description:
design description: H3K4me1 ChIP-Seq analysis of foreskin keratinocyte from skin03 (A15572) using Illumina HiSeq 2000
library name: A15572
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 134-471 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
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: GSM958161_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me1.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15572-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13914
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 80,401,389
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.2852
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.3346
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9712
IROC_PERCENTILE: 53
POISSON_SCORE: 0.5008
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM958161_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me1.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15572-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13965
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 8
BROWSER_TRACK_NAME: PFK H3K4me1 03 72
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15572 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 80,401,389
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.2852
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.3346
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9712
IROC_PERCENTILE: 53
POISSON_SCORE: 0.5008
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.98

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


title: UW_DnaseSeq_Retina_adult-8wks_C57BL/6

status: Public on Oct 03 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Retina

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeUwDnase

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell

value: Retina

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

value: M

tag: age

tag: age description

value: Adult 8 weeks

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse

tag: labexpid

tag: labversion

tag: replicate


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: H3K4me3 ChIP-Seq analysis of foreskin fibroblast from skin03 (A15566) using Illumina HiSeq 2000
library name: A15566
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 10 ug
SIZE_FRACTION: 130-445 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM958158_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15566-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13925
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,092,900
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 17
FINDPEAKS_SCORE: 0.4005
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4087
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4699
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM958158_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15566-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13976
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 8
BROWSER_TRACK_NAME: PFF H3K4me3 03 66
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin03 Library A15566 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,092,900
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 17
FINDPEAKS_SCORE: 0.4005
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4087
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4699
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

organism: Homo sapiens

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

tag: histological type

value: Fibroblast

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: foreskin fibroblast


title: UW_DnaseSeq_HeadlessEmbryo_E11.5_CD-1

source_name: HeadlessEmbryo

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: cell

value: HeadlessEmbryo

value: Whole embryos with heads removed

value: Embryonic day 11.5

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


description:
design description: H3K27ac ChIP-Seq analysis of foreskin melanocyte from skin03 (A15584) using Illumina HiSeq 2000
library name: A15584
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 96-433 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
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: GSM958157_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27ac.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15584-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13921
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,762,999
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 24
FINDPEAKS_SCORE: 0.2074
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.2546
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9962
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3661
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM958157_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27ac.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15584-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13972
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 8
BROWSER_TRACK_NAME: PFM H3K27ac 03 84
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27ac Donor skin03 Library A15584 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,762,999
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 24
FINDPEAKS_SCORE: 0.2074
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.2546
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9962
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3661
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Melanocyte

value: foreskin melanocyte


title: UW_DnaseSeq_mG/ER_adult-8wks_C57BL/6

source_name: mG/ER

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

value: DNaseI HS Sequencing

value: mG/ER

tag: cell organism

tag: cell description

value: MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with Β-estradiol treatment

tag: cell sex

tag: age

tag: age description


title: UW_DnaseSeq_NIH-3T3_immortalized_NIH/Swiss

value: mouse

value: fibroblast

value: M

value: immortalized

value: Immortal cells

tag: strain

value: NIH/Swiss

tag: strain description

value: An outbred Swiss mouse  used as a general-purpose stock. Used extensively for pertussis HSF testing.

tag: labexpid

tag: labversion

tag: replicate


title: UW_DnaseSeq_Patski_immortalized_Spretus.BL6-Xist

source_name: Patski

value: Patski

value: Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res.  2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic  kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is  always the inactive X. This is an adherent cell line.


description:
design description: H3K27ac ChIP-Seq analysis of foreskin keratinocyte from skin03 (A15577) using Illumina HiSeq 2000
library name: A15577
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 121-459 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
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: GSM958156_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27ac.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15577-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13931
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 71,960,455
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 24
FINDPEAKS_SCORE: 0.1812
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.2087
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9955
IROC_PERCENTILE: 38
POISSON_SCORE: 0.3064
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM958156_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27ac.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15577-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13982
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 8
BROWSER_TRACK_NAME: PFK H3K27ac 03 77
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27ac Donor skin03 Library A15577 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 71,960,455
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 24
FINDPEAKS_SCORE: 0.1812
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.2087
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9955
IROC_PERCENTILE: 38
POISSON_SCORE: 0.3064
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

