title: ChIP-Seq analysis of H3K36me3;inf temp lobe cls; Lib:XZ:20100924:17--ChIP:XZ:20100914:17:inferior temporal lobe:H3K36Me3

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:17--ChIP:XZ:20100914:17:inferior temporal lobe:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5752
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5933
****************
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: GSM670011_BI.Brain_Inferior_Temporal_Lobe.H3K36me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:17--ChIP:XZ:20100914:17:inferior temporal lobe:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Inferior Temporal Lobe, Donor 112 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.6576
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.1086
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1894
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9296
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3414
POISSON_PERCENTILE: 23

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

ANALYSIS FILE NAME: GSM670011_BI.Brain_Inferior_Temporal_Lobe.H3K36me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:17--ChIP:XZ:20100914:17:inferior temporal lobe:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 112 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.6786
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BITL H3K36me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K36me3 Donor 112 Library Lib:XZ:20100924:17--ChIP:XZ:20100914:17:inferior temporal lobe:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.1086
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1894
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9296
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3414
POISSON_PERCENTILE: 23

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:17--ChIP:XZ:20100914:17:inferior temporal lobe:H3K36Me3

value: Brain, Inferior Temporal Lobe

value: Inferior Temporal Lobe

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac in cingulate gyrus cells; Lib:XZ:20100924:12--ChIP:XZ:20100914:12:cingulate gyrus:H3K9Ac

status: Public on Mar 31 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:12--ChIP:XZ:20100914:12:cingulate gyrus:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5773
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5934
****************
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: GSM670032_BI.Brain_Cingulate_Gyrus.H3K9ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:12--ChIP:XZ:20100914:12:cingulate gyrus:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Brain Cingulate Gyrus, Donor 112 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.6473
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1712
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2278
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.988
IROC_PERCENTILE: 12
POISSON_SCORE: 0.3249
POISSON_PERCENTILE: 68

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

ANALYSIS FILE NAME: GSM670032_BI.Brain_Cingulate_Gyrus.H3K9ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:12--ChIP:XZ:20100914:12:cingulate gyrus:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 112 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.6683
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BCG H3K9ac 12
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K9ac Donor 112 Library Lib:XZ:20100924:12--ChIP:XZ:20100914:12:cingulate gyrus:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1712
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2278
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.988
IROC_PERCENTILE: 12
POISSON_SCORE: 0.3249
POISSON_PERCENTILE: 68

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

molecule: genomic DNA

organism: Homo sapiens

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:12--ChIP:XZ:20100914:12:cingulate gyrus:H3K9Ac

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Brain, Cingulate Gyrus

value: post-mortem

tag: molecule

value: genomic DNA

tag: disease

value: Cingulate Gyrus

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K4me3; hippocampus mid cls; Lib:XZ:20100921:09--ChIP:XZ:20100914:09:hippocampus middle:H3K4Me3

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:09--ChIP:XZ:20100914:09:hippocampus middle:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5763
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5937
****************
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: GSM670022_BI.Brain_Hippocampus_Middle.H3K4me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:09--ChIP:XZ:20100914:09:hippocampus middle:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Hippocampus Middle, Donor 112 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.6571
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.1271
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1582
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.999
IROC_PERCENTILE: 60
POISSON_SCORE: 0.1988
POISSON_PERCENTILE: 4

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

ANALYSIS FILE NAME: GSM670022_BI.Brain_Hippocampus_Middle.H3K4me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:09--ChIP:XZ:20100914:09:hippocampus middle:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 112 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.6781
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BHM H3K4me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K4me3 Donor 112 Library Lib:XZ:20100921:09--ChIP:XZ:20100914:09:hippocampus middle:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.1271
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1582
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.999
IROC_PERCENTILE: 60
POISSON_SCORE: 0.1988
POISSON_PERCENTILE: 4

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:09--ChIP:XZ:20100914:09:hippocampus middle:H3K4Me3

value: Brain, Hippocampus Middle

value: Hippocampus Middle

value: Millipore

value: Histone H3K4me3


title: hCG+7

status: Public on Apr 01 2011

city: Shantou

first: Zeng-Ming

last: Yang

address: 263 Daxue Road

department: Biology

country: China

institute: Shantou University

description:
small RNA(18-35nt)
small RNA deep sequencing of hCG+7

library_source: transcriptomic

data_processing: the 3’ end of the read was determined by the 3’ most perfect match to the first 8 nt of the 3’ adaptor (build: hg19).

