description:
design description: MeDIP-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A02758) using Illumina Genome Analyzer IIx
library name: A02758
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 1 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
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: GSM707023_UCSF-UBC.Brain_Germinal_Matrix.MeDIP-Seq.HuFGM02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02758-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Brain Germinal Matrix MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Brain Germinal Matrix, Donor HuFGM02 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.7930
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 79,145,077
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.0174
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1612
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.7825
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3329
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707023_UCSF-UBC.Brain_Germinal_Matrix.MeDIP-Seq.HuFGM02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02758-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 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.7935
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: BGM MeDIP 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix MeDIP-Seq Donor HuFGM02 Library A02758-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 79,145,077
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.0174
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1612
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.7825
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3329
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

extract_protocol: library construction protocol: Refer to document 'MeDIP-seq library construction protocol v2' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: male

tag: body site

value: Brain

tag: histological type

value: Germinal matrix tissue

tag: is tumor

value: No

value: primary tissue

value: brain (germinal matrix) tissue


title: Reference Epigenome: ChIP-Seq Input from Mesenchymal Stem Cells; renlab.Input.MSC.02.01

status: Public on Jul 27 2011

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Mesenchymal Stem Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK444
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7923
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914
****************
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: GSM767354_UCSD.H1_Derived_Mesenchymal_Stem_Cells.Input.SK444.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.MSC.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on H1 Derived Mesenchymal Stem Cells, Library SK444, 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.10445
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,275,745
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.08
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.17
IROC_PERCENTILE: 35
POISSON_SCORE: 0.15
POISSON_PERCENTILE: 97
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM767354_UCSD.H1_Derived_Mesenchymal_Stem_Cells.Input.SK444.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.MSC.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK444, 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.10518
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 5
BROWSER_TRACK_NAME: HDMSC Input 44
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells ChIP-Seq Input Library SK444 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,275,745
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.08
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.17
IROC_PERCENTILE: 35
POISSON_SCORE: 0.15
POISSON_PERCENTILE: 97
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.Input.MSC.02.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sample alias

tag: sample common name

value: H1 Derived Mesenchymal Stem Cells

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Publication in progress

tag: passage

tag: medium

tag: Sex

value: Male

tag: batch

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: MeDIP-Seq analysis of foreskin keratinocyte from skin01 (A02302) using Illumina Genome Analyzer IIx
library name: A02302
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 0.7 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
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: GSM707022_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MeDIP-Seq.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02302-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.7929
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 75,998,520
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4269
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4702
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9803
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5478
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707022_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MeDIP-Seq.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02302-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.7934
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: PFK MeDIP 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin01 Library A02302-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 75,998,520
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4269
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4702
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9803
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5478
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: male

value: Penis

value: Keratinocyte

value: primary cell culture

tag: cell type

value: foreskin keratinocyte


description:
design description: MeDIP-Seq analysis of fetal brain tissue from H22510 (A02296) using Illumina Genome Analyzer IIx
library name: A02296
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 2 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 1 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
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: GSM707019_UCSF-UBC.Fetal_Brain.MeDIP-Seq.H22510.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02296-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Brain MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Fetal Brain, Donor H22510 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.7932
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 71,844,146
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.1283
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.2919
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9164
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4402
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707019_UCSF-UBC.Fetal_Brain.MeDIP-Seq.H22510.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02296-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Fetal Brain, Donor H22510 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.7937
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: FB MeDIP 10
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H22510 Library A02296-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 71,844,146
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.1283
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.2919
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9164
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4402
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Brain

value: Brain tissue

value: No

value: primary tissue

value: fetal brain tissue


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Mesenchymal Stem Cells; renlab.H3K4me1.MSC.02.01

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Mesenchymal Stem Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK465
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7927
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914
****************
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: GSM767347_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4me1.SK465.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.MSC.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library SK465, 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.10441
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,517,388
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.39
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.49
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.99
IROC_PERCENTILE: 63
POISSON_SCORE: 0.58
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM767347_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4me1.SK465.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.MSC.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK465, 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.10514
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 5
BROWSER_TRACK_NAME: HDMSC H3K4me1 65
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me1 Library SK465 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,517,388
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.39
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.49
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.99
IROC_PERCENTILE: 63
POISSON_SCORE: 0.58
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K4me1.MSC.02.01

value: H1 Derived Mesenchymal Stem Cells

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Histone H3K4me1

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Mesenchymal Stem Cells; renlab.H3K4me3.MSC.02.01

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Mesenchymal Stem Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK467
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7919
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914
****************
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: GSM767349_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4me3.SK467.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.MSC.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library SK467, 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.10459
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,471,779
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.38
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.49
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.89
IROC_PERCENTILE: 13
POISSON_SCORE: 0.49
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM767349_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4me3.SK467.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.MSC.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK467, 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.10532
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 5
BROWSER_TRACK_NAME: HDMSC H3K4me3 67
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me3 Library SK467 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,471,779
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.38
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.49
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.89
IROC_PERCENTILE: 13
POISSON_SCORE: 0.49
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K4me3.MSC.02.01

value: Publication in progress

value: Male

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: Active Motif


description:
design description: MRE-Seq analysis of foreskin keratinocyte from skin01 (A02305) using Illumina Genome Analyzer IIx
library name: A02305
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document '5xMRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV
MRE_PROTOCOL_SIZE_FRACTION: 182-442 bp
****************
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: GSM707018_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02305-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.7942
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,593,644
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 94.5
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707018_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02305-1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.7946
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: PFK MRE 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin01 Library A02305-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,593,644
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 94.5
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: NA