tag: histological type

value: Keratinocyte

tag: is tumor

value: No

value: primary cell culture

value: foreskin keratinocyte


description:
design description: H3K4me3 ChIP-Seq analysis of foreskin keratinocyte from skin03 (A15573) using Illumina HiSeq 2000
library name: A15573
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 10 ug
SIZE_FRACTION: 158-473 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM958155_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15573-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13929
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,330,966
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 17
FINDPEAKS_SCORE: 0.6939
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.6926
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9999
IROC_PERCENTILE: 80
POISSON_SCORE: 0.6979
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM958155_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15573-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13980
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 8
BROWSER_TRACK_NAME: PFK H3K4me3 03 73
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15573 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,330,966
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 17
FINDPEAKS_SCORE: 0.6939
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.6926
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9999
IROC_PERCENTILE: 80
POISSON_SCORE: 0.6979
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

tag: cell type


title: UW_DnaseSeq_ZhBTc4_E0_129/Ola

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell

value: Undifferentiated mouse embryonic stem cells

value: Embryonic day 0 (stem cell)

value: The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice.


title: UW_DnaseSeq_GenitalFatPad_adult-8wks_C57BL/6

source_name: GenitalFatPad

value: GenitalFatPad

tag: cell organism

value: mouse

tag: cell description

value: Genital Adipose tissue

tag: cell sex

value: M

tag: age

tag: age description

value: Adult 8 weeks

value: C57 black 6, the most common inbred strain of laboratory mouse


title: UW_DnaseSeq_ForelimbBud_E11.5_CD-1

source_name: ForelimbBud

value: ForelimbBud

value: embryo forelimb buds

value: Embryonic day 11.5

tag: strain

tag: strain description

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.

tag: labversion

tag: replicate


description:
design description: H3K27me3 ChIP-Seq analysis of foreskin fibroblast from skin03 (A15568) using Illumina HiSeq 2000
library name: A15568
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 133-410 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00242
****************
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: GSM958154_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K27me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15568-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13916
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 61,765,652
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.0382
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.1101
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.8695
IROC_PERCENTILE: 56
POISSON_SCORE: 0.3442
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM958154_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K27me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15568-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13967
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 8
BROWSER_TRACK_NAME: PFF H3K27me3 03 68
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin03 Library A15568 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 61,765,652
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.0382
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.1101
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.8695
IROC_PERCENTILE: 56
POISSON_SCORE: 0.3442
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

tag: histological type

value: Fibroblast

value: No

value: primary cell culture

value: foreskin fibroblast


title: UW_DnaseSeq_B-cell_(CD43-)_adult-8wks_C57BL/6

description: SRR579076, which is associated with SRX191028/GSM1014170, and SRR574026, which is associated with SRX188640/GSM1003813, are the same runs.

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

value: DNaseI HS Sequencing

value: mouse spleen B cells, CD43-,CD11b-

tag: labexpid


description:
design description: H3K9me3 ChIP-Seq analysis of foreskin keratinocyte from skin03 (A15574) using Illumina HiSeq 2000
library name: A15574
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 138-446 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
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: GSM958153_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K9me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15574-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13918
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,470,006
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 18
FINDPEAKS_SCORE: 0.0771
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.1136
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.8514
IROC_PERCENTILE: 44
POISSON_SCORE: 0.3833
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM958153_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K9me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15574-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13969
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 8
BROWSER_TRACK_NAME: PFK H3K9me3 03 74
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15574 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,470,006
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 18
FINDPEAKS_SCORE: 0.0771
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.1136
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.8514
IROC_PERCENTILE: 44
POISSON_SCORE: 0.3833
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Keratinocyte

tag: is tumor

tag: cell type

value: foreskin keratinocyte


title: UW_DnaseSeq_Cerebrum_adult-8wks_C57BL/6

source_name: Cerebrum

tag: datatype

tag: datatype description

tag: cell

value: Cerebrum

tag: cell organism

value: mouse

tag: cell description

value: M

value: Adult 8 weeks

value: C57 black 6, the most common inbred strain of laboratory mouse


title: UW_DnaseSeq_A20_immortalized_BALB/cAnN

value: B cell lymphoma line derived from a spontaneous reticulum cell neoplasm

tag: cell sex

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: strain

value: BALB/cAnN

tag: strain description

value: ccMyeloma high incidence H2d


description:
design description: H3K4me1 ChIP-Seq analysis of foreskin melanocyte from skin03 (A15579) using Illumina HiSeq 2000
library name: A15579
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 97-408 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
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: GSM958152_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me1.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15579-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13928
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 56,786,318
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.2804
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.3281
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9651
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4973
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM958152_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me1.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15579-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13979
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 8
BROWSER_TRACK_NAME: PFM H3K4me1 03 79
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15579 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 56,786,318
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.2804
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.3281
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9651
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4973
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

