title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in iPS 6.9 Cells; renlab.H3K4me3.iPS-6.9_01.01

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in iPS 6.9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK398
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6891
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6880
****************
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: GSM706075_UCSD.iPS_DF_6.9.H3K4me3.SK398.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.iPS-6.9_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the iPS DF 6.9 Cell Line, Library SK398 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.8280
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,938,026
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
FINDPEAKS_SCORE: 0.5322
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.5371
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5307
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706075_UCSD.iPS_DF_6.9.H3K4me3.SK398.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.iPS-6.9_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the iPS DF 6.9 Cell Line, Library SK398 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.8299
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 4
BROWSER_TRACK_NAME: iD6.9 H3K4me3 98
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line Histone H3K4me3 Library SK398 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,938,026
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
FINDPEAKS_SCORE: 0.5322
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.5371
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5307
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K4me3.iPS-6.9_01.01

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: mTeSR

value: Male

value: Histone H3K4me3

value: Millipore


title: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 6.9; methylC-seq_ff_ips_6_9_r1b

status: Public on Apr 13 2011

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 6.9 derived from reprogramming of foreskin fibroblasts
Library name: methylC-seq_ff_ips_6_9_r1b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6925
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6923
****************
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: GSM706058_UCSD.iPS_DF_6.9.Bisulfite-Seq.methylC-seq_ff_ips_6_9_r1b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_6_9_r1b.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 6.9 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 6.9 Cell Line, Library methylC-seq_ff_ips_6_9_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.7650
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 4
BROWSER_TRACK_NAME: iD6.9 BS 1b
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line Bisulfite-Seq Library methylC-seq_ff_ips_6_9_r1b EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 457,987,977
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.18
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 11

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

ANALYSIS FILE NAME: GSM706058_UCSD.iPS_DF_6.9.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_6_9_r1a-methylC-seq_ff_ips_6_9_r1b.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 6.9 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 6.9 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.7656
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 4
BROWSER_TRACK_NAME: iD6.9 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line Bisulfite-Seq Combined Libraries EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,058,102,841
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.19

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

SPECIAL NOTE: generated from combined data in GSM706057, GSM706058 (thus .wig files on these records are identical)

molecule: genomic DNA

organism: Homo sapiens

source_name: iPS cell line clone 6.9 derived from reprogramming of foreskin fibroblasts, biological replicate 1 (r1); methylC-seq_ff_ips_6_9_r1b

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 16degC 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: 95degC 2 min, 98degC 30 sec, then 4-8 cycles of 98degC 15 sec, 60degC 30 sec and 72degC 4 min, ending with one 72degC 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 three independent libraries from the same biological sample.

tag: sample alias

tag: sample common name

value: iPS DF 6.9 Cell Line

tag: molecule

value: genomic DNA

tag: disease

value: Thomson Laboratory

value: Cell Line

tag: line

value: iPS DF 6.9

tag: lineage

value: induced pluripotent stem cell

tag: passage

tag: medium

value: TeSR

tag: Sex

tag: batch

value: Replicate 1

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: 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: >30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

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

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 19.11; methylC-seq_ff_ips_19_11_r1a

description:
Design description: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts
Library name: methylC-seq_ff_ips_19_11_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6902
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6900
****************
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: GSM706053_UCSD.iPS_DF_19.11.Bisulfite-Seq.methylC-seq_ff_ips_19_11_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_19_11_r1a.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 19.11 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 19.11 Cell Line, Library methylC-seq_ff_ips_19_11_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.7653
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 4
BROWSER_TRACK_NAME: iD19.11 BS 1a
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Bisulfite-Seq Library methylC-seq_ff_ips_19_11_r1a EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 749,941,431
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.25
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 44

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

ANALYSIS FILE NAME: GSM706053_UCSD.iPS_DF_19.11.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_19_11_r1a-methylC-seq_ff_ips_19_11_r1b-methylC-seq_ff_ips_19_11_r2a-methylC-seq_ff_ips_19_11_r2b.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 19.11 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 19.11 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.7654
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 4
BROWSER_TRACK_NAME: iD19.11 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Bisulfite-Seq Combined Libraries EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,347,396,659
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.24

