

label_protocol: Standard NimbleGen label protocol

extract_protocol:
Total genomic DNA prepared for Illumina GA sequencing
Methods are described in Gehring et al (submitted)


title: Exp2_2_2005121948low

tag: Patient with trisomy 18, confirmed by karyotyping and FISH


title: Exp4_1_2005121952b


title: Exp3_3_2005121312a

tag: Patient with duplication on chromosome 15

tag: Patient with duplication on chromosome 7


title: Embryo DNA methylation IP/total DNA (MGE_220227)

description: Methylated embryo DNA and embryo gDNA (200-300 bp) were prepared for Illumina GA sequencing, labeled with Cy3 and Cy5, and hybridized to arrays

source_name: Methylated DNA isolated from embryo total genomic DNA

label_protocol: Standard NimbleGen labeling protocol (http://www.nimblegen.com/products/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

extract_protocol:
Embryo DNA isolated by 5-methylcytosine antibody IP and prepared for Illumina GA sequencing
Methods are described in Gehring et al (submitted)

value: Columbia-glabrous Age:Torpedo-stage seeds Tissue:Embryo

source_name: Embryo total genomic DNA


title: BM-MSC culture rep 3

description:
Gene expression data of human bone marrow derived mesenchymal stem cells.
BM-MSC of a female 74-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2 for 1 passage.

source_name: bone marrow MSC in culture from normal donor 3

value: female

value: 74 years


title: Exp3_2_2005121312b

tag: Patient with deletion on chromosome 10


title: Exp3_1_2005121311b


title: H9 embryonic stem cells (leukocyte study)

status: Public on Nov 01 2007

city: Winston-Salem

first: Jennifer

middle: A

last: Hipp

state: NC

address: Medical Center Blvd

department: Institute for Regenerative Medicine

institute: Wake Forest School of Medicine

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr.

scan_protocol: Once the probe array has been hybridized, washed, and stained, it is scanned.

data_processing: The data were analyzed with Robust Multi-Chip Analysis (RMA).

source_name: H9 undifferentiated embryonic stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: see supplementary information Lu et.al, Nature Methods, 2007 Jun;4(6):501-9.

extract_protocol: Total RNA was extracted by Qiagen RNAeasy kiit and was performed according to the manufacturer's instructions.

tag: derived from H9


title: H1 blast cells - GFP (leukocyte study)

source_name: H1 blast cells - GFP

treatment_protocol: see supplementary information Lu et.al, Nature Methods, 2007 Jun;4(6):501-9.

tag: derived from H1-GFP labeled


title: H1 embryonic stem cells - GFP (leukocyte study)

source_name: H1 undifferentiated embryonic stem cells - GFP


title: S_25014370 (leukocyte study)

description: Data for Inflamation and Host Reponse to Injury, NIH Glue Grant, Study or Experiment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GCOS version 1.2.0

label: paper supplemental material "A Network-Based Analysis of Systemic Inflammation in Humans" at www.gluegrant.org

source_name: whole blood

label_protocol: not available

extract_protocol: not available

tag: Six healthy subjects at 0, 2, 6 hours post endotoxin administration


title: S_21437514 (leukocyte study)


title: S_27557812 (leukocyte study)


title: H9 embryoid bodies (leukocyte study)

source_name: H9 day3.5 embryoid bodies

tag: derived from H10


title: H1 blast cells - GFP (stromal study)


title: H1 embryoid bodies - GFP (stromal cell study)

source_name: H1 day3.5 embryoid bodies - GFP


title: H9 blast cells (stromal cell study)

source_name: H9 blast cells

tag: derived from H11


title: H9 embryonic stem cells (stromal cell study)


title: H1 embryonic stem cells - GFP (stromal cell study)


title: H9 blast cells (leukocyte study)


title: H9 embryoid bodies (stromal cell study)


title: S_31212545 (leukocyte study)


title: H1 embryoid bodies - GFP (endothelial study)


title: H1 blast cells - GFP (endothelial study)


title: S_11976839 (leukocyte study)


title: H9 embryoid bodies (endothelial study)


title: H1 embryoid bodies - GFP (leukocyte study)


title: S_3761772 (leukocyte study)


title: H1 embryonic stem cells - GFP (endothelial study)


title: H9 blast cells (endothelial study)


title: NB87 U133p2 (breast epithelial study)