value: Melanocyte

value: No

value: primary cell culture

value: foreskin melanocyte


title: UW_DnaseSeq_Heart_adult-8wks_C57BL/6

source_name: Heart

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

value: DNaseI HS Sequencing

value: Heart

tag: labversion

tag: replicate


title: UW_DnaseSeq_FatPad_adult-8wks_C57BL/6

source_name: FatPad

tag: datatype

value: FatPad

value: mouse

value: Adipose tissue

value: M

value: Adult 8 weeks

value: C57 black 6, the most common inbred strain of laboratory mouse


title: Human_T24_RNA-seq

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

description:
RNA seq of human thyroid primary cell at 24 hr after  G28.5 treatment
human_24hour

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  human hg18 or mouse mm9 exon and exon junction sequences  and contamination datanases using bwa algorithm
After filtering reads mapped to contamination databases, the reads that  have one or no mismatch and are uniquely aligned to each exon and splicing-junction sites were extracted and then counted. The read count for each RefSeq transcript was calculated by combining the counts for exons and splicing junctions of corresponding transcript.
Supplementary_files_format_and_content: tab-delimited txt file including  count values for RefSeq transcripts
Genome_build: hg18 or mm9

molecule: total RNA

source_name: primary thyroid cell line

growth_protocol: Human thyroid primary cells were prepared from fresh, non-cancerous thyroid tissue adjacent to thyroid tumors that were removed at surgery. Tissue was minced and digested in a 50 ml falcon tube with type II collagenase at a concentration of 5 mg/ml for three hours at 37 degrees celsius. After three hours, 10ml of medium [DMEM, 4.0 mM L-glutamine and sodium pyruvate, 10% FBS, 1% antibiotic anti-mycotic solution  was added to the tube, and the product was strained through a 70 um cell strainer into another 50 ml falcon tube. The tube was centrifuged at 1000 rpm for 5 minutes. The supernatant was carefully removed from the pellet and the pellet was washed with another 10 ml of medium. Again, the tube was spun at 1000 rpm for 5 minutes. The medium was removed from the pellet. The pellet was suspended in 10 ml of medium, and the cells were plated in a 25 cm2 flask, and placed in an incubator at 37 degrees celsius with 5% CO2.

extract_protocol: According to Illumina mRNA Sequencing Sample Preparation Guide. Briefly, 2ug total RNA hybridized to poly dT magnetic beads to capture polyA mRNA molecules. Chemical fragmentation, first strand synthesis with RTase, randomers second strand synthesis. Then end repair, 3' A overhang, multiplex adapter ligation (from Illumina indexing kit), size selection by electrophoresis and cut at 200bp. 18 cycles of PCR with a primer bearing an indexing barcode.

treatment_protocol: Primary thyroid cell cultures were washed with 10ml PBS after 24 hours, and then 10mL of medium [DMEM, 4.0 mM L-glutamine and sodium pyruvate, 10% FBS, 1% antibiotic anti-mycotic solution (all from Hyclone/Thermo Fisher Waltham, MA)] were added to the flask. This was allowed to incubate at 37oC with 5% CO2 overnight. Cell were washed with PBS, and plated evenly in a 12 well plate. Cells were incubated 24 hours to allow for adherence to the wells. Again, the cells were washed and at this time the cells were treated for 0 or 24 hours with 1 ug of anti-CD40 stimulating antibody (G28.5).