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

SPECIAL NOTE: generated from combined data in GSM706053, GSM706054, GSM706055, GSM706056 (thus .wig files on these records are identical)

source_name: iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts, biological replicate 1 (r1); methylC-seq_ff_ips_19_11_r1a

value: iPS DF 19.11 Cell Line

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: iPS DF 19.11

value: induced pluripotent stem cell

value: Male

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


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me2 in hESC H9 Cells; renlab.H3K79me2.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me2 in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK143
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6952
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6947
****************
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: GSM706078_UCSD.H9.H3K79me2.AK143.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.hESC.H9.02.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me2 ChIP-Seq on the H9 Cell Line, Library AK143 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.8292
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,205,607
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0105
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0409
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0973
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.58

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

ANALYSIS FILE NAME: GSM706078_UCSD.H9.H3K79me2.AK143.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.hESC.H9.02.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me2 ChIP-Seq read mappings from the H9 Cell Line, Library AK143 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.8311
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 4
BROWSER_TRACK_NAME: H9 H3K79me2 43
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K79me2 Library AK143 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,205,607
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0105
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0409
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0973
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.58

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K79me2.hESC.H9.02.01

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

value: H9 Cell Line

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: Between 30 and 50

value: mTeSER

value: Female

value: Histone H3K79me2

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Whole genome shotgun bisulfite sequencing of the H9 cell line; methylC-seq_h9_r1b

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of the H9 cell line
Library name: methylC-seq_h9_r1b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6863
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6860
****************
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: GSM706060_UCSD.H9.Bisulfite-Seq.methylC-seq_h9_r1b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h9_r1b.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of H9 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H9 Cell Line, Library methylC-seq_h9_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.7651
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 4
BROWSER_TRACK_NAME: H9 BS 1b
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Bisulfite-Seq Library methylC-seq_h9_r1b EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 361,168,627
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.98
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 89

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

ANALYSIS FILE NAME: GSM706060_UCSD.H9.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h9_r1a-methylC-seq_h9_r1b-methylC-seq_h9_r2a.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of H9 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H9 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.7655
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 4
BROWSER_TRACK_NAME: H9 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Bisulfite-Seq Combined Libraries EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 979,100,755
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.85

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

SPECIAL NOTE: generated from combined data in GSM706059, GSM706060, GSM706061 (thus .wig files on these records are identical)

source_name: H9 cell line, biological replicate 1 (r1); methylC-seq_h9_r1b

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell

value: TeSR

value: Replicate 1

value: DNA Methylation

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

value: Covaris S2

value: Standard fragment express, 4 cycles

value: 5 µg

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

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: >30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

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

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in iPS 19.11 Cells; renlab.H3K9me3.iPS-19.11_01.01

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in iPS 19.11 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK232
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6822
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6813
****************
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: GSM706079_UCSD.iPS_DF_19.11.H3K9me3.SK232.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.iPS-19.11_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the iPS DF 19.11 Cell Line, Library SK232 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.8294
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,587,946
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0817
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1507
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9266
IROC_PERCENTILE: 67
POISSON_SCORE: 0.2441
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706079_UCSD.iPS_DF_19.11.H3K9me3.SK232.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.iPS-19.11_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the iPS DF 19.11 Cell Line, Library SK232 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.8313
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 4
BROWSER_TRACK_NAME: iD19.11 H3K9me3 32
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Histone H3K9me3 Library SK232 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,587,946
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0817
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1507
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9266
IROC_PERCENTILE: 67
POISSON_SCORE: 0.2441
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K9me3.iPS-19.11_01.01

value: iPS DF 19.11 Cell Line

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: Between 30 and 40

value: mTeSR

value: Male

value: Histone H3K9me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Whole genome shotgun bisulfite sequencing of the H9 cell line; methylC-seq_h9_r1a

description:
Design description: Whole genome shotgun bisulfite sequencing of the H9 cell line
Library name: methylC-seq_h9_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6862
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6860
****************
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: GSM706059_UCSD.H9.Bisulfite-Seq.methylC-seq_h9_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h9_r1a.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of H9 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H9 Cell Line, Library methylC-seq_h9_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.7648
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 4
BROWSER_TRACK_NAME: H9 BS 1a
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Bisulfite-Seq Library methylC-seq_h9_r1a EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 212,424,100
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.00
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM706059_UCSD.H9.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h9_r1a-methylC-seq_h9_r1b-methylC-seq_h9_r2a.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of H9 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H9 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.7655
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 4
BROWSER_TRACK_NAME: H9 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Bisulfite-Seq Combined Libraries EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 979,100,755
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.85