molecule: total RNA

growth_protocol: A total of 10 women patients (age range, 27-38 years; body mass index or BMI range, 17.4-22.3 kg/m2) undergoing IVF treatment

extract_protocol:
Total RNAs were extracted with TRIzol reagent. The small RNA fragments of 18~30 bases long were isolated and purified from 10 μg total RNA using 15% TBE-Urea PAGE gel. The 5’ adaptors (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’) and 3’ adaptors (5’- pUCGUAUGCCGUCUUCUGCUUGidT-3’) were added to the ends of fragments. Reverse transcription PCR (RT-PCR) was performed using a RT-PCR kit (Invitrogen). The fragments were purified using 6% TBE PAGE gel and used for high-throughput sequencing with an Illumina Genome Analyzer IIx sequencer at Huada Genomics Institute Co. Ltd, China. Each small RNA sample was sequenced in a single lane.
18-35nt small RNA by gel

treatment_protocol: Endometrial biopsies were obtained from two groups of patients using different experimental designs. In the first group, we aimed to study endometrial receptivity during natural cycles. In the second group, ovarian stimulation was performed using the long protocol. Endometrial biopsies were obtained on days hCG+4 (n=5) and hCG+7 (n=5) from women who did not have embryo transfer after IVF treatment because of fertilization failure.

tag: tissue

value: endometrium


title: ChIP-Seq analysis of H3K4me1; inf. temp lobe cls; Lib:XZ:20100924:15--ChIP:XZ:20100914:15:inferior temporal lobe:H3K4Me1

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:15--ChIP:XZ:20100914:15:inferior temporal lobe:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5777
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5933
****************
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: GSM670036_BI.Brain_Inferior_Temporal_Lobe.H3K4me1.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:15--ChIP:XZ:20100914:15:inferior temporal lobe:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Inferior Temporal Lobe, Donor 112 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.6549
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.1383
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.234
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9349
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3994
POISSON_PERCENTILE: 29

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

ANALYSIS FILE NAME: GSM670036_BI.Brain_Inferior_Temporal_Lobe.H3K4me1.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:15--ChIP:XZ:20100914:15:inferior temporal lobe:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 112 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.6759
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BITL H3K4me1 12
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K4me1 Donor 112 Library Lib:XZ:20100924:15--ChIP:XZ:20100914:15:inferior temporal lobe:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.1383
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.234
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9349
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3994
POISSON_PERCENTILE: 29

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:15--ChIP:XZ:20100914:15:inferior temporal lobe:H3K4Me1

value: Brain, Inferior Temporal Lobe

value: post-mortem

value: genomic DNA

value: Inferior Temporal Lobe

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in mid frontal lobe cells; Lib:XZ:20100924:01--ChIP:XZ:20100914:01:mid frontal lobe:H3K4Me1

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:01--ChIP:XZ:20100914:01:mid frontal lobe:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5756
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5939
****************
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: GSM670015_BI.Brain_Mid_Frontal_Lobe.H3K4me1.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:01--ChIP:XZ:20100914:01:mid frontal lobe:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Mid Frontal Lobe, Donor 112 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.6572
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.0437
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.1575
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.8498
IROC_PERCENTILE: 4
POISSON_SCORE: 0.3314
POISSON_PERCENTILE: 4

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

ANALYSIS FILE NAME: GSM670015_BI.Brain_Mid_Frontal_Lobe.H3K4me1.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:01--ChIP:XZ:20100914:01:mid frontal lobe:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Mid Frontal Lobe, Donor 112 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.6782
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMFL H3K4me1 12
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K4me1 Donor 112 Library Lib:XZ:20100924:01--ChIP:XZ:20100914:01:mid frontal lobe:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.0437
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.1575
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.8498
IROC_PERCENTILE: 4
POISSON_SCORE: 0.3314
POISSON_PERCENTILE: 4

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:01--ChIP:XZ:20100914:01:mid frontal lobe:H3K4Me1

value: Brain, Mid Frontal Lobe

value: Mid Frontal Lobe

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Protein A-Sepharose 4B


title: ChIP-Seq analysis of H3K4me1 in cingulate gyrus cells; Lib:XZ:20100924:08--ChIP:XZ:20100914:08:cingulate gyrus:H3K4Me1