tag: cell line

value: primary thyroid cell line

tag: treatment protocol

value: G28.5 treatment (1 ug, 24 hour)


description:
design description: H3K36me3 ChIP-Seq analysis of foreskin fibroblast from skin03 (A15569) using Illumina HiSeq 2000
library name: A15569
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 122-444 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
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: GSM958149_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K36me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15569-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13932
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 65,981,725
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.2702
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.2235
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9718
IROC_PERCENTILE: 40
POISSON_SCORE: 0.5037
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM958149_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K36me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15569-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13983
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 8
BROWSER_TRACK_NAME: PFF H3K36me3 03 69
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin03 Library A15569 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 65,981,725
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.2702
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.2235
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9718
IROC_PERCENTILE: 40
POISSON_SCORE: 0.5037
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: male

value: Penis

tag: histological type

value: Fibroblast

tag: is tumor

tag: cell type

value: foreskin fibroblast


description:
design description: H3K27me3 ChIP-Seq analysis of foreskin melanocyte from skin03 (A15582) using Illumina HiSeq 2000
library name: A15582
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 77-388 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00242
****************
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: GSM958150_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15582-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13920
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,622,487
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.1029
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.1706
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9566
IROC_PERCENTILE: 72
POISSON_SCORE: 0.3985
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM958150_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15582-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13971
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 8
BROWSER_TRACK_NAME: PFM H3K27me3 03 82
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15582 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,622,487
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.1029
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.1706
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9566
IROC_PERCENTILE: 72
POISSON_SCORE: 0.3985
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: Melanocyte

value: No

value: primary cell culture

value: foreskin melanocyte


description:
design description: H3K27me3 ChIP-Seq analysis of foreskin keratinocyte from skin03 (A15575) using Illumina HiSeq 2000
library name: A15575
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 135-459 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00242
****************
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: GSM958162_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15575-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13930
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 61,535,175
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.101
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.154
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9947
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3432
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM958162_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15575-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13981
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 8
BROWSER_TRACK_NAME: PFK H3K27me3 03 75
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15575 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 61,535,175
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.101
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.154
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9947
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3432
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: Keratinocyte

value: foreskin keratinocyte


title: UW_DnaseSeq_Liver_E14.5_129

source_name: Liver

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell

value: Liver

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

tag: age

value: Embryonic day 14.5

value: Strain 129, has widely available embryonic stem cells

tag: labexpid


title: UW_DnaseSeq_EPC_(CD117+,CD71+,TER119-)_E14.5_CD-1

tag: lab

value: liver fraction CD117+,CD71+,TER119-

value: M

tag: age description

tag: strain

tag: strain description

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: UW_DnaseSeq_Cerebellum_adult-8wks_C57BL/6

source_name: Cerebellum

value: tissue

value: cerebellum

tag: lab description

tag: datatype

value: Cerebellum

value: Adult 8 weeks

value: C57 black 6, the most common inbred strain of laboratory mouse

tag: labversion

tag: replicate


title: UW_DnaseSeq_ES-WW6_E0_Unknown

value: ES-cells isolated from mix of ~20% C57/B6J, ~75% 129/Sv and ~5% SJL strains

value: Embryonic day 0 (stem cell)

value: Unknown

value: Unknown strain origin


title: UW_DnaseSeq_416B_immortalized_B6D2F1/J

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

value: DNaseI HS Sequencing

value: myeloid progenitor cells, CD34+

value: immortalized

value: Immortal cells

value: Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1.


title: UW_DnaseSeq_EPC_(CD117+,CD71+,TER119+)_E14.5_CD-1

value: mouse

value: liver fraction CD117+,CD71+,TER119+

value: M

value: Embryonic day 14.5

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: Bisulfite-Seq analysis of RRBS_Lib 268 derived from human cingulate gyrus cells; RRBS_Lib 268

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 268
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11785
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9759
****************
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: GSM916090_BI.Brain_Cingulate_Gyrus.RRBS.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS_Lib 268.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Cingulate Gyrus RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Brain Cingulate Gyrus, Donor 149 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13906
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BCG RRBS 49 68
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus RRBS Donor 149 Library RRBS_Lib 268 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,594,472
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.4
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; RRBS_Lib 268

extract_protocol: Library construction protocol: Smith et al., Methods 48, 226-232

tag: sample alias

tag: sample common name

value: Brain, Cingulate Gyrus

value: Post-Mortem

value: no AD evident at demise

tag: molecule

value: genomic DNA

tag: disease

value: Cingulate Gyrus

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: 2x5hrs Epitect Kit

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina TruSeq adapter

value: Illumina TruSeq primer

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Illumina TruSeq primer pair

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS_Lib 274 derived from human substantia nigra cells; RRBS_Lib 274