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

SPECIAL NOTE: generated from combined data in GSM706059, GSM706060, GSM706061 (thus .wig files on these records are identical)

source_name: H9 cell line, biological replicate 1 (r1); methylC-seq_h9_r1a

value: H9 Cell Line

value: Thomson Laboratory

value: embryonic stem cell

value: TeSR

value: Female

value: Replicate 1

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: 16degC 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: >30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

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

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 19.11; methylC-seq_ff_ips_19_11_r1b

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts
Library name: methylC-seq_ff_ips_19_11_r1b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6903
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6900
****************
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: GSM706054_UCSD.iPS_DF_19.11.Bisulfite-Seq.methylC-seq_ff_ips_19_11_r1b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_19_11_r1b.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 19.11 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 19.11 Cell Line, Library methylC-seq_ff_ips_19_11_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.7645
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 4
BROWSER_TRACK_NAME: iD19.11 BS 1b
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Bisulfite-Seq Library methylC-seq_ff_ips_19_11_r1b EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 537,787,960
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.19
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM706054_UCSD.iPS_DF_19.11.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_19_11_r1a-methylC-seq_ff_ips_19_11_r1b-methylC-seq_ff_ips_19_11_r2a-methylC-seq_ff_ips_19_11_r2b.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 19.11 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 19.11 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.7654
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 4
BROWSER_TRACK_NAME: iD19.11 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Bisulfite-Seq Combined Libraries EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,347,396,659
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.24

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

SPECIAL NOTE: generated from combined data in GSM706053, GSM706054, GSM706055, GSM706056 (thus .wig files on these records are identical)

source_name: iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts, biological replicate 1 (r1); methylC-seq_ff_ips_19_11_r1b

value: iPS DF 19.11 Cell Line

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: iPS DF 19.11

value: induced pluripotent stem cell

value: TeSR

value: Male


title: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 19.11; methylC-seq_ff_ips_19_11_r2b

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts
Library name: methylC-seq_ff_ips_19_11_r2b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6905
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6901
****************
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: GSM706056_UCSD.iPS_DF_19.11.Bisulfite-Seq.methylC-seq_ff_ips_19_11_r2b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_19_11_r2b.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 19.11 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 19.11 Cell Line, Library methylC-seq_ff_ips_19_11_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.7652
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 4
BROWSER_TRACK_NAME: iD19.11 BS 2b
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Bisulfite-Seq Library methylC-seq_ff_ips_19_11_r2b EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 749,941,431
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.59
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM706056_UCSD.iPS_DF_19.11.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_19_11_r1a-methylC-seq_ff_ips_19_11_r1b-methylC-seq_ff_ips_19_11_r2a-methylC-seq_ff_ips_19_11_r2b.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 19.11 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 19.11 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.7654
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 4
BROWSER_TRACK_NAME: iD19.11 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Bisulfite-Seq Combined Libraries EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,347,396,659
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.24

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

SPECIAL NOTE: generated from combined data in GSM706053, GSM706054, GSM706055, GSM706056 (thus .wig files on these records are identical)

source_name: iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts, biological replicate 2 (r2); methylC-seq_ff_ips_19_11_r2b

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


title: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 19.11; methylC-seq_ff_ips_19_11_r2a

description:
Design description: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts
Library name: methylC-seq_ff_ips_19_11_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6904
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6901
****************
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: GSM706055_UCSD.iPS_DF_19.11.Bisulfite-Seq.methylC-seq_ff_ips_19_11_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_19_11_r2a.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 19.11 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 19.11 Cell Line, Library methylC-seq_ff_ips_19_11_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.7649
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 4
BROWSER_TRACK_NAME: iD19.11 BS 2a
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Bisulfite-Seq Library methylC-seq_ff_ips_19_11_r2a EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,391,307
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.58
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 56