description: RNA from bulk normal breast or normal breast organoid

hyb_protocol: was not provided

scan_protocol: was not provided

data_processing: GCRMA

label_protocol: was not provided

extract_protocol: was not provided


title: NB60 U133p2 (breast epithelial study)

tag: bulk normal breast or normal breast organoid


title: H9 embryonic stem cells (endothelial study)


title: NB64 U133p2 (breast epithelial study)


title: NB83 U133p2 (breast epithelial study)


title: NB58 U133p2 (breast epithelial study)


title: H9 embryoid bodies (breast epithelial study)


title: NB69 U133p2 (breast epithelial study)


title: NB42 U133p2 (breast epithelial study)


title: H9 embryonic stem cells (breast epithelial study)


title: H9 blast cells (breast epithelial study)


title: H1 embryoid bodies - GFP (breast epithelial study)


title: H1 embryonic stem cells - GFP (breast epithelial study)


title: H1 blast cells - GFP (breast epithelial study)


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-424 - mAdbID:68597

status: Public on Oct 25 2007

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: mAdb experiment ID: 68597

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42øC for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100øC for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42øC just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42øC in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: not provided

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

label_protocol: Cy5 Sample Labeling Protocol - generic

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

tag: Tissue

value: liver

tag: Disease state

value: HBV positive Hepatocellular Carcinoma (HCC)

tag: Individual

tag: Genotype/Genetic variation

value: EpCAM negative

source_name: 02-424B - Control

label_protocol: Cy3 Sample Labeling Protocol - generic

value: HBV-infected with chirrhosis


title: cord blood 18

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: Gene expression data from newborn cord blood

hyb_protocol: Following fragmentation, cRNA was hybridized on HGU 133 plus 2.0

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Robust multichip analysis

source_name: cord blood arsenic exposure level 0.2

extract_protocol: globin reduction protocol rna easy extraction

tag: Cord blood arsenic exposure level 0.2


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-460 - mAdbID:68604

description: mAdb experiment ID: 68604

source_name: 03-460B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-237 - mAdbID:68594

description: mAdb experiment ID: 68594

source_name: 03-237B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-416 - mAdbID:68603

description: mAdb experiment ID: 68603

value: EpCAM positive

source_name: 03-416B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-058 - mAdbID:68591

description: mAdb experiment ID: 68591

source_name: 03-058B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-343 - mAdbID:68602

description: mAdb experiment ID: 68602

source_name: 03-343B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-150 - mAdbID:68600

description: mAdb experiment ID: 68600

source_name: 03-150B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-251 - mAdbID:68595

description: mAdb experiment ID: 68595

source_name: 03-251B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-423 - mAdbID:68590

description: mAdb experiment ID: 68590

source_name: 02-423B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-233 - mAdbID:68601

description: mAdb experiment ID: 68601

source_name: 03-233B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-439 - mAdbID:68596

description: mAdb experiment ID: 68596

source_name: 03-439B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-355 - mAdbID:68605

description: mAdb experiment ID: 68605

source_name: 02-355B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-070 - mAdbID:68599

description: mAdb experiment ID: 68599

source_name: 03-070B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-227 - mAdbID:68607

description: mAdb experiment ID: 68607

source_name: 03-227B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-358 - mAdbID:68606

description: mAdb experiment ID: 68606

source_name: 02-358B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-105 - mAdbID:68582

description: mAdb experiment ID: 68582

source_name: 03-105B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-269 - mAdbID:68589

description: mAdb experiment ID: 68589

source_name: 02-269B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-366 - mAdbID:68585

description: mAdb experiment ID: 68585

source_name: 03-366B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-208 - mAdbID:68593

description: mAdb experiment ID: 68593

source_name: 03-208B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-089 - mAdbID:68065

description: mAdb experiment ID: 68065

source_name: 03-089B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-325 - mAdbID:68576

description: mAdb experiment ID: 68576

source_name: 02-325B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-309 - mAdbID:68575

description: mAdb experiment ID: 68575

source_name: 02-309B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-048 - mAdbID:68580

description: mAdb experiment ID: 68580

source_name: 03-048B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-361 - mAdbID:68579

description: mAdb experiment ID: 68579

source_name: 02-361B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-219 - mAdbID:68066

description: mAdb experiment ID: 68066

source_name: 03-219B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-285 - mAdbID:68063

description: mAdb experiment ID: 68063

source_name: 02-285B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-301 - mAdbID:68064

description: mAdb experiment ID: 68064

source_name: 02-301B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-270 - mAdbID:68060