description:
sample_term_id: UBERON_0002038
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 274
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11781
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9444
****************
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: GSM916086_BI.Brain_Substantia_Nigra.RRBS.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS_Lib 274.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Substantia Nigra RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Brain Substantia Nigra, Donor 149 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13905
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BSN RRBS 49 74
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra RRBS Donor 149 Library RRBS_Lib 274 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,761,269
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; RRBS_Lib 274

value: Brain, Substantia Nigra

value: Post-Mortem

value: no AD evident at demise

value: genomic DNA

value: Substantia Nigra


title: Bisulfite-Seq analysis of RRBS_Lib 267 and 277 derived from human mid frontal lobe cells; RRBS_Lib 267 and RRBS_Lib 277

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 267 and RRBS_Lib 277
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11780
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9448
****************
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: GSM916085_BI.Brain_Mid_Frontal_Lobe.RRBS.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS_Lib 267-RRBS_Lib 277.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Mid Frontal Lobe RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Brain Mid Frontal Lobe, Donor 149 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13907
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BMFL RRBS 49 67
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe RRBS Donor 149 Library RRBS_Lib 267 and RRBS_Lib 277 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 59,549,360
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.75
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; RRBS_Lib 267 and RRBS_Lib 277

value: Brain, Mid Frontal Lobe

value: Mid Frontal Lobe

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center


title: UW_DnaseSeq_Liver_E14.5_129.DLCR/DLCR

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell

value: Liver

tag: cell organism

value: mouse

value: M

value: Embryonic day 14.5

value: 129 strain mouse with homozygous deletion of the beta-globin LCR region, see Bender et. al. (2000). Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region.


title: UW_DnaseSeq_EPC_(CD117-,CD71+,TER119+)_E14.5_CD-1

tag: cell description

value: liver fraction CD117-,CD71+,TER119+

tag: cell sex

tag: age

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: Bisulfite-Seq analysis of RRBS_Lib 273 derived from human anterior caudate cells; RRBS_Lib 273

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 273
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11774
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5936
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916079_BI.Brain_Anterior_Caudate.RRBS.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS_Lib 273.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Anterior Caudate RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Brain Anterior Caudate, Donor 112 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13910
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BAC RRBS 12 73
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate RRBS Donor 112 Library RRBS_Lib 273 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,783,056
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.81
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: human post mortem brain region from a non Alzheimer's donor; RRBS_Lib 273

value: Brain, Anterior Caudate

value: post-mortem

value: genomic DNA

value: Anterior Caudate

value: Female

value: brain

value: 2x5hrs Epitect Kit

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina TruSeq adapter

value: Illumina TruSeq primer

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Illumina TruSeq primer pair

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS_Lib 271 derived from human angular gyrus cells; RRBS_Lib 271

description:
sample_term_id: UBERON_0002686
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 271
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11782
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9456
****************
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: GSM916087_BI.Brain_Angular_Gyrus.RRBS.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS_Lib 271.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Angular Gyrus RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Brain Angular Gyrus, Donor 149 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13903
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BAG RRBS 49 71
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus RRBS Donor 149 Library RRBS_Lib 271 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,684,751
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.95
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; RRBS_Lib 271

value: Brain, Angular Gyrus

value: Post-Mortem

value: no AD evident at demise

value: Angular gyrus

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years


title: UW_DnaseSeq_ES-E14_E0_129/Ola

tag: lab

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

value: DNaseI HS Sequencing

tag: line

value: mouse

value: mouse embryonic stem cells

value: M

tag: age description

value: Embryonic day 0 (stem cell)

value: The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice.