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

ANALYSIS FILE NAME: GSM706055_UCSD.iPS_DF_19.11.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_19_11_r1a-methylC-seq_ff_ips_19_11_r1b-methylC-seq_ff_ips_19_11_r2a-methylC-seq_ff_ips_19_11_r2b.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 19.11 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 19.11 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.7654
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 4
BROWSER_TRACK_NAME: iD19.11 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Bisulfite-Seq Combined Libraries EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,347,396,659
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.24

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

SPECIAL NOTE: generated from combined data in GSM706053, GSM706054, GSM706055, GSM706056 (thus .wig files on these records are identical)

source_name: iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts, biological replicate 2 (r2); methylC-seq_ff_ips_19_11_r2a

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: >30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

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

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole genome shotgun bisulfite sequencing of the H9 cell line; methylC-seq_h9_r2a

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of the H9 cell line
Library name: methylC-seq_h9_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6864
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6861
****************
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: GSM706061_UCSD.H9.Bisulfite-Seq.methylC-seq_h9_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h9_r2a.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of H9 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H9 Cell Line, Library methylC-seq_h9_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.7646
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 4
BROWSER_TRACK_NAME: H9 BS 2a
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Bisulfite-Seq Library methylC-seq_h9_r2a EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 405,508,028
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.69
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 78

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

ANALYSIS FILE NAME: GSM706061_UCSD.H9.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h9_r1a-methylC-seq_h9_r1b-methylC-seq_h9_r2a.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of H9 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H9 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.7655
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 4
BROWSER_TRACK_NAME: H9 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Bisulfite-Seq Combined Libraries EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 979,100,755
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.85

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

SPECIAL NOTE: generated from combined data in GSM706059, GSM706060, GSM706061 (thus .wig files on these records are identical)

source_name: H9 cell line, biological replicate 2 (r2); methylC-seq_h9_r2a

value: H9 Cell Line

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell

value: TeSR

value: Female

value: Standard fragment express, 4 cycles


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in iPS 6.9 Cells; renlab.H3K4me1.iPS-6.9_01.01

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in iPS 6.9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK397
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6885
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6880
****************
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: GSM706073_UCSD.iPS_DF_6.9.H3K4me1.SK397.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.iPS-6.9_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the iPS DF 6.9 Cell Line, Library SK397 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.8298
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,929,073
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.0919
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2169
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.8894
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3688
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706073_UCSD.iPS_DF_6.9.H3K4me1.SK397.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.iPS-6.9_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the iPS DF 6.9 Cell Line, Library SK397 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.8317
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 4
BROWSER_TRACK_NAME: iD6.9 H3K4me1 97
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line Histone H3K4me1 Library SK397 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,929,073
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.0919
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2169
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.8894
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3688
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K4me1.iPS-6.9_01.01

value: iPS DF 6.9 Cell Line

value: James Thompson Laboratory

value: iPS 6.9

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: mTeSR

value: Male

value: iPSC 6.9

value: Histone H3K4me1

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in hESC H9 Cells; renlab.H3K4me1.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK141
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6948
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6947
****************
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: GSM706071_UCSD.H9.H3K4me1.AK141.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.hESC.H9.02.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the H9 Cell Line, Library AK141 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.8288
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,076,429
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.0076
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0886
HOTSPOT_PERCENTILE: 8
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1827
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.78

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

ANALYSIS FILE NAME: GSM706071_UCSD.H9.H3K4me1.AK141.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.hESC.H9.02.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H9 Cell Line, Library AK141 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.8307
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 4
BROWSER_TRACK_NAME: H9 H3K4me1 41
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K4me1 Library AK141 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,076,429
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.0076
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0886
HOTSPOT_PERCENTILE: 8
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1827
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.78

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K4me1.hESC.H9.02.01

value: H9 Cell Line

value: genomic DNA

value: Cell Line

value: Embryonic Stem Cell

value: Between 30 and 50

value: mTeSER

value: Female


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in iPS 19.11 Cells; renlab.H3K4me1.iPS-19.11_01.01

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in iPS 19.11 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK401
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6820