description: mAdb experiment ID: 68060

source_name: 03-270B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-235 - mAdbID:68059

description: mAdb experiment ID: 68059

source_name: 03-235B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-447 - mAdbID:68055

description: mAdb experiment ID: 68055

source_name: 02-447B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-314 - mAdbID:68061

description: mAdb experiment ID: 68061

source_name: 03-314B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-082 - mAdbID:68056

description: mAdb experiment ID: 68056

source_name: 03-082B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-042 - mAdbID:67929

description: mAdb experiment ID: 67929

source_name: 03-042B - Control


title: EpCAM positive HBV-infected with cirrhosis02-339 - mAdbID:68577

description: mAdb experiment ID: 68577

source_name: 02-339B - Control

value: HBV-infected with cirrhosis


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-457 - mAdbID:67927

description: mAdb experiment ID: 67927

source_name: 02-457B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-151 - mAdbID:68057

description: mAdb experiment ID: 68057

source_name: 03-151B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-272 - mAdbID:67930

description: mAdb experiment ID: 67930

source_name: 03-272B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-321 - mAdbID:67904

description: mAdb experiment ID: 67904

source_name: 02-321B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-395 - mAdbID:68054

description: mAdb experiment ID: 68054

source_name: 02-395B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-215 - mAdbID:68058

description: mAdb experiment ID: 68058

source_name: 03-215B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-405 - mAdbID:67932

description: mAdb experiment ID: 67932

source_name: 03-405B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-315 - mAdbID:67909

description: mAdb experiment ID: 67909

source_name: 02-315B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-384 - mAdbID:67905

description: mAdb experiment ID: 67905

source_name: 02-384B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-460 - mAdbID:67928

description: mAdb experiment ID: 67928

source_name: 02-460B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-055 - mAdbID:68598

description: mAdb experiment ID: 68598

source_name: 03-055B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-119 - mAdbID:67847

description: mAdb experiment ID: 67847

source_name: 03-119B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-205 - mAdbID:67746

description: mAdb experiment ID: 67746

source_name: 03-205B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-344 - mAdbID:67867

description: mAdb experiment ID: 67867

source_name: 02-344B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-354 - mAdbID:67843

description: mAdb experiment ID: 67843

source_name: 02-354B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-374 - mAdbID:67751

description: mAdb experiment ID: 67751

source_name: 03-374B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-443 - mAdbID:67872

description: mAdb experiment ID: 67872

source_name: 03-443B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-407 - mAdbID:67926

description: mAdb experiment ID: 67926

source_name: 02-407B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-295 - mAdbID:67722

description: mAdb experiment ID: 67722

source_name: 03-295B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-015 - mAdbID:67869

description: mAdb experiment ID: 67869

source_name: 03-015B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-261 - mAdbID:67749

description: mAdb experiment ID: 67749

source_name: 03-261B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-305 - mAdbID:67849

description: mAdb experiment ID: 67849

source_name: 03-305B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-397 - mAdbID:67871

description: mAdb experiment ID: 67871

source_name: 03-397B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-286 - mAdbID:67865

description: mAdb experiment ID: 67865

source_name: 02-286B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-162 - mAdbID:67719

description: mAdb experiment ID: 67719

source_name: 03-162B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-284 - mAdbID:67750

description: mAdb experiment ID: 67750

source_name: 03-284B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-326 - mAdbID:67723

description: mAdb experiment ID: 67723

source_name: 03-326B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-309 - mAdbID:67907

description: mAdb experiment ID: 67907

source_name: 03-309B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-301 - mAdbID:67848

description: mAdb experiment ID: 67848

source_name: 03-301B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-383 - mAdbID:67870

description: mAdb experiment ID: 67870

source_name: 03-383B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-214 - mAdbID:67720

description: mAdb experiment ID: 67720

source_name: 03-214B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-337 - mAdbID:67866

description: mAdb experiment ID: 67866

source_name: 02-337B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-234 - mAdbID:67748

description: mAdb experiment ID: 67748

source_name: 03-234B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-273 - mAdbID:67721

description: mAdb experiment ID: 67721

source_name: 03-273B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-431 - mAdbID:67844

description: mAdb experiment ID: 67844

source_name: 02-431B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-466 - mAdbID:67868

description: mAdb experiment ID: 67868

source_name: 02-466B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-025 - mAdbID:67718

description: mAdb experiment ID: 67718

source_name: 03-025B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-457 - mAdbID:67687