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:08--ChIP:XZ:20100914:08:cingulate gyrus:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5774
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5934
****************
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: GSM670033_BI.Brain_Cingulate_Gyrus.H3K4me1.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:08--ChIP:XZ:20100914:08:cingulate gyrus:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Cingulate Gyrus, Donor 112 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.6468
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.0918
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.2017
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8996
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3775
POISSON_PERCENTILE: 18

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

ANALYSIS FILE NAME: GSM670033_BI.Brain_Cingulate_Gyrus.H3K4me1.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:08--ChIP:XZ:20100914:08:cingulate gyrus:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 112 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.6678
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BCG H3K4me1 12
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K4me1 Donor 112 Library Lib:XZ:20100924:08--ChIP:XZ:20100914:08:cingulate gyrus:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.0918
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.2017
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8996
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3775
POISSON_PERCENTILE: 18

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:08--ChIP:XZ:20100914:08:cingulate gyrus:H3K4Me1

value: Brain, Cingulate Gyrus

value: Cingulate Gyrus

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam


title: ChIP-Seq analysis of H3K9ac in mid frontal lobe cells; Lib:XZ:20100924:05--ChIP:XZ:20100914:05:mid frontal lobe:H3K9Ac

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:05--ChIP:XZ:20100914:05:mid frontal lobe:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5762
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5939
****************
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: GSM670021_BI.Brain_Mid_Frontal_Lobe.H3K9ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:05--ChIP:XZ:20100914:05:mid frontal lobe:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Brain Mid Frontal Lobe, Donor 112 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.6586
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1223
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.1811
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9871
IROC_PERCENTILE: 8
POISSON_SCORE: 0.2746
POISSON_PERCENTILE: 28

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

ANALYSIS FILE NAME: GSM670021_BI.Brain_Mid_Frontal_Lobe.H3K9ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:05--ChIP:XZ:20100914:05:mid frontal lobe:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Brain Mid Frontal Lobe, Donor 112 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.6796
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMFL H3K9ac 12
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K9ac Donor 112 Library Lib:XZ:20100924:05--ChIP:XZ:20100914:05:mid frontal lobe:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1223
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.1811
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9871
IROC_PERCENTILE: 8
POISSON_SCORE: 0.2746
POISSON_PERCENTILE: 28

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:05--ChIP:XZ:20100914:05:mid frontal lobe:H3K9Ac

value: post-mortem

value: genomic DNA

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K4me3 in mid frontal lobe cells; Lib:XZ:20100924:02--ChIP:XZ:20100914:02:mid frontal lobe:H3K4Me3

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:02--ChIP:XZ:20100914:02:mid frontal lobe:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5757
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5939
****************
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: GSM670016_BI.Brain_Mid_Frontal_Lobe.H3K4me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:02--ChIP:XZ:20100914:02:mid frontal lobe:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Mid Frontal Lobe, Donor 112 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.6489
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.1774
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2001
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2343
POISSON_PERCENTILE: 12

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

ANALYSIS FILE NAME: GSM670016_BI.Brain_Mid_Frontal_Lobe.H3K4me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:02--ChIP:XZ:20100914:02:mid frontal lobe:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Mid Frontal Lobe, Donor 112 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.6699
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMFL H3K4me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K4me3 Donor 112 Library Lib:XZ:20100924:02--ChIP:XZ:20100914:02:mid frontal lobe:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.1774
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2001
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2343
POISSON_PERCENTILE: 12

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:02--ChIP:XZ:20100914:02:mid frontal lobe:H3K4Me3

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3; ant. caudate cls; Lib:XZ:20100921:18--ChIP:XZ:20100914:18:anterior caudate

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:18--ChIP:XZ:20100914:18:anterior caudate
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5767
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5936
****************
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: GSM670026_BI.Brain_Anterior_Caudate.H3K36me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:18--ChIP:XZ:20100914:18:anterior caudate.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Anterior Caudate, Donor 112 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.6593
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.0894
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.1756
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9213
IROC_PERCENTILE: 31
POISSON_SCORE: 0.3426
POISSON_PERCENTILE: 27