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

extract_protocol: library construction protocol: Refer to document '5xMRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: male

value: Penis

value: Keratinocyte

value: No

value: primary cell culture

value: foreskin keratinocyte


description:
design description: MeDIP-Seq analysis of foreskin melanocyte from skin01 (A02300) using Illumina Genome Analyzer IIx
library name: A02300
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 0.87 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
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: GSM707020_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MeDIP-Seq.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02300-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin01 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.7931
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 62,242,542
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.3865
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4446
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9749
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5457
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707020_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MeDIP-Seq.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02300-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin01 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.7936
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: PFM MeDIP 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin01 Library A02300-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 62,242,542
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.3865
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4446
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9749
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5457
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Melanocyte

value: foreskin melanocyte


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Neural Progenitor Cells; renlab.H3K27ac.NPC.02.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Neural Progenitor Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK504
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7904
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7903
****************
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: GSM767343_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27ac.SK504.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.NPC.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library SK504, 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.10468
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,716,737
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.08
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.14
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.99
IROC_PERCENTILE: 59
POISSON_SCORE: 0.19
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

ANALYSIS FILE NAME: GSM767343_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27ac.SK504.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.NPC.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library SK504, 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.10541
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 5
BROWSER_TRACK_NAME: HDNP H3K27ac 04
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library SK504 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,716,737
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.08
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.14
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.99
IROC_PERCENTILE: 59
POISSON_SCORE: 0.19
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K27ac.NPC.02.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Between 20 and 30

value: Histone H3K27ac

value: magnetic anti-rabbit


title: fibroblast_miRNA

city: Storrs

first: James

middle: R

last: Lindsay

state: CT

address: 354 Mansfield Road, Unit 2131

department: Molecular and Cell Biology

institute: University of Connecticut

description: size fractionated small RNA

library_source: transcriptomic

data_processing: custom pipeline to remove adapters and size select reads for the appropriate class

molecule: total RNA

organism: Notamacropus eugenii

source_name: pouch young fibroblasts

extract_protocol: Hannon Protocol

tag: age

value: 125 days

tag: sample origin

value: pouch young fibroblasts

tag: small rna classes

value: miRNA


description:
design description: MeDIP-Seq analysis of foreskin fibroblast from skin01 (A02301) using Illumina Genome Analyzer IIx
library name: A02301
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 0.57 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
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: GSM707021_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MeDIP-Seq.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02301-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin01 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.7933
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 65,855,098
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4023
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4579
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9772
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5496
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707021_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MeDIP-Seq.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02301-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin01 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.7938
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: PFF MeDIP 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin01 Library A02301-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 65,855,098
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4023
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4579
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9772
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5496
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

tag: submitted sample id

value: male

tag: body site

value: Penis

value: Fibroblast

value: foreskin fibroblast


description:
design description: MRE-Seq analysis of foreskin fibroblast from skin01 (A02304) using Illumina Genome Analyzer IIx
library name: A02304
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document '5xMRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV
MRE_PROTOCOL_SIZE_FRACTION: 175-421 bp
****************
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: GSM707017_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MRE-Seq.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02304-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin01 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.7941
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 55,654,361
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 95.2
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707017_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MRE-Seq.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02304-1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin01 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.7945
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: PFF MRE 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin01 Library A02304-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 55,654,361
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 95.2
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: NA

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

tag: histological type

tag: is tumor

value: No

value: primary cell culture


description:
design description: MRE-Seq analysis of fetal brain tissue from H22510 (A04895) using Illumina Genome Analyzer IIx
library name: A04895
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, SsiI
MRE_PROTOCOL_SIZE_FRACTION: 168-400 bp
****************
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: GSM707015_UCSF-UBC.Fetal_Brain.MRE-Seq.H22510.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A04895-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Brain MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Fetal Brain, Donor H22510 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.7940
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,477,014
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.6
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707015_UCSF-UBC.Fetal_Brain.MRE-Seq.H22510.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A04895-1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Fetal Brain, Donor H22510 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.7944
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: FB MRE 10
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain MRE-Seq Donor H22510 Library A04895-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,477,014
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.6
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

extract_protocol: library construction protocol: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: Brain

value: Brain tissue

value: primary tissue

value: fetal brain tissue


description:
design description: MRE-Seq analysis of foreskin melanocyte from skin01 (A02303) using Illumina Genome Analyzer IIx
library name: A02303
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document '5xMRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV
MRE_PROTOCOL_SIZE_FRACTION: 147-454 bp
****************
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: GSM707016_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MRE-Seq.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02303-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin01 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.7939
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,517,339
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 94.7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM707016_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MRE-Seq.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02303-1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin01 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.7943
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: PFM MRE 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin01 Library A02303-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,517,339
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 94.7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Melanocyte

value: foreskin melanocyte


title: CD14+CD16++

status: Public on Jul 24 2011

city: Frankfurt am Main

first: Björn

last: Rotter

country: Germany

institute: GenXPro-GmbH

description: RNA from 12 volunteers was matched

data_processing:
Illumina GA-20, Version IIX SuperSAGE/deepSuperSAGE Normalization. Data processing: Quantification of tags, Annotation to Refseq Human RNA, if no hit in this database the Human Refseq-genomics and Refseq all vertebrate mammalian database were used as reference databases in the respective order. The tags were normalized to one million reads per sample (Tag count/sum of all tags per experiment*1000000). Only tags which were present at least twice were included.
Exact genome build information is unknown, but DBs (human RNA and genomic) were downloaded November 13th, 2010, the vertebrate mammalian was downloaded the 14th of November 2010.

