title: Reference Epigenome: ChIP-Seq Analysis of H3K4me2 in hESC Cells; renlab.H3K4me2.hESC-03.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me2 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL96
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3464
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
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: GSM602261_UCSD.H1.H3K4me2.YL96.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.hESC-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on the H1 Cell Line, Library YL96 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.5153
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.5604
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.5517
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9992
IROC_PERCENTILE: 63
POISSON_SCORE: 0.5943
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM602261_UCSD.H1.H3K4me2.YL96.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.hESC-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the H1 Cell Line, Library YL96 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.4520
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K4me2 96
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4me2 Library YL96 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.5604
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.5517
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9992
IROC_PERCENTILE: 63
POISSON_SCORE: 0.5943
POISSON_PERCENTILE: 25

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K4me2.hESC-03.01

value: Cell Line

value: Histone H3K4me2

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in hESC Cells; renlab.H2AK5ac.hESC-01.01

status: Public on Oct 07 2010

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2AK5ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL97
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3426
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM602257_UCSD.H1.H2AK5ac.YL97.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2AK5ac ChIP-Seq on the H1 Cell Line, Library YL97 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.5163
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.1575
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2032
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8377
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3752
POISSON_PERCENTILE: 17

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

ANALYSIS FILE NAME: GSM602257_UCSD.H1.H2AK5ac.YL97.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2AK5ac ChIP-Seq read mappings from the H1 Cell Line, Library YL97 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.4527
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H2AK5ac 97
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2AK5ac Library YL97 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.1575
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2032
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8377
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3752
POISSON_PERCENTILE: 17

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2AK5ac.hESC-01.01

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

tag: molecule

value: genomic DNA

tag: disease

value: James Thompson Laboratory

tag: line

tag: lineage

value: Embryonic Stem Cell

tag: passage

value: Between 20 and 40

tag: medium

value: mTeSER

tag: Sex

value: Male

tag: batch

value: Histone H2AK5ac

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in hESC Cells; renlab.H3K18ac.hESC-02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K18ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: SAK208
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3457
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3459
****************
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: GSM602259_UCSD.H1.H3K18ac.SAK208.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.hESC-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K18ac ChIP-Seq on the H1 Cell Line, Library SAK208 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.5177
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.2431
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.1969
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8539
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4305
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM602259_UCSD.H1.H3K18ac.SAK208.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.hESC-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K18ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK208 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.4486
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K18ac 08
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K18ac Library SAK208 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.2431
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.1969
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8539
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4305
POISSON_PERCENTILE: 25

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K18ac.hESC-02.01

value: Histone H3K18ac


title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; methylC-seq_h1+bmp4_r2b

description:
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days
Library name: methylC-seq_h1+bmp4_r2b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3383
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3378
****************
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: GSM602255_UCSD.H1-BMP4.Bisulfite-Seq.methylC-seq_h1+bmp4_r2b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r2b.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line, Library methylC-seq_h1+bmp4_r2b 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5125
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS 2b
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Library methylC-seq_h1+bmp4_r2b EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.47
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 65

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

ANALYSIS FILE NAME: GSM602255_UCSD.H1-BMP4.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r1a-methylC-seq_h1+bmp4_r1b-methylC-seq_h1+bmp4_r1c-methylC-seq_h1+bmp4_r2a-methylC-seq_h1+bmp4_r2b-methylC-seq_h1+bmp4_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line combined libraries 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5129
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Combined Libraries EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.32
SPECIAL NOTE: generated from combined data in GSM602251, GSM602252, GSM602253, GSM602254, GSM602255, GSM602256 (thus .wig files on these records are identical)

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

source_name: H1 Cell Line treated with BMP4, biological replicate 2 (r2); methylC-seq_h1+bmp4_r2b

extract_protocol: Library construction protocol: Five µg of genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 100-150 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 31 µM dNTPs, 1 µl Primer 1, 1 µl Primer 2 (50 µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 4-8 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample.