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

ANALYSIS FILE NAME: GSM670026_BI.Brain_Anterior_Caudate.H3K36me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:18--ChIP:XZ:20100914:18:anterior caudate.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Anterior Caudate, Donor 112 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.6803
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BAC H3K36me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K36me3 Donor 112 Library Lib:XZ:20100921:18--ChIP:XZ:20100914:18:anterior caudate EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.0894
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.1756
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9213
IROC_PERCENTILE: 31
POISSON_SCORE: 0.3426
POISSON_PERCENTILE: 27

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:18--ChIP:XZ:20100914:18:anterior caudate

value: Brain, Anterior Caudate

value: Anterior Caudate

value: Female

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K9me3; inf. temp lobe cls; Lib:XZ:20100924:20--ChIP:XZ:20100914:20:inferior temporal lobe:H3K9Me3

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:20--ChIP:XZ:20100914:20:inferior temporal lobe:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5746
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5933
****************
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: GSM670005_BI.Brain_Inferior_Temporal_Lobe.H3K9me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:20--ChIP:XZ:20100914:20:inferior temporal lobe:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Inferior Temporal Lobe, Donor 112 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.6474
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0198
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.0816
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.7569
IROC_PERCENTILE: 23
POISSON_SCORE: 0.1716
POISSON_PERCENTILE: 23

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

ANALYSIS FILE NAME: GSM670005_BI.Brain_Inferior_Temporal_Lobe.H3K9me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:20--ChIP:XZ:20100914:20:inferior temporal lobe:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 112 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.6684
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BITL H3K9me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K9me3 Donor 112 Library Lib:XZ:20100924:20--ChIP:XZ:20100914:20:inferior temporal lobe:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0198
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.0816
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.7569
IROC_PERCENTILE: 23
POISSON_SCORE: 0.1716
POISSON_PERCENTILE: 23

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:20--ChIP:XZ:20100914:20:inferior temporal lobe:H3K9Me3

value: Brain, Inferior Temporal Lobe

value: Inferior Temporal Lobe

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Protein A-Sepharose 4B

value: Histone H3K9me3


title: ChIP-Seq analysis of WCE; inf. temp. lobe cls; Lib:XZ:20100924:21--ChIP:XZ:20100914:21:inferior temporal lobe:WCE

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:21--ChIP:XZ:20100914:21:inferior temporal lobe:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5751
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5933
****************
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: GSM670010_BI.Brain_Inferior_Temporal_Lobe.Input.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:21--ChIP:XZ:20100914:21:inferior temporal lobe:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Inferior Temporal Lobe, Donor 112 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.6555
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0095
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0361
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM670010_BI.Brain_Inferior_Temporal_Lobe.Input.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:21--ChIP:XZ:20100914:21:inferior temporal lobe:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Inferior Temporal Lobe, Donor 112 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.6765
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BITL Input 12
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe ChIP-Seq Input Donor 112 Library Lib:XZ:20100924:21--ChIP:XZ:20100914:21:inferior temporal lobe:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0095
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0361
POISSON_PERCENTILE: 33

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:21--ChIP:XZ:20100914:21:inferior temporal lobe:WCE

value: post-mortem

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me3; ant. caudate cls; Lib:XZ:20100921:16--ChIP:XZ:20100914:16:anterior caudate :H3K4Me3

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:16--ChIP:XZ:20100914:16:anterior caudate :H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5772
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5936
****************
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: GSM670031_BI.Brain_Anterior_Caudate.H3K4me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:16--ChIP:XZ:20100914:16:anterior caudate :H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Anterior Caudate, Donor 112 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.6554
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2131
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.2409
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2842
POISSON_PERCENTILE: 32

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

ANALYSIS FILE NAME: GSM670031_BI.Brain_Anterior_Caudate.H3K4me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:16--ChIP:XZ:20100914:16:anterior caudate :H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Anterior Caudate, Donor 112 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.6764
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BAC H3K4me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K4me3 Donor 112 Library Lib:XZ:20100921:16--ChIP:XZ:20100914:16:anterior caudate :H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2131
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.2409
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2842
POISSON_PERCENTILE: 32