source_name: isolated monocyte subset

extract_protocol: SuperSAGE/deepSuperSAGE. SuperSAGE library preparation by GenXPro-GmbH, essentially as described by Matsumura et al. 2010; Total RNA from monocyte subsets was isolated and same aliquots from each donor and monocyte subset were matched for SuperSAGE. Three SuperSAGE libraries (CD14++CD16-, CD14++CD16+ and CD14+CD16++) were generated.

treatment_protocol: Human monocyte subsets (CD14++CD16-, CD14++CD16+, CD14+CD16++) were isolated from 12 healthy volunteers based on MACS technology. RNA extraction using RNAeasy Kit (Qiagen)

value: monocytes

tag: health status

value: healthy

tag: cell type subset


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Mesenchymal Stem Cells; renlab.H3K4me3.MSC.01.01

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Mesenchymal Stem Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK463
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7901
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7874
****************
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: GSM767348_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4me3.SK463.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.MSC.01.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library SK463, 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.10453
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,255,149
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.21
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.37
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.88
IROC_PERCENTILE: 7
POISSON_SCORE: 0.42
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM767348_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4me3.SK463.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.MSC.01.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK463, 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.10526
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 5
BROWSER_TRACK_NAME: HDMSC H3K4me3 63
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me3 Library SK463 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,255,149
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.21
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.37
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.88
IROC_PERCENTILE: 7
POISSON_SCORE: 0.42
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K4me3.MSC.01.01

tag: sample alias

tag: sample common name

value: H1 Derived Mesenchymal Stem Cells

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Publication in progress

value: Male

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: CD14++CD16+

description: RNA from 12 volunteers was matched


title: testis_miRNA

description: size fractionated small RNA

source_name: pouch young testis

value: 125 days

value: pouch young testis

value: miRNA


title: CD14++CD16-

description: RNA from 12 volunteers was matched

value: monocytes

value: healthy


title: testis_crasiRNA

description: size fractionated small RNA

value: crasiRNA


title: INPUT_H1299_ChipSeq

status: Public on Jul 25 2011

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

description: Chromatin IP against sonicated genomic DNA

data_processing: DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the HG18 genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described in (Koch et al, Nat Struct Mol Biol (2011), advance online doi:10.1038/nsmb.2085) . As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

source_name: H1299 Cell line

growth_protocol: H1299 cells were grown in DMEM, supplemented with 10% FCS, 100 U ml-1 penicillin-streptomycin and 2mM L-glutamine. Cells were crosslinked with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 50mM Hepes pH 7.8) for a final formaldehyde concentration of 1% for 10 minutes at room temperature. The reaction was quenched with the addition of 250mM glycine and an incubation at room temperature for 5 minutes. Cells were washed twice with cold DPBS and counted using a Vi-CELL cell counter (Beckman Coulter, France). Aliquots of 5x107 cells were snap-frozen in liquid nitrogen and stored at -80C for later use.

extract_protocol: Library were prepared in accordance with the Illumina protocol for ChIP-Seq experiments.

treatment_protocol:
EDTA-free protease inhibitors (Roche, France) were added to all buffers to a final concentration of 1x together with 0.2mM PMSF and 1µg/ml pepstatin. Aliquots of 5x107 cells were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at 4°C. Chromatin was collected by centrifugation for 5 minutes at 4°C and 1.350g in a tabletop centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc, USA) sonicator for 12 cycles (30 seconds on, 30 seconds off, amplitude 40) with the tubes submerged in ice-cold sonication solution (500mM NaCl, 20% Ethanol). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g and 4°C for 20 minutes. For batch processing, supernatants were combined, mixed thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at -80°C until use and 50µl aliquots were taken to serve as input controls.
All experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G. Beads were washed 3x with 1ml and subsequently resuspended in 250µl of blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody (santa cruz N-20, ref sc-899x for RNA polymerase II and Abcam ab9050 for H3k36me3), the beads were incubated at 4°C overnight on a rotating wheel. Unbound antibodies were removed through three further washes with 1ml of blocking solution. Beads were resuspended in 100µl of blocking solution, extracts were added and the mix was incubated overnight at 4°C on a rotating wheel.
Beads were washed 8 times in RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 10 mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE+ (10mM Tris pH8, 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps at 65°C for 15 and 10 minutes in 110µl and 100µl of elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65°C overnight (13-15 hours) for crosslink reversal. DNA was purified as described for the input.