description: mAdb experiment ID: 67687

source_name: 03-457B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-291 - mAdbID:67684

description: mAdb experiment ID: 67684

source_name: 03-291B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-422 - mAdbID:67686

description: mAdb experiment ID: 67686

source_name: 03-422B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-284 - mAdbID:67716

description: mAdb experiment ID: 67716

source_name: 02-284B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-290 - mAdbID:67717

description: mAdb experiment ID: 67717

source_name: 02-290B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-223 - mAdbID:67632

description: mAdb experiment ID: 67632

source_name: 03-223B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-349 - mAdbID:67635

description: mAdb experiment ID: 67635

source_name: 03-349B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-429 - mAdbID:67680

description: mAdb experiment ID: 67680

source_name: 02-429B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-456 - mAdbID:67681

description: mAdb experiment ID: 67681

source_name: 02-456B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-450 - mAdbID:67638

description: mAdb experiment ID: 67638

source_name: 03-450B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-434 - mAdbID:67636

description: mAdb experiment ID: 67636

source_name: 03-434B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-238 - mAdbID:67634

description: mAdb experiment ID: 67634

source_name: 03-238B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-133 - mAdbID:67481

description: mAdb experiment ID: 67481

source_name: 03-133B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-279 - mAdbID:67550

description: mAdb experiment ID: 67550

source_name: 03-279B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-180 - mAdbID:67683

description: mAdb experiment ID: 67683

source_name: 03-180B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-351 - mAdbID:67546

description: mAdb experiment ID: 67546

source_name: 02-351B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-073 - mAdbID:67480

description: mAdb experiment ID: 67480

source_name: 03-073B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-093 - mAdbID:67325

description: mAdb experiment ID: 67325

source_name: 03-093B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-441 - mAdbID:67637

description: mAdb experiment ID: 67637

source_name: 03-441B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-432 - mAdbID:67479

description: mAdb experiment ID: 67479

source_name: 02-432B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-277 - mAdbID:67327

description: mAdb experiment ID: 67327

source_name: 03-277B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-329 - mAdbID:67685

description: mAdb experiment ID: 67685

source_name: 03-329B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-409 - mAdbID:67324

description: mAdb experiment ID: 67324

source_name: 02-409B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-311 - mAdbID:67328

description: mAdb experiment ID: 67328

source_name: 03-311B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-430 - mAdbID:67478

description: mAdb experiment ID: 67478

source_name: 02-430B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-146 - mAdbID:67682

description: mAdb experiment ID: 67682

source_name: 03-146B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-114 - mAdbID:67549

description: mAdb experiment ID: 67549

source_name: 03-114B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-369 - mAdbID:67330

description: mAdb experiment ID: 67330

source_name: 03-369B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-271 - mAdbID:67323

description: mAdb experiment ID: 67323

source_name: 02-271B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-289 - mAdbID:67631

description: mAdb experiment ID: 67631

source_name: 02-289B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-333 - mAdbID:67272

description: mAdb experiment ID: 67272

source_name: 03-333B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-037 - mAdbID:67268

description: mAdb experiment ID: 67268

source_name: 03-037B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-387 - mAdbID:67151

description: mAdb experiment ID: 67151

source_name: 03-387B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-370 - mAdbID:67265

description: mAdb experiment ID: 67265

source_name: 02-370B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-262 - mAdbID:67205

description: mAdb experiment ID: 67205

source_name: 03-262B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-313 - mAdbID:67200

description: mAdb experiment ID: 67200

source_name: 02-313B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-164 - mAdbID:67204

description: mAdb experiment ID: 67204

source_name: 03-164B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-064 - mAdbID:67269

description: mAdb experiment ID: 67269

source_name: 03-064B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-312 - mAdbID:67271

description: mAdb experiment ID: 67271

source_name: 03-312B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-416 - mAdbID:67149

description: mAdb experiment ID: 67149

source_name: 02-416B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-361 - mAdbID:67206

description: mAdb experiment ID: 67206

source_name: 03-361B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-285 - mAdbID:67270

description: mAdb experiment ID: 67270

source_name: 03-285B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-302 - mAdbID:67146

description: mAdb experiment ID: 67146

source_name: 02-302B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-087 - mAdbID:67150

description: mAdb experiment ID: 67150

source_name: 03-087B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-043 - mAdbID:67202

description: mAdb experiment ID: 67202

source_name: 03-043B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-195 - mAdbID:66622