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:16--ChIP:XZ:20100914:16:anterior caudate :H3K4Me3

value: genomic DNA

value: 10 million cells

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: hCG+4

description:
small RNA(18-35nt)
small RNA deep sequencing of hCG+4

value: endometrium


title: ChIP-Seq analysis of H3K9me3; hippocampus mid cls; Lib:XZ:20100921:13--ChIP:XZ:20100914:13:hippocampus middle:H3K9Me3

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:13--ChIP:XZ:20100914:13:hippocampus middle:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5742
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5937
****************
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: GSM670001_BI.Brain_Hippocampus_Middle.H3K9me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:13--ChIP:XZ:20100914:13:hippocampus middle:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Hippocampus Middle, Donor 112 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.6529
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.016
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.053
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.8792
IROC_PERCENTILE: 69
POISSON_SCORE: 0.1304
POISSON_PERCENTILE: 8

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

ANALYSIS FILE NAME: GSM670001_BI.Brain_Hippocampus_Middle.H3K9me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:13--ChIP:XZ:20100914:13:hippocampus middle:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 112 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.6739
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BHM H3K9me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K9me3 Donor 112 Library Lib:XZ:20100921:13--ChIP:XZ:20100914:13:hippocampus middle:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.016
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.053
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.8792
IROC_PERCENTILE: 69
POISSON_SCORE: 0.1304
POISSON_PERCENTILE: 8

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:13--ChIP:XZ:20100914:13:hippocampus middle:H3K9Me3

value: Brain, Hippocampus Middle

value: Hippocampus Middle

value: Female

value: Primary Tissue

value: Abcam


title: LH+2

description:
small RNA(18-35nt)
small RNA deep sequencing of LH+2


title: ChIP-Seq analysis of H3K9me3 in Cultured CD34 cells; Lib:RI:20101012:03--ChIP:MA:20100927:03:CD34 expanded:H3K9Me3

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:03--ChIP:MA:20100927:03:CD34 expanded:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5736
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3896
****************
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: GSM669995_BI.CD34_Cultured_Cells.H3K9me3.123.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:03--ChIP:MA:20100927:03:CD34 expanded:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD34 Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD34 Cultured Cells, Donor 123 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.6523
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0898
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.1571
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.8668
IROC_PERCENTILE: 46
POISSON_SCORE: 0.2739
POISSON_PERCENTILE: 35

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

ANALYSIS FILE NAME: GSM669995_BI.CD34_Cultured_Cells.H3K9me3.123.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:03--ChIP:MA:20100927:03:CD34 expanded:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD34 Cultured Cells, Donor 123 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.6733
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CD34 H3K9me3 23
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells Histone H3K9me3 Donor 123 Library Lib:RI:20101012:03--ChIP:MA:20100927:03:CD34 expanded:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0898
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.1571
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.8668
IROC_PERCENTILE: 46
POISSON_SCORE: 0.2739
POISSON_PERCENTILE: 35

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

source_name: flow sorted CD34+ cells from cord blood expanded in short term culture; Lib:RI:20101012:03--ChIP:MA:20100927:03:CD34 expanded:H3K9Me3

value: CD34 Cultured Cells

tag: markers

value: short term

value: cultured CD34

value: Unknown

value: Primary Cell

value: FHCRC

value: Protein A-Sepharose 4B

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K9ac in HUES48 cells; Lib:MC:20101025:11--ChIP:MC:20101020:11:ES cell HUES_48:H3K9Ac

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20101025:11--ChIP:MC:20101020:11:ES cell HUES_48:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5754
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5930
****************
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: GSM670013_BI.HUES48.H3K9ac.Lib_MC_20101025_11--ChIP_MC_20101020_11_ES_cell_HUES_48_H3K9Ac.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:11--ChIP:MC:20101020:11:ES cell HUES_48:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES48 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the HUES48 Cell Line, Library Lib:MC:20101025:11--ChIP:MC:20101020:11:ES cell HUES_48:H3K9Ac 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.6547
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1216
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.181
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.998
IROC_PERCENTILE: 92
POISSON_SCORE: 0.2059
POISSON_PERCENTILE: 12