value: Thomson Laboratory

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

value: 25, including 10 passages in TeSR

value: TeSR

value: Replicate 2

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95ËšC 2 min; 98ËšC 30 sec, 4 cycles of 98ËšC 15 sec, 60ËšC 30 sec, 72ËšC 4 min; 72ËšC 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; methylC-seq_h1+bmp4_r2a

description:
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days
Library name: methylC-seq_h1+bmp4_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3382
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3378
****************
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: GSM602254_UCSD.H1-BMP4.Bisulfite-Seq.methylC-seq_h1+bmp4_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r2a.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line, Library methylC-seq_h1+bmp4_r2a 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5122
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS 2a
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Library methylC-seq_h1+bmp4_r2a EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.47
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 65

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

ANALYSIS FILE NAME: GSM602254_UCSD.H1-BMP4.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r1a-methylC-seq_h1+bmp4_r1b-methylC-seq_h1+bmp4_r1c-methylC-seq_h1+bmp4_r2a-methylC-seq_h1+bmp4_r2b-methylC-seq_h1+bmp4_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line combined libraries 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5129
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Combined Libraries EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.32
SPECIAL NOTE: generated from combined data in GSM602251, GSM602252, GSM602253, GSM602254, GSM602255, GSM602256 (thus .wig files on these records are identical)

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

source_name: H1 Cell Line treated with BMP4, biological replicate 2 (r2); methylC-seq_h1+bmp4_r2a

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

value: 25, including 10 passages in TeSR

value: TeSR

value: Male


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me2 in hESC Cells; renlab.H3K4me2.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me2 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: LL322
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3462
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1595
****************
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: GSM602260_UCSD.H1.H3K4me2.LL322.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.hESC-02.01-renlab.H3K4me2.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on the H1 Cell Line, Library LL322 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.5158
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.6379
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.6394
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7027
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM602260_UCSD.H1.H3K4me2.LL322.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.hESC-02.01-renlab.H3K4me2.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the H1 Cell Line, Library LL322 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.4549
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K4me2 22
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4me2 Library LL322 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.6379
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.6394
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7027
POISSON_PERCENTILE: 75

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K4me2.hESC-01.01

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: Between 25 and 45

value: mTeSER

value: Histone H3K4me2

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; methylC-seq_h1+bmp4_r2c

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days
Library name: methylC-seq_h1+bmp4_r2c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3384
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3378
****************
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: GSM602256_UCSD.H1-BMP4.Bisulfite-Seq.methylC-seq_h1+bmp4_r2c.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line, Library methylC-seq_h1+bmp4_r2c 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5110
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS 2c
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Library methylC-seq_h1+bmp4_r2c EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.46
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 53

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

ANALYSIS FILE NAME: GSM602256_UCSD.H1-BMP4.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r1a-methylC-seq_h1+bmp4_r1b-methylC-seq_h1+bmp4_r1c-methylC-seq_h1+bmp4_r2a-methylC-seq_h1+bmp4_r2b-methylC-seq_h1+bmp4_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line combined libraries 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5129
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Combined Libraries EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.32
SPECIAL NOTE: generated from combined data in GSM602251, GSM602252, GSM602253, GSM602254, GSM602255, GSM602256 (thus .wig files on these records are identical)

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

source_name: H1 Cell Line treated with BMP4, biological replicate 2 (r2); methylC-seq_h1+bmp4_r2c

value: genomic DNA

value: Thomson Laboratory

value: Replicate 2

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95ËšC 2 min; 98ËšC 30 sec, 4 cycles of 98ËšC 15 sec, 60ËšC 30 sec, 72ËšC 4 min; 72ËšC 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; methylC-seq_h1+bmp4_r1c

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days
Library name: methylC-seq_h1+bmp4_r1c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3381
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
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: GSM602253_UCSD.H1-BMP4.Bisulfite-Seq.methylC-seq_h1+bmp4_r1c.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r1c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line, Library methylC-seq_h1+bmp4_r1c 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5112
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS 1c
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Library methylC-seq_h1+bmp4_r1c EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 41