tag: tumor stage

value: Immortalized

tag: tissue

value: Lung carcinoma

tag: chip antibody


title: cell_crasiRNA

description: size fractionated small RNA

source_name: pouch young cell

value: pouch young cell


title: CSHL_RnaSeq_HeLa-S3_cell_longPolyA (superseded by GSE86661)

status: Public on Jul 22 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
****************************
GSM765402 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE86661
****************************

molecule: polyA RNA

value: immortalized cell line

tag: line

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell lineage

value: ectoderm

tag: rnaextract

value: longPolyA

tag: rnaextract description

value: Poly(A)+ RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Paired 76 nt directed reads

tag: replicate

tag: spikeinpool

value: Paired 76 n.t. directed reads

tag: replicate description

value: tier 1


title: CSHL_RnaSeq_K562_cell_longPolyA (superseded by GSE86660)

description:
****************************
GSM765405 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE86660
****************************

tag: localization description

value: Whole cell


title: CSHL_RnaSeq_NHEK_cytosol_longPolyA (superseded by GSE78593)

description:
****************************
GSM765400 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78593
****************************

source_name: NHEK

tag: cell sex

value: F

value: tier 3


title: CSHL_RnaSeq_AG04450_cell_longNonPolyA (superseded by GSE78599)

description:
****************************
GSM765396 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78599
****************************

value: longNonPolyA

value: Poly(A)- RNA longer than 200 nt


title: CSHL_RnaSeq_NHLF_cell_longPolyA (superseded by GSE78595)

description:
****************************
GSM765394 record metadata submitted on July 11, 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78595
****************************

source_name: NHLF

tag: cell description

value: lung fibroblasts

tag: cell karyotype

value: normal


title: CSHL_RnaSeq_K562_nucleolus_total (superseded by GSE90239)

description:
****************************
GSM765393 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90239
****************************

molecule: nuclear RNA

tag: datatype

value: total

value: Total RNA extract (longer than 200 nt)

value: The part of the nucleus where ribosomal RNA is actively transcribed


title: CSHL_RnaSeq_NHEK_cell_longPolyA (superseded by GSE78594)

description:
****************************
GSM765401 record metadata submitted on July 11, 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78594
****************************

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression


title: CSHL_RnaSeq_NHEK_cell_longNonPolyA (superseded by GSE78591)

description:
****************************
GSM765398 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78591
****************************


title: CSHL_RnaSeq_SK-N-SH_RA_cell_longPolyA (superseded by GSE90232)

description:
****************************
GSM765395 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90232
****************************

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: longPolyA

value: Poly(A)+ RNA longer than 200 nt


title: CSHL_RnaSeq_K562_chromatin_total (superseded by GSE90238)

description:
****************************
GSM765392 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90238
****************************

value: iIDR

value: Paired 76 nt directed reads

value: Nuclear DNA and associated proteins

value: Paired 76 n.t. directed reads


title: Trypanosoma brucei brucei strain 247MelCyR procyclic culture library 2

status: Public on Jul 28 2011

city: Glasgow

first: Anneli

last: Cooper

address: GBRC, 120 University Place

department: Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

data_processing: Read sequences were trimmed to 21bp (4bp NlaIII site + 17bp), then tag counts collated for each read sequence in each library using a custom written script with Perl 5.10.0.

organism: Trypanosoma brucei brucei

source_name: Trypanosoma brucei brucei strain 247MelCyR procyclic culture 2

growth_protocol: Procyclic form T.b.brucei strains STIB 247 and  247MelCyR were grown in SDM-79 media supplemented with 10% fetal bovine serum and harvested during mid-log phase (approximately 4,500,000 cells per library).

extract_protocol: The cells were pelleted at 1100g for 10 mins at 4ºC and immediately re-suspended in RLT buffer (Qiagen RNeasy kit). The cells were disrupted by serial passage through a 26 gauge needle and stored at -80ºC before use. RNA was isolated from the cells using RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase treatment step, to ensure that there was no DNA contamination. The RNA was measured for quantity and quality by Nanodrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer according to the manufacturer’s instructions. Sequence tag preparation was performed with Digital Gene Expression Tag Profile Kit (Illumina) using NlaIII, according to the manufacturer’s instructions.

tag: strain

tag: drug sensitivity

value: Cymelarsan resistant

tag: lifecycle stage

value: procyclic culture

tag: library


title: CSHL_RnaSeq_HSMM_cell_longNonPolyA (superseded by GSE78597)

description:
****************************
GSM765391 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78597
****************************

source_name: HSMM

value: skeletal muscle myoblasts

tag: rnaextract

value: longNonPolyA

tag: rnaextract description

value: Poly(A)- RNA longer than 200 nt

tag: biorep

tag: labexpid

value: tier 1


title: CSHL_RnaSeq_K562_nucleoplasm_total (superseded by GSE90240)

description:
****************************
GSM765390 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90240
****************************

value: total

value: Total RNA extract (longer than 200 nt)

tag: labversion

tag: readtype

tag: readtype description

tag: replicate

value: That part of the nuclear content other than the chromosomes or the nucleolus

value: tier 3


title: CSHL_RnaSeq_NHLF_cell_longNonPolyA (superseded by GSE78598)

description:
****************************
GSM765389 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78598
****************************