tag: labexpid


title: Bisulfite-Seq analysis of RRBS_Lib 272 derived from human substantia nigra cells; RRBS_Lib 272

description:
sample_term_id: UBERON_0002038
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 272
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11773
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5938
****************
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: GSM916078_BI.Brain_Substantia_Nigra.RRBS.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS_Lib 272.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Substantia Nigra RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Brain Substantia Nigra, Donor 112 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13904
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BSN RRBS 12 72
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra RRBS Donor 112 Library RRBS_Lib 272 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,404,731
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.25
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: human post mortem brain region from a non Alzheimer's donor; RRBS_Lib 272

value: Brain, Substantia Nigra

value: post-mortem

value: genomic DNA

value: Substantia Nigra

value: Female

value: brain

value: 2x5hrs Epitect Kit

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina TruSeq adapter

value: Illumina TruSeq primer

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Illumina TruSeq primer pair

value: Pfu Turbo Cx hot start


title: UW_DnaseSeq_CH12_immortalized_B10.H-2aH-4bp/Wts

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

value: DNaseI HS Sequencing

value: mouse

value: B-cell lymphoma (GM12878 analog)

value: F

value: immortalized

value: immortalized cell line

tag: strain

tag: strain description

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: UW_DnaseSeq_ZhBTc4_E0_diffProtB_6hr_129/Ola

value: Undifferentiated mouse embryonic stem cells

value: M

value: Embryonic day 0 (stem cell)

tag: treatment

tag: treatment description

value: Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 6 hours. Doxycycline added to a final concentration of 100 ng/ml. (Stam)

value: The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice.

tag: labversion

tag: replicate


title: UW_DnaseSeq_ZhBTc4_E0_diffProtB_24hr_129/Ola

tag: datatype description

tag: cell

value: Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam)


title: UW_DnaseSeq_EPC_(CD117+,CD71-,TER119-)_E14.5_CD-1

tag: cell organism

tag: cell description

value: liver fraction CD117+,CD71-,TER119-

value: Embryonic day 14.5

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


description:
design description: H3K4me3 ChIP-Seq analysis of foreskin melanocyte from skin03 (A15580) using Illumina HiSeq 2000
library name: A15580
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 10 ug
SIZE_FRACTION: 87-374 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM958151_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15580-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13917
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,505,750
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 17
FINDPEAKS_SCORE: 0.5002
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.5032
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.2715
IROC_PERCENTILE: 7
POISSON_SCORE: 0.5009
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM958151_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15580-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13968
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 8
BROWSER_TRACK_NAME: PFM H3K4me3 03 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15580 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,505,750
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 17
FINDPEAKS_SCORE: 0.5002
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.5032
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.2715
IROC_PERCENTILE: 7
POISSON_SCORE: 0.5009
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

tag: histological type

value: Melanocyte

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: foreskin melanocyte


title: Human_T0_RNA_seq

description:
RNA seq of human thyroid primary cell without treatment
human_0hour

tag: cell line

value: primary thyroid cell line

tag: treatment protocol

value: no treatment


title: UW_DnaseSeq_THelper-Activated_adult-8wks_C57BL/6

source_name: THelper-Activated

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

value: DNaseI HS Sequencing

value: THelper-Activated

value: mouse

value: Activated primary CD4 effector cells, isolated ex vivo

tag: cell sex

tag: age

tag: age description

value: Adult 8 weeks

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse

tag: labexpid


title: Bisulfite-Seq analysis of RRBS_Lib 276 derived from human anterior caudate cells; RRBS_Lib 276

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 276
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11769
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9447
****************
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: GSM916074_BI.Brain_Anterior_Caudate.RRBS.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS_Lib 276.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Anterior Caudate RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Brain Anterior Caudate, Donor 149 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13899
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BAC RRBS 49 76
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate RRBS Donor 149 Library RRBS_Lib 276 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,916,721
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.18
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; RRBS_Lib 276

tag: sample alias

tag: sample common name

value: Brain, Anterior Caudate

value: Post-Mortem

value: no AD evident at demise

tag: molecule

value: genomic DNA

tag: disease

value: Anterior Caudate

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: 2x5hrs Epitect Kit

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina TruSeq adapter

value: Illumina TruSeq primer

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Illumina TruSeq primer pair

value: Pfu Turbo Cx hot start


title: UW_DnaseSeq_WholeBrain_adult-8wks_C57BL/6

source_name: WholeBrain

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell

value: WholeBrain

tag: cell organism

value: mouse

tag: cell description

value: Whole Brain

value: M

value: Adult 8 weeks

value: C57 black 6, the most common inbred strain of laboratory mouse

tag: labversion

tag: replicate


title: UW_DnaseSeq_ES-WW6_F1KO_E0_Unknown

tag: lab

tag: lab description

tag: datatype

value: Histone H1c, H1d, H1e triple null mouse embryonic stem cell line derived from ES-WW6 cells.