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

ANALYSIS FILE NAME: GSM602253_UCSD.H1-BMP4.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r1a-methylC-seq_h1+bmp4_r1b-methylC-seq_h1+bmp4_r1c-methylC-seq_h1+bmp4_r2a-methylC-seq_h1+bmp4_r2b-methylC-seq_h1+bmp4_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line combined libraries 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5129
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Combined Libraries EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.32
SPECIAL NOTE: generated from combined data in GSM602251, GSM602252, GSM602253, GSM602254, GSM602255, GSM602256 (thus .wig files on these records are identical)

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

source_name: H1 Cell Line treated with BMP4, biological replicate 1 (r1); methylC-seq_h1+bmp4_r1c

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

value: 27, including 16 passages in TeSR

value: TeSR

value: Male

value: Replicate 1


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in hESC Cells; renlab.H3K4me1.hESC-03.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL131
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3534
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3533
****************
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: GSM605312_UCSD.H1.H3K4me1.YL131.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.hESC-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the H1 Cell Line, Library YL131 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.4396
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3669
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.3905
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9826
IROC_PERCENTILE: 45
POISSON_SCORE: 0.5398
POISSON_PERCENTILE: 44

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

ANALYSIS FILE NAME: GSM605312_UCSD.H1.H3K4me1.YL131.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.hESC-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H1 Cell Line, Library YL131 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.4503
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K4me1 31
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4me1 Library YL131 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3669
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.3905
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9826
IROC_PERCENTILE: 45
POISSON_SCORE: 0.5398
POISSON_PERCENTILE: 44

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K4me1.hESC-03.01

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: mTeSER

value: Histone H3K4me1

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; methylC-seq_h1+bmp4_r1b

description:
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days
Library name: methylC-seq_h1+bmp4_r1b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3380
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
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: GSM602252_UCSD.H1-BMP4.Bisulfite-Seq.methylC-seq_h1+bmp4_r1b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r1b.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line, Library methylC-seq_h1+bmp4_r1b 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5111
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS 1b
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Library methylC-seq_h1+bmp4_r1b EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.24
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 47

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

ANALYSIS FILE NAME: GSM602252_UCSD.H1-BMP4.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r1a-methylC-seq_h1+bmp4_r1b-methylC-seq_h1+bmp4_r1c-methylC-seq_h1+bmp4_r2a-methylC-seq_h1+bmp4_r2b-methylC-seq_h1+bmp4_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line combined libraries 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5129
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Combined Libraries EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.32
SPECIAL NOTE: generated from combined data in GSM602251, GSM602252, GSM602253, GSM602254, GSM602255, GSM602256 (thus .wig files on these records are identical)

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

source_name: H1 Cell Line treated with BMP4, biological replicate 1 (r1); methylC-seq_h1+bmp4_r1b

value: genomic DNA

value: Thomson Laboratory

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95ËšC 2 min; 98ËšC 30 sec, 4 cycles of 98ËšC 15 sec, 60ËšC 30 sec, 72ËšC 4 min; 72ËšC 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; methylC-seq_h1+bmp4_r1a

description:
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days
Library name: methylC-seq_h1+bmp4_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3379
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
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: GSM602251_UCSD.H1-BMP4.Bisulfite-Seq.methylC-seq_h1+bmp4_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r1a.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line, Library methylC-seq_h1+bmp4_r1a 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5126
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS 1a
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Library methylC-seq_h1+bmp4_r1a EA Release 2

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 41

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

ANALYSIS FILE NAME: GSM602251_UCSD.H1-BMP4.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1+bmp4_r1a-methylC-seq_h1+bmp4_r1b-methylC-seq_h1+bmp4_r1c-methylC-seq_h1+bmp4_r2a-methylC-seq_h1+bmp4_r2b-methylC-seq_h1+bmp4_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1-BMP4 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1-BMP4 Cell Line combined libraries 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. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5129
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1BMP4 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line Bisulfite-Seq Combined Libraries EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.32
SPECIAL NOTE: generated from combined data in GSM602251, GSM602252, GSM602253, GSM602254, GSM602255, GSM602256 (thus .wig files on these records are identical)