value: RnaSeq

value: Sequencing analysis of RNA expression

value: lung fibroblasts

value: normal

tag: spikeinpool

tag: replicate description


title: CSHL_RnaSeq_MCF-7_cell_longPolyA (superseded by GSE90237)

description:
****************************
GSM765388 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90237
****************************

value: immortalized cell line

tag: line

tag: cell description

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: longPolyA

value: Poly(A)+ RNA longer than 200 nt

value: iIDR

value: Paired 76 nt directed reads


title: CSHL_RnaSeq_HeLa-S3_cytosol_longPolyA (superseded by GSE90234)

description:
****************************
GSM765404 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90234
****************************

tag: datatype

tag: datatype description

tag: cell lineage

value: ectoderm

value: Paired 76 n.t. directed reads


title: exponentialculture-dcr1-

status: Public on Jul 21 2011

city: Cold Spring Harbor

first: Mikel

last: Zaratiegui

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

description: small RNA from dcr1 KO

data_processing: Reads were aligned to the Schysosaccahromyces pombe May 2008 release reference sequence using MAQ (http://maq.sourceforge.net/) using the map function.

organism: Schizosaccharomyces pombe

source_name: exponential growing cells

growth_protocol: exponential stage growth in YEA media, harvested at OD=0.5

extract_protocol: Total RNA extracted by hot phenol method. Low molecular weight RNA enriched by FLASH-PAGE method, then small RNAs (size 15-30nt) isolated by Urea-PAGE gel, cutting band and get extraction. Ligation of adapters, size selection and PCR following manufactures's instructions (Illumina)

tag: strain

tag: developmental stage

value: exponential growing culture

tag: genotype

value: h-, Ddcr1::kanMX6, otr1R(SphI)::ura4, ura4-DS/E, ade6-210, leu1-32, his7-366


title: CSHL_RnaSeq_HMEC_cell_longNonPolyA (superseded by GSE78596)

description:
****************************
GSM765397 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78596
****************************

source_name: HMEC

value: mammary epithelial cells

tag: cell karyotype

tag: rnaextract

value: longNonPolyA

tag: rnaextract description

value: Poly(A)- RNA longer than 200 nt

value: tier 1


title: CSHL_RnaSeq_HeLa-S3_nucleus_longPolyA (superseded by GSE90235)

description:
****************************
GSM765403 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90235
****************************

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: biorep

tag: labexpid

tag: labversion


title: CSHL_RnaSeq_GM12878_nucleus_longPolyA (superseded by GSE90233)

description:
****************************
GSM765386 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90233
****************************

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: readtype

tag: readtype description

tag: replicate


title: Sech_RNASeq

city: Los Angeles

first: Sudeep

last: Srivastava

address: 1050 Childs Way

institute: University of Southern California

data_processing:
Alignment: Sequence reads from all samples were mapped using PerM [57] to the D. melanogaster genome sequence (FlyBase version FB2010_07) allowing 12 mismatches per 72 base pair read. MapSplice was used to map the remaining reads to de-novo junctions.
Gene annotations in D. melanogaster (FlyBase version FB2010_07) were used to assign gene identity for transcriptome quantification.  Gene expression levels were quantified using a two-parameter generalized Poisson (GP) model (http://www-rcf.usc.edu/~liangche/software.html)

organism: Drosophila sechellia

source_name: D. sechellia w

growth_protocol: RNA was extracted from adult male flies. All stocks were maintained on standard cornmeal, yeast , dextrose medium at 25 degrees celsius with a 12 hour light : dark cycle.

extract_protocol: samples were fragmented to ~250 b.p. by chemical fragmentation.  First strand cDNA was synthesized using SuperScriptÂ® II Reverse Transcriptase (Invitrogen) and a combination of random hexamer and oligo (dT) primers; second strand cDNA was synthesized using DNA polymerase I in combination with ribonuclease H.  Double stranded cDNA templates were blunt ended using End-Itâ¢ Repair Kit (Epicentre), and A-overhangs were added at both ends with Klenow fragment (3'â5' exo-minus).  Illumina GAII sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Linkâ¢ DNA Ligation Kit (Epicentre).  We then enriched for cDNA templates by performing multiplex incorporating PCR reactions and isolated 250-550 base pair fragments by gel purification.  During PCR, unique index sequences (Illumina) were incorporated into each biological sample to allow identification of reads from each sample when multiple samples were sequenced on a single lane of the flow cell.  Paired-end sequencing was carried out by loading the samples onto four lanes (three samples per lane) of a flow cell and run on an Illumina Genome Analyzer IIx sequencer using 72 cycles per end of each paired-end read.  Biological replicates of each genotype were loaded onto separate lanes.  Images were processed using Illumina's GenomeStudio software.