value: Embryonic day 0 (stem cell)

value: Unknown

value: Unknown strain origin


title: Hrp3-del_rep1_MNaseSeq

status: Public on Oct 02 2012

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
MNase-seq reads were aligned to the S.pombe (EF2) genome assembly using the Bowtie alignment program (Langmead et al., 2009).
The center of fragments was calcualted from paired-end reads and the fragment size was set to 140 bp.
The fragments were normalized and processed by the nucleR program (Flores & Orozco, 2011).
Genome_build: EF2
Supplementary_files_format_and_content: wig files were generated using the nucleR program.

organism: Schizosaccharomyces pombe

growth_protocol: Grow up cells in  YES medium at 30°C

extract_protocol: Cells were suspended in 200 ml of culture medium at a density of 2x107 cells/ml, and then cross-linked with formaldehyde (final concentration of 1% v/v) for 15 minutes at room temperature. The fixed cells were subjected to chromatin isolation and MNase digestion as described above(Bernardi et al., 1991). Pelleted nuclei were digested with 600 U of micrococcal nuclease (NEB) at 37°C for 20 min, and samples were subjected to proteinase K treatment followed by overnight de-cross-linking at 65°C. Naked DNA was prepared from genomic DNA digested with 100 U of micrococcal nuclease. Mono-nucleosomal fragments were gel purified from 1.5% agarose gels run in TAE, and DNA was extracted with QIAGEN gel extraction kits and subject to paired end sequencing using the Illumina platform.

tag: genotype


title: Hrp1-del_MNaseSeq


title: Hrp3-del_MNaseSeq


title: Mit1-del_MNaseSeq


title: WT_MNaseSeq


title: K279 WT Exp plus TEX

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Removal of polyA-tails from Fasta sequences
Size filtering: discarding reads shorter than 12 nt
Read mapping using segemehl version 0.1.2
Genome_build: AM743169.1
Supplementary_files_format_and_content: wiggle
Normalized (by total number of mapped reads) read coverages in wiggle format

organism: Stenotrophomonas maltophilia

source_name: bacterial

extract_protocol: Sample processing, library construction and deep sequencing analysis were performed as previously described (Sharma 2010). Briefly, total RNA was extracted from K279a and Delta-hfq cultures in exponential growth, and primary transcripts were enriched by a selective degradation of RNAs containing a 5’ mono-phosphate (5’P) by treatment with 5’P-dependent terminator exonuclease (Epicentre). Specifically, equal amounts of RNA were incubated for 60 min at 30°C with terminator exonuclease (TEX treated library) or in buffer alone (untreated library). Following phenol/chloroform extraction, the RNA was precipitated, and treated with 1 unit TAP (tobacco acid pyrophosphatase; Epicentre) for 1 h at 37°C to generate 5’ mono-phosphates for linker ligation, and again purified by organic extraction and precipitation as above. cDNA libraries for Illumina GAIIx sequencing were constructed by vertis Biotechnology AG, Germany (http://www.vertisbiotech.com/). First, -/+TEX treated RNA samples were poly(A)-tailed using poly(A) polymerase, followed by ligation of an RNA adapter to the 5´ P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV RNase H- reverse transcriptase. The resulting cDNAs were PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase. Incubation temperatures were 42°C for 20 min, ramp to 55°C, followed by 55°C for 5 min. Each library contains a specific barcode sequence, which is attached to the 5’ end of the cDNAs. The primers used for PCR amplification were designed for amplicon sequencing according to the instructions of Illumina/Solexa.

treatment_protocol: RNA was isolated from S. maltophilia wild-type and Δhfq cultures at different growth phases. Culture aliquots were removed and mixed with 0.2 vol of stop-mix (5% water-saturated phenol, 95% ethanol), snap-frozen in liquid nitrogen and stored at –80°C until RNA isolation. After thawing on ice, bacteria were centrifuged, and RNA was isolated using the TRIzol method followed by treatment with DNase I (Sittka 2008).

tag: genetic background

value: wt

tag: treatment

value: plus TEX


title: K279 dHfq Exp minus TEX

growth_protocol: RNA was isolated from S. maltophilia wild-type and Δhfq cultures at different growth phases.

value: delta hfq

value: minus TEX