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

source_name: H1 Cell Line treated with BMP4, biological replicate 1 (r1); methylC-seq_h1+bmp4_r1a

value: genomic DNA

value: Cell Line

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

value: 27, including 16 passages in TeSR

value: TeSR

value: Male

value: Replicate 1


title: HPC7_Meis1

city: Cambridge

first: Samuel

middle: David

last: Foster

state: Cambridgeshire

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

department: Department of Haematology

country: United Kingdom

institute: Cambridge Institute for Medical Research

description: Chromatin IP against Meis1 protein

data_processing: Processed alignment files include either .map.txt or .export.txt files. The .map.txt files were created using the Maq software package using the default alignment settings. The .export.txt files were created using the Eland software package, again using the standard settings. All alignments were made to the mm9 mouse genome. Column headings for both file types can be found in the linked Readme file. The .bedgraph files were created using an in house script and show the sequence read denisty across the mm9 mouse genome.

organism: Mus musculus

source_name: HPC-7 Cell Line

growth_protocol: HPC-7 cells were grown in 10% conditioned mSCF and were routinely counted and split every day to be kept at a confluence between 0.7-2 x 106 cells per ml).

extract_protocol: Chromatin was fixed in 0.4% formaldehyde, sheared to 200-500bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

treatment_protocol: No treatment beyond normal growth protocol was used.

tag: cell type

value: Early haematopoietic cell line derived from ES cells


title: HPC7_Pu1

description: Chromatin IP against Pu.1 protein


title: HPC7_Scl

description: Chromatin IP against Scl protein


title: HPC7_Gata2

description: Chromatin IP against Gata2 protein


title: HPC7_Lmo2

description: Chromatin IP against Lmo2 protein


title: HPC7_IgG

description: Chromatin IP against IgG protein


title: HPC7_Gfi1b

description: Chromatin IP against Gfi1b protein


title: HPC7_Runx1

description: Chromatin IP against Runx1 protein


title: HPC7_Fli1

description: Chromatin IP against Fli1 protein


title: HPC7_H3AcK9

description: Chromatin IP against H3AcK9


title: Reference Epigenome: ChIP-Seq Input from hESC H1 Cells; renlab.Input.hESC-05.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from hESC H1 Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: YL154
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3721
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3510
****************
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: GSM605337_UCSD.H1.Input.YL154.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-05.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library YL154 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.4422
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0374
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.1195
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.6362
IROC_PERCENTILE: 40
POISSON_SCORE: 0.2415
POISSON_PERCENTILE: 61

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

ANALYSIS FILE NAME: GSM605337_UCSD.H1.Input.YL154.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-05.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library YL154 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.4467
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 Input 54
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line ChIP-Seq Input Library YL154 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0374
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.1195
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.6362
IROC_PERCENTILE: 40
POISSON_SCORE: 0.2415
POISSON_PERCENTILE: 61

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

source_name: Human embryonic stem cells; H1 cell line; renlab.Input.hESC-05.01

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: mTeSER

value: ChIP-Seq Input

value: Branson Tip Sonicator

value: Input

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H4K20me1 in hESC Cells; renlab.H4K20me1.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K20me1 in hESC Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: YL253
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3561
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3456
****************
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: GSM605329_UCSD.H1.H4K20me1.YL253.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K20me1.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H4K20me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K20me1 ChIP-Seq on the H1 Cell Line, Library YL253 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.5190
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H4K20me1_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.3061
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.1863
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8472
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4136
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM605329_UCSD.H1.H4K20me1.YL253.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K20me1.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H4K20me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K20me1 ChIP-Seq read mappings from the H1 Cell Line, Library YL253 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.4499
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H4K20me1 53
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H4K20me1 Library YL253 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K20me1_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.3061
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.1863
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8472
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4136
POISSON_PERCENTILE: 33