tag: gender

value: male

tag: tissue

value: Genital Disc


title: Maur_RNASeq

organism: Drosophila mauritiana

source_name: D. mauritiana P-insertion Q1


title: Q1A_RNASeq

organism: Drosophila sechellia x Drosophila mauritiana

source_name: hybrid introgression line 3Q1(A)


title: CSHL_RnaSeq_NHEK_nucleus_longPolyA (superseded by GSE78592)

description:
****************************
GSM765399 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78592
****************************

tag: datatype

tag: cell sex

value: F

value: longPolyA

tag: spikeinpool

tag: replicate description

value: tier 3


title: 3A_RNASeq

source_name: hybrid introgression line Q1(A)


title: CSHL_RnaSeq_K562_nucleus_longPolyA (superseded by GSE90236)

description:
****************************
GSM765387 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90236
****************************

tag: datatype description

value: Poly(A)+ RNA longer than 200 nt

value: iIDR

value: Paired 76 nt directed reads

tag: localization description

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: BJ-tert Dnase I hypersensitivity

status: Public on Jul 20 2011

city: Sydney

first: Tim

middle: R.

last: Mercer

state: New South Wales

address: 384 Victoria Street Darlinghurst NSW 2010

country: Australia

institute: Garvan

description: Dnase I cleaved DNA fragments

data_processing: Sequence data were evaluated and aligned to the reference mitochondrial genome using BowTie (Langmead et al., 2009) using default parameters and returning only unique aligning read. The 5â termini of the sequenced reads, corresponding to the cleavage sites, was used to assign each nucleotide within the mitochondrial genome an integer score corresponding to DNase I cleavage frequency. The subsequent DNase I cleavage profiles were subject to de-spiking to account for DNase I dinucleotide cleavage bias was corrected in cleavage frequencies as previously described (Hesselberth et al., 2009).

source_name: BJ-tert

growth_protocol: BJ-tert cells were cultured as described previously (http://genome.ucsc.edu/ENCODE/protocols/cell/human/BJ-tert_Stam_protocol.pdf)

extract_protocol: Samples were firstly size fractionated by sucrose gradient centrifugation to obtain fragments that were cleaved on both ends by DNase I, referred to as DNase I double-hit fragments, as  previously described (Sabo et al. ,2006).  Resultant fragments of 100-500 bp in length were then used to construct DNaseI libraries according to Illumina's genomic prep kit protocol with minor modifications as previously described (Hesselberth et al., 2009). Libraries were sequenced to produce 36 bp reads according to standard sequencing-by-synthesis methodology on an Illumina Genome Analyzer (GAII).

treatment_protocol: DNase footprinting was done as previously described (Hesselberth et al., 2009).

tag: subcellular

value: Whole cell

tag: cell type

value: BJ-tert


title: Mitochondria PARE 5' end sequencing (rep1)

description: Total RNA, no rRNA depletion

data_processing: Sequenced reads were aligned with BowTie (Langmead et al., 2009) using default parameters and returning only unique aligning read. Following alignment, reads were trimmed to the 5' terminal mononucleotide to correspond to sites of RNA cleavage.

source_name: 143B cells

growth_protocol: 143B osteosarcoma cells were cultured at 37C under humidified 95% air/5% CO2 in Dulbecco's modified Eagle's medium (DMEM, Invitrogen) containing glucose (4.5 g.l-1), 1 mM pyruvate, 2 mM glutamine, penicillin (100 U.ml-1), streptomycin sulfate (100 µg.ml-1) and 10 % fetal bovine serum (FBS).

extract_protocol: RNA was extracted from 143B mitochondria using the miRNeasy kit (Qiagen) and PARE libraries prepared as described previously (German et al. 2009). RNA was polyadenylated with E.coli poly(A) polymerase, ethanol precipitated and cytoplasmic rRNA was depleted using the RiboMinus kit (Invitrogen). RNA adaptor (5'-GUUCAGAGUUCUACAGUCCGAC-3') was ligated using T4 RNA ligase (Ambion) and RNA was extracted with phenol / chloroform, ethanol precipitated and purified using an Oligotex kit (Qiagen). RNA was then reverse transcribed (SuperscriptII, Invitrogen) using the primer (5'-CGAGCACAGAATTAATACGACT(18)V-3') and amplified by PCR (Phusion DNA Polymerase, Finnzymes) using the primers (5'-GTTCAGAGTTCTACAGTCCGAC-3' and 5'-CGAGCACAGAATTAATACGAC-3'). PCR conditions were 5 cycles of 98 °C for 20 s, 60 °C for 30 s and 72 °C for 3 min, followed by a 7 min incubation at 72C. Products were gel purified, cleaved with MmeI (New England Biolabs) and dephosphorylated (FastAP, Fermentas). Samples were run on a 12% polyacrylamide gel and a 42 nt band excised. DNA was eluted from the gel overnight with 0.3 M NaCl, filtered through a Millex 0.45 µM column and ethanol precipitated. Products were then ligated using T4 DNA ligase (Fermentas) to one of 6 double-stranded DNA adaptors (top 5'-P-TCGTATGCCGTCTTCTGCTTG-3', bottom NN: 3'-NNAGCATACGGCAGAAGACGAAC-5') that varied in the composition of an additional first 6 nucleotides (not in the given sequence) to enable barcoding of the separate tissue samples. Another 12% polyacrylamide gel was run and a 92 nt band excised and purified as above followed by PCR amplification using the following conditions : 21 cycles of 98 °C for 20 s, 60 °C for 30 s and 72 °C for 15s, followed by an incubation at 72C for 3 min. The product was run on a polyacrylamide gel and purified prior to high-throughput sequencing using the Illumina GA platform.