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

ANALYSIS FILE NAME: GSM670013_BI.HUES48.H3K9ac.Lib_MC_20101025_11--ChIP_MC_20101020_11_ES_cell_HUES_48_H3K9Ac.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:11--ChIP:MC:20101020:11:ES cell HUES_48:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the HUES48 Cell Line, Library Lib:MC:20101025:11--ChIP:MC:20101020:11:ES cell HUES_48:H3K9Ac 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.6757
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES48 H3K9ac Ac
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K9ac Library Lib:MC:20101025:11--ChIP:MC:20101020:11:ES cell HUES_48:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1216
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.181
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.998
IROC_PERCENTILE: 92
POISSON_SCORE: 0.2059
POISSON_PERCENTILE: 12

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

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:11--ChIP:MC:20101020:11:ES cell HUES_48:H3K9Ac

value: HUES48 stem cells

value: HUES48 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

value: genomic DNA

tag: passage

tag: line

tag: batch

value: ES cell HUES_48-1

value: Cell Line

value: undifferentiated

tag: Sex

value: Harvard University

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K36me3; hippocampus mid cls; Lib:XZ:20100921:10--ChIP:XZ:20100914:10:hippocampus middle:H3K36Me3

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:10--ChIP:XZ:20100914:10:hippocampus middle:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5743
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5937
****************
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: GSM670002_BI.Brain_Hippocampus_Middle.H3K36me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:10--ChIP:XZ:20100914:10:hippocampus middle:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Hippocampus Middle, Donor 112 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.6454
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.0728
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.1637
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9114
IROC_PERCENTILE: 23
POISSON_SCORE: 0.302
POISSON_PERCENTILE: 15

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

ANALYSIS FILE NAME: GSM670002_BI.Brain_Hippocampus_Middle.H3K36me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:10--ChIP:XZ:20100914:10:hippocampus middle:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 112 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.6664
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BHM H3K36me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K36me3 Donor 112 Library Lib:XZ:20100921:10--ChIP:XZ:20100914:10:hippocampus middle:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.0728
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.1637
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9114
IROC_PERCENTILE: 23
POISSON_SCORE: 0.302
POISSON_PERCENTILE: 15

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:10--ChIP:XZ:20100914:10:hippocampus middle:H3K36Me3

value: Brain, Hippocampus Middle

value: post-mortem

value: Hippocampus Middle

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: LH+7

description:
small RNA(18-35nt)
small RNA deep sequencing of LH+7

value: endometrium


title: ChIP-Seq analysis of WCE in cingulate gyrus cells; Lib:XZ:20100924:14--ChIP:XZ:20100914:14:cingulate gyrus:WCE

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:14--ChIP:XZ:20100914:14:cingulate gyrus:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5744
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5934
****************
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: GSM670003_BI.Brain_Cingulate_Gyrus.Input.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:14--ChIP:XZ:20100914:14:cingulate gyrus:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Cingulate Gyrus, Donor 112 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.6567
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.0046
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0263
POISSON_PERCENTILE: 17

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

ANALYSIS FILE NAME: GSM670003_BI.Brain_Cingulate_Gyrus.Input.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:14--ChIP:XZ:20100914:14:cingulate gyrus:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Cingulate Gyrus, Donor 112 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.6777
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BCG Input 12
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus ChIP-Seq Input Donor 112 Library Lib:XZ:20100924:14--ChIP:XZ:20100914:14:cingulate gyrus:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.0046
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0263
POISSON_PERCENTILE: 17

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:14--ChIP:XZ:20100914:14:cingulate gyrus:WCE

value: Brain, Cingulate Gyrus

value: genomic DNA

value: Cingulate Gyrus

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me3; inf. temp lobe cls; Lib:XZ:20100924:16--ChIP:XZ:20100914:16:inferior temporal lobe:H3K4Me3

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:16--ChIP:XZ:20100914:16:inferior temporal lobe:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5733
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5933
****************
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: GSM669992_BI.Brain_Inferior_Temporal_Lobe.H3K4me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:16--ChIP:XZ:20100914:16:inferior temporal lobe:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Inferior Temporal Lobe, Donor 112 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.6520
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2017
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2304
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9998
IROC_PERCENTILE: 88
POISSON_SCORE: 0.2677
POISSON_PERCENTILE: 20