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H4K20me1.hESC-01.01

value: Histone H4K20me1

value: Biorupter

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me2 in hESC Cells; renlab.H3K79me2.hESC-02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me2 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL204
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3696
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3673
****************
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: GSM605322_UCSD.H1.H3K79me2.YL204.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.hESC-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me2 ChIP-Seq on the H1 Cell Line, Library YL204 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.5149
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.2744
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1514
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.7911
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4251
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM605322_UCSD.H1.H3K79me2.YL204.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.hESC-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me2 ChIP-Seq read mappings from the H1 Cell Line, Library YL204 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.4515
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K79me2 04
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K79me2 Library YL204 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.2744
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1514
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.7911
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4251
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K79me2.hESC-02.01

value: genomic DNA

value: Cell Line

value: Histone H3K79me2


title: Reference Epigenome: ChIP-Seq Analysis of H2BK20ac in hESC Cells; renlab.H2BK20ac.hESC-02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK20ac in hESC Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: SAK205
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3517
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3459
****************
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: GSM605301_UCSD.H1.H2BK20ac.SAK205.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK20ac.hESC-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2BK20ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK20ac ChIP-Seq on the H1 Cell Line, Library SAK205 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.5191
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2BK20ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.2679
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1512
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8142
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4311
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM605301_UCSD.H1.H2BK20ac.SAK205.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK20ac.hESC-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2BK20ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK20ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK205 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.4460
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H2BK20ac 05
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2BK20ac Library SAK205 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK20ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.2679
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1512
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8142
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4311
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2BK20ac.hESC-02.01

value: Male

value: Histone H2BK20ac

value: Upstate

value: upstate 07-347


title: Reference Epigenome: ChIP-Seq Analysis of H2BK5ac in hESC Cells; renlab.H2BK5ac.hESC-02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK5ac in hESC Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: SAK202
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3500
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3459
****************
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: GSM605303_UCSD.H1.H2BK5ac.SAK202.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.hESC-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK5ac ChIP-Seq on the H1 Cell Line, Library SAK202 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.5172
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.3507
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1906
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8784
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4428
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM605303_UCSD.H1.H2BK5ac.SAK202.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.hESC-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK5ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK202 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.4492
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H2BK5ac 02
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2BK5ac Library SAK202 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.3507
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1906
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8784
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4428
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2BK5ac.hESC-02.01

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: mTeSER

value: Histone H2BK5ac

value: Active Motif


title: Reference Epigenome: ChIP-Seq Input from hESC H1 Cells; renlab.Input.hESC-04.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from hESC H1 Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: YL262
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3719
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3456
****************
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: GSM605336_UCSD.H1.Input.YL262.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-04.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library YL262 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.4418
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0545
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.0803
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.3687
IROC_PERCENTILE: 26
POISSON_SCORE: 0.2465
POISSON_PERCENTILE: 64

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

ANALYSIS FILE NAME: GSM605336_UCSD.H1.Input.YL262.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-04.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library YL262 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.4451
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 Input 62
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line ChIP-Seq Input Library YL262 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0545
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.0803
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.3687
IROC_PERCENTILE: 26
POISSON_SCORE: 0.2465
POISSON_PERCENTILE: 64

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

source_name: Human embryonic stem cells; H1 cell line; renlab.Input.hESC-04.01

value: ChIP-Seq Input

value: Input

value: 500 micrograms


title: epitheliumbreast-cancer-C7

status: Public on Oct 05 2010

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Sage-Seq

library_source: transcriptomic

data_processing: Sequencing was carried out at the Wistar Institute. The first 17bps of each read is used as a tag. The number of each unique tag is counted.   Processed data file includes tag sequences (17bps) in the first column and counts (frequencies) in the second column. Illumina software pipeline OLB version 1.6, 1.7, 1.8 with CASAVA 1.5 was used for generation  of sequence: frequency processed files.

molecule: total RNA

source_name: biopsy and surgery

extract_protocol:
cDNA made from polyA RNA isolated from purified cells using antibody attached to beads were fragmented with NlaIII/MmeI restriction enzyme with subsequent adapter ligation.
Details of antibodies used in study:
CD24-Antibody: Vendor: BD-Pharmingen, Cat.#: 555426
CD44-Antibody: Vendor: BD-Pharmingen, Cat.#: 550988
CD201(EPCR)-Antibody: Vendor: BD-Pharmingen, Cat.#: 552500