treatment_protocol: Mitochondria were prepared from 2 x 107 143B cells grown overnight in 15 cm2 dishes. Cells in PBS were sedimented (150 g for 5 min at 4 °C), resuspended in 4 ml of ice-cold 10 mM NaCl, 1.5 mM MgCl2 and 10 mM Tris-HCl, pH 7.5. Cells were allowed to swell for 5 min on ice and briefly homogenised with a 7 ml glass homogenizer. The sucrose concentration was then adjusted to 250 mM by adding 2 M sucrose in 10 mM Tris-HCl and 1 mM EDTA, pH 7.6 (T10E20 buffer). The nuclei from this suspension were sedimented (1,300 g for 3 min at 4 °C), and the centrifugation step was repeated for the supernatant once more. Mitochondria were sedimented from the supernatant by centrifugation (15,000 g for 15 min at 4 °C). The mitochondrial suspension was layered on a discontinuous sucrose gradient (1.0 and 1.7 M) in T10E20 buffer and centrifuged at 70,000 g for 40 min at 4C. The mitochondrial fraction was recovered from the interface between the two sucrose cushions, diluted with 400 µl of 250 mM sucrose in T10E20 buffer and washed once in the same solution. The final mitochondrial pellet was resuspended in 100 µl of 250 mM sucrose in T10E20 buffer and protein concentration as determined by the bicinchoninic acid (BCA) assay using bovine serum albumin (BSA) as a standard.

value: Mitochondria

value: 143B cells


title: Mitochondria Small RNA

description: Total RNA, fractionated (15-30nt)

data_processing: Small RNA sequenced reads were aligned to the human genome (hg18) with ZOOM requiring exact and unique matches (Lin et al., 2008).

extract_protocol: Small RNAs were harvested from isolated mitochondria using the miRNeasy RNA extraction kit (Qiagen). RNA purity and integrity was confirmed by BioAnalyser (Agilent, CA). Deep sequencing of the mitochondrial small RNA was performed on the Illumina GAII (Illumina, CA) according to the manufacturer's instructions with one modification to sample isolation from the PAGE gel after adaptor ligation was performed with a modified set of size markers to facilitate sequencing of small RNAs between 15-30nt.


title: Mitoplast RNAseq

description: Total RNA, directional, no rRNA depletion

data_processing: Sequenced reads were aligned with BowTie (Langmead et al., 2009) using default parameters and returning only unique aligning read.

extract_protocol: Deep sequencing of the isolated mitoplast RNA was performed on the Illumina GAII platform (Illumina, CA) according to the Illumina Directional RNA-Seq protocol. Notably, to capture tRNA and rRNA transcripts that are usually omitted from standard RNA sequencing approaches we employed random hexamer primers for cDNA library generation, and omitted depletion steps to preserve rRNA expression and size selection steps to preserve tRNA expression.

treatment_protocol: Mitochondria were isolated from ten 15 cm2 dishes as described above. Mitochondria were washed and suspended in STE containing 0.1% (w/v) fat-free BSA (STE/BSA) in the last step. The final pellet was suspended in a minimal amount of STE/BSA and the protein concentration was measured by the BCA assay. The mitochondria were diluted with STE/BSA to a final concentration of 50 mg.ml-1 and stirred on ice. 0.5 ml of digitonin (6.25 mg.ml-1) was added dropwise over 2 minutes and the solution was kept on ice for a further 13 minutes. 3 volumes of STE/BSA were added and the mixture was homogenised 4 times with a tight homogenizer. The mitoplasts were collected by centrifugation for 10 minutes at 10,000 g and the concentration was measured using the BCA assay. Immunoblotting was carried out to confirm the absence of the outer membrane from the mitoplasts.

value: Mitoplast


title: Hela Dnase I hypersensitivity

description: Dnase I cleaved DNA fragments

source_name: Hela

growth_protocol: Hela cells were cultured as described previously (http://genome.ucsc.edu/ENCODE/protocols/cell/human/HeLa-S3_protocol.pdf)

value: Hela


title: Mitochondria RNAseq

extract_protocol: Deep sequencing of the isolated mitochondrial RNA was performed on the Illumina GAII platform (Illumina, CA) according to the Illumina Directional RNA-Seq protocol. Notably, to capture tRNA and rRNA transcripts that are usually omitted from standard RNA sequencing approaches we employed random hexamer primers for cDNA library generation, and omitted depletion steps to preserve rRNA expression and size selection steps to preserve tRNA expression.


title: wild type control 111U-3

city: Bethesda

first: David

middle: Johannes

last: Clark

state: MD

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

data_processing: ELAND was used to align the reads to the NCBI Saccharomyces cerevisiae genome sequence Build 2.1

organism: Saccharomyces cerevisiae

source_name: wild type control

growth_protocol: Cells grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium (control), or in synthetic complete medium lacking histidine, with 10 mM 3-aminotriazole for 20 mins prior to harvesting (+3AT).

extract_protocol: The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

treatment_protocol: Nuclei were prepared and digested to mono-nucleosomes with micrococcal nuclease. Mono-nucleosomal DNA was gel-purified.