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

ANALYSIS FILE NAME: GSM669992_BI.Brain_Inferior_Temporal_Lobe.H3K4me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:16--ChIP:XZ:20100914:16:inferior temporal lobe:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 112 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.6730
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BITL H3K4me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K4me3 Donor 112 Library Lib:XZ:20100924:16--ChIP:XZ:20100914:16:inferior temporal lobe:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2017
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2304
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9998
IROC_PERCENTILE: 88
POISSON_SCORE: 0.2677
POISSON_PERCENTILE: 20

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:16--ChIP:XZ:20100914:16:inferior temporal lobe:H3K4Me3

value: Brain, Inferior Temporal Lobe

value: Inferior Temporal Lobe

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of WCE in fetal lung cells (superseded by GSE120319)

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:08--ChIP:XZ:20100726:08:fetal lung:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5734
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5943
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
****************************
This sample record's metadata may be obsolete; up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE120319
****************************

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

ANALYSIS FILE NAME: GSM669993_BI.Fetal_Lung.Input.UW_H23284.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:08--ChIP:XZ:20100726:08:fetal lung:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Fetal Lung, Donor UW H23284 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.6533
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0054
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0298
POISSON_PERCENTILE: 27

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

ANALYSIS FILE NAME: GSM669993_BI.Fetal_Lung.Input.UW_H23284.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:08--ChIP:XZ:20100726:08:fetal lung:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Fetal Lung, Donor UW H23284 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.6743
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: FL Input 84
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung ChIP-Seq Input Donor UW H23284 Library Lib:XZ:20100731:08--ChIP:XZ:20100726:08:fetal lung:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0054
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0298
POISSON_PERCENTILE: 27

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

source_name: Primary fetal lung tissue; Lib:XZ:20100731:08--ChIP:XZ:20100726:08:fetal lung:WCE

value: Fetal Lung

value: surgery

value: Fetal lung

value: Female

value: Primary Tissue

value: lung

value: UW

value: 96 days


title: ChIP-Seq analysis of H3K36me3 in cingulate gyrus cells; Lib:XZ:20100924:10--ChIP:XZ:20100914:10:cingulate gyrus:H3K36Me3

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:10--ChIP:XZ:20100914:10:cingulate gyrus:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5726
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5934
****************
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: GSM669985_BI.Brain_Cingulate_Gyrus.H3K36me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:10--ChIP:XZ:20100914:10:cingulate gyrus:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Cingulate Gyrus, Donor 112 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.6448
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.0807
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.1696
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9124
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3265
POISSON_PERCENTILE: 19

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

ANALYSIS FILE NAME: GSM669985_BI.Brain_Cingulate_Gyrus.H3K36me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:10--ChIP:XZ:20100914:10:cingulate gyrus:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 112 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.6658
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BCG H3K36me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K36me3 Donor 112 Library Lib:XZ:20100924:10--ChIP:XZ:20100914:10:cingulate gyrus:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.0807
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.1696
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9124
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3265
POISSON_PERCENTILE: 19

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:10--ChIP:XZ:20100914:10:cingulate gyrus:H3K36Me3

value: Brain, Cingulate Gyrus

value: post-mortem

value: genomic DNA

value: Cingulate Gyrus

value: brain

value: Rush University Medical Center

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: ChIP-Seq analysis of WCE; ant. caudate cls; Lib:XZ:20100921:21--ChIP:XZ:20100914:21:anterior caudate :WCE

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:21--ChIP:XZ:20100914:21:anterior caudate :WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5719
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5936
****************
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: GSM669978_BI.Brain_Anterior_Caudate.Input.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:21--ChIP:XZ:20100914:21:anterior caudate :WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Anterior Caudate ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Anterior Caudate, Donor 112 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.6508
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.0065
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0298
POISSON_PERCENTILE: 27

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

ANALYSIS FILE NAME: GSM669978_BI.Brain_Anterior_Caudate.Input.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:21--ChIP:XZ:20100914:21:anterior caudate :WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Anterior Caudate, Donor 112 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.6718
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BAC Input 12
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate ChIP-Seq Input Donor 112 Library Lib:XZ:20100921:21--ChIP:XZ:20100914:21:anterior caudate :WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.0065
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0298
POISSON_PERCENTILE: 27

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:21--ChIP:XZ:20100914:21:anterior caudate :WCE

value: Brain, Anterior Caudate

value: Anterior Caudate

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input