description: mAdb experiment ID: 66622

source_name: 03-195B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-283 - mAdbID:67199

description: mAdb experiment ID: 67199

source_name: 02-283B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-404 - mAdbID:67266

description: mAdb experiment ID: 67266

source_name: 02-404B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-315 - mAdbID:66624

description: mAdb experiment ID: 66624

source_name: 03-315B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-360 - mAdbID:66626

description: mAdb experiment ID: 66626

source_name: 03-360B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-287 - mAdbID:67144

description: mAdb experiment ID: 67144

source_name: 02-287B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-228 - mAdbID:66620

description: mAdb experiment ID: 66620

source_name: 03-228B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-314 - mAdbID:67147

description: mAdb experiment ID: 67147

source_name: 02-314B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-322 - mAdbID:66625

description: mAdb experiment ID: 66625

source_name: 03-322B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-200 - mAdbID:66621

description: mAdb experiment ID: 66621

source_name: 03-200B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-062 - mAdbID:66623

description: mAdb experiment ID: 66623

source_name: 03-062B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-306 - mAdbID:67145

description: mAdb experiment ID: 67145

source_name: 03-306B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-265 - mAdbID:66586

description: mAdb experiment ID: 66586

source_name: 03-265B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-317 - mAdbID:66587

description: mAdb experiment ID: 66587

source_name: 03-317B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-263 - mAdbID:66619

description: mAdb experiment ID: 66619

source_name: 03-263B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-226 - mAdbID:66585

description: mAdb experiment ID: 66585

source_name: 03-226B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-269 - mAdbID:65740

description: mAdb experiment ID: 65740

source_name: 03-269B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-147 - mAdbID:66583

description: mAdb experiment ID: 66583

source_name: 03-147B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-225 - mAdbID:65739

description: mAdb experiment ID: 65739

source_name: 03-225B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-102 - mAdbID:66582

description: mAdb experiment ID: 66582

source_name: 03-102B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-394 - mAdbID:65741

description: mAdb experiment ID: 65741

source_name: 03-394B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-425 - mAdbID:65717

description: mAdb experiment ID: 65717

source_name: 03-425B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-345 - mAdbID:65736

description: mAdb experiment ID: 65736

source_name: 02-345B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-375 - mAdbID:67148

description: mAdb experiment ID: 67148

source_name: 02-375B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-354 - mAdbID:65653

description: mAdb experiment ID: 65653

source_name: 03-354B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-050 - mAdbID:65733

description: mAdb experiment ID: 65733

source_name: 03-050B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-438 - mAdbID:65743

description: mAdb experiment ID: 65743

source_name: 03-438B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-244 - mAdbID:65651

description: mAdb experiment ID: 65651

source_name: 03-244B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-336 - mAdbID:65714

description: mAdb experiment ID: 65714

source_name: 03-336B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-421 - mAdbID:65709

description: mAdb experiment ID: 65709

source_name: 02-421B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-448 - mAdbID:65710

description: mAdb experiment ID: 65710

source_name: 02-448B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-196 - mAdbID:65649

description: mAdb experiment ID: 65649

source_name: 03-196B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-268 - mAdbID:65652

description: mAdb experiment ID: 65652

source_name: 03-268B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-057 - mAdbID:65646

description: mAdb experiment ID: 65646

source_name: 03-057B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-281 - mAdbID:65642

description: mAdb experiment ID: 65642

source_name: 03-281B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-458 - mAdbID:65638

description: mAdb experiment ID: 65638

source_name: 02-458B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-017 - mAdbID:65647

description: mAdb experiment ID: 65647

source_name: 03-017B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-323 - mAdbID:65635

description: mAdb experiment ID: 65635

source_name: 02-323B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-088 - mAdbID:65386

description: mAdb experiment ID: 65386

source_name: 03-088B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-077 - mAdbID:65648

description: mAdb experiment ID: 65648

source_name: 03-077B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-454 - mAdbID:65637

description: mAdb experiment ID: 65637

source_name: 02-454B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-230 - mAdbID:65639

description: mAdb experiment ID: 65639

source_name: 03-230B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-213 - mAdbID:65387

description: mAdb experiment ID: 65387

source_name: 03-213B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-081 - mAdbID:65385

description: mAdb experiment ID: 65385

source_name: 03-081B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-375 - mAdbID:65643

description: mAdb experiment ID: 65643

source_name: 03-375B - Control