tag: strain

tag: genotype

tag: average length (bp) +/-sd

tag: assayed molecule

value: nucleosomal DNA


title: exponentialculture-wt

description: small RNA from wt

tag: developmental stage

value: exponential growing culture


title: wild type +3AT 111A-2

source_name: wild type +3AT


title: Trypanosoma brucei brucei strain STIB 247 procyclic culture library 1

source_name: Trypanosoma brucei brucei strain STIB 247 procyclic culture 1

value: STIB 247

tag: drug sensitivity

value: Cymelarsan sensitive

tag: lifecycle stage

value: procyclic culture

tag: library


title: input_6hr_WCE_ChIPSeq

status: Public on Jul 19 2011

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: input DNA

data_processing:
Alignment: Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the mouse genome (NCBI build 37, UCSC mm9) or the human genome (UCSC hg19) using the bowtie (Langmead et al., 2009) alignment tool, version 0.12.7. Only those sequences that matched uniquely to the genome with up to two mismatches were retained.
Peaks: Enriched regions of ChIP-seq signal were determined by the "MACS" (Zhang et al.,2008) peak-finding program, version 1.4.0rc2. Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively. The effective genome size was configured appropriately for mouse and human datasets, and the p-value cutoff was set to 1.00e-08 or FDR <= 1%, and a foldchange greater than five.

organism: Mus musculus

growth_protocol: Mouse embryonic stem cells (KH2) were cultured under feeder-free medium ESGRO (Millipore).  HCT-116 cells were grown in McCoyâs 5A medium supplemented with 10% FBS.

extract_protocol: Chromatin immunoprecipitation (ChIP) was performed according to previously described protocols (Wang et al. 2009 [MCB]).  Briefly,  ES cells were cross-linked by 1% formaldehyde and sonicated. 10 ug of antibodies were used in the ChIP assays. The ChIP Libraries were prepared with the Illumina DNA Sample Kit (Part# 0801-0303) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols.  Antibodies for Pol II are from Covance, 8WG16, catalog #MMS-126R.  Other antibodies were sourced from the original work of Lin et al. 2010 (Mol. Cell)

treatment_protocol: For RA induction, mouse ES cells were treated with 0.3 uM of all-trans retinoic acid for 6 hours. For serum stimulation, cells were first starved by washing cells 2x in PBS, then culturing for 40 hours in McCoy's 5A without serum. Cells were then either left untreated or treated with serum for 30 minutes before harvesting.

value: C57BL/6 (female)  x 129/S (male)

value: mES

tag: cell passage

tag: chip antibody


title: wild type +3AT 111A-3


title: Thy1+ SSC-enriched rep1

city: houston

first: Zhiyv

last: Niu

state: tx

address: One baylor plaza, 506E

department: Animal Biology

institute: University of Pennsylvania

data_processing: Individual small RNA sequences (referred to as âreadsâ) were initially analyzed using Flicker bioinformatics software using ELAND short read aligner (Illumina, Inc). To process the small RNA reads for each sample library, adaptor sequences (ATCTCGTATGCCGTCTTCTGCTTG) were aligned to respective raw reads, taking into account substitutions, inserts and deletions. The adaptor sequences were aligned to the 3â ends of the raw reads and the best matching scores was trimmed from each read. The trimmed reads were subsequently aligned to FASTA formatted pre-miRNA and mature-miRNA sequences derived from miRBase database (Release 12.0; www.mirbase.org). The statistical significance of differential miR expression between Thy1+ SSC-enriched and Thy1- somatic cell-enriched libraries was analyzed using DESeq statistic package, where the statistical significance (p) of differential miR expression was further adjusted (padj) using the Benjamimi-Hochbergâs FDR (false recovery rate).

source_name: Freshly isolated SSC enriched testis population

extract_protocol: Small RNA libraries from Thy1+ SSC-enriched and Thy1- somatic cell-enriched testis cell populations, or germ cell cultures were isolated using Trizol (Invitrogen) and purified using the Illumina manufacturer protocols âPreparing Samples for Analysis of Small RNAâ and âPreparing Samples for Small RNA Sequencing Using the Alternative v1.5 Protocolâ. The final libraries of small RNAs for each sample were gel-purified and measured using Agilent Bioanalyzer (Agilent Technologies).

value: Thy1+ spermatogonial stem cell

tag: source tissue

value: Testis

tag: passages

tag: macs antibody

value: Thy1.2 MACS Antibody


title: Thy1+ SSC-enriched rep2


title: AFF4_0hr_ChIPSeq

description: Chromatin IP against AFF4

value: Lin et al. 2010 (Mol. Cell)


title: Pol_II_6hr_ChIPSeq

description: Chromatin IP against Pol II

value: Pol II  8WG16 Covance (Mono)


title: Thy1- Somatic-enriched rep1

source_name: Freshly isolated SSC depleted testis population

value: Thy1- spermatogonial stem cell


title: Thy1- Somatic-enriched rep2


title: SSC-enriched germ cell culture 1

source_name: SSC enriched germ cell culture derived from Thy1+ SSC-enriched cell population

value: spermatogonial stem cell enriched cell culture


title: ELL2_6hr_ChIPSeq

description: Chromatin IP against ELL2


title: AFF4_6hr_ChIPSeq

description: Chromatin IP against AFF4

value: Lin et al. 2010 (Mol. Cell.)