tag: tissue

value: breast

value: epithelial cell

tag: disease state

value: cancer

tag: cell marker


title: Reference Epigenome: ChIP-Seq Analysis of H2BK12ac in hESC Cells; renlab.H2BK12ac.hESC-02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK12ac in hESC Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: SAK203
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3508
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3459
****************
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: GSM605297_UCSD.H1.H2BK12ac.SAK203.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.hESC-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK12ac ChIP-Seq on the H1 Cell Line, Library SAK203 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.5161
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.4795
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.202
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8701
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4939
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM605297_UCSD.H1.H2BK12ac.SAK203.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.hESC-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK12ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK203 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.4530
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H2BK12ac 03
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2BK12ac Library SAK203 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.4795
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.202
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8701
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4939
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2BK12ac.hESC-02.01

value: genomic DNA

value: Cell Line

value: Histone H2BK12ac

value: Biorupter

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: epitheliumbreast-cancer-C6

description: Sage-Seq

value: EPCR


title: epitheliumbreast-cancer-C5

description: Sage-Seq


title: epitheliumbreast-cancer-C3

description: Sage-Seq


title: epitheliumbreast-cancer-C4

description: Sage-Seq


title: epitheliumbreast-cancer-C2

description: Sage-Seq


title: HPC7_Lyl1

description: Chromatin IP against Lyl1 protein

value: Early haematopoietic cell line derived from ES cells


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in hESC Cells; renlab.H2BK15ac.hESC-02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK15ac in hESC Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: SAK204
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3513
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3459
****************
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: GSM605299_UCSD.H1.H2BK15ac.SAK204.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.hESC-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK15ac ChIP-Seq on the H1 Cell Line, Library SAK204 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.5137
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED: 5
FINDPEAKS_SCORE: 0.3599
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.1444
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.8011
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4506
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM605299_UCSD.H1.H2BK15ac.SAK204.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.hESC-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK15ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK204 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.4476
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H2BK15ac 04
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2BK15ac Library SAK204 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED: 5
FINDPEAKS_SCORE: 0.3599
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.1444
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.8011
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4506
POISSON_PERCENTILE: 40

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2BK15ac.hESC-02.01

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: mTeSER

value: Male

value: Histone H2BK15ac


title: epitheliumbreast-cancer-C1

description: Sage-Seq

value: breast


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in hESC Cells; renlab.H2AK5ac.hESC-02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2AK5ac in hESC Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: SAK201
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3460
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3459
****************
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: GSM602258_UCSD.H1.H2AK5ac.SAK201.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.hESC-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2AK5ac ChIP-Seq on the H1 Cell Line, Library SAK201 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.5130
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.2594
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1178
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.7339
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4269
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM602258_UCSD.H1.H2AK5ac.SAK201.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.hESC-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2AK5ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK201 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.4501
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H2AK5ac 01
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2AK5ac Library SAK201 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.2594
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1178
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.7339
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4269
POISSON_PERCENTILE: 33

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2AK5ac.hESC-02.01

value: Histone H2AK5ac

value: 500 micrograms


title: epitheliumbreast-normal-N7

description: Sage-Seq

source_name: reduction mammoplasty

value: epithelial cell

value: normal


title: epitheliumbreast-normal-N4

description: Sage-Seq


title: epitheliumbreast-normal-N6

description: Sage-Seq


title: epitheliumbreast-normal-N5

description: Sage-Seq


title: epitheliumbreast-normal-N3

description: Sage-Seq


title: epitheliumbreast-normal-N2

description: Sage-Seq


title: Reference Epigenome: ChIP-Seq Analysis of H4K91ac in hESC Cells; renlab.H4K91ac.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K91ac in hESC Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: YL254
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3559
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3456
****************
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: GSM605332_UCSD.H1.H4K91ac.YL254.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K91ac ChIP-Seq on the H1 Cell Line, Library YL254 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.5196
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.3479
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1945
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8655
IROC_PERCENTILE: 33
POISSON_SCORE: 0.461
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM605332_UCSD.H1.H4K91ac.YL254.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K91ac ChIP-Seq read mappings from the H1 Cell Line, Library YL254 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.4551
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H4K91ac 54
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H4K91ac Library YL254 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.3479
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1945
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8655
IROC_PERCENTILE: 33
POISSON_SCORE: 0.461
POISSON_PERCENTILE: 33

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H4K91ac.hESC-01.01

value: genomic DNA

value: Cell Line

value: Histone H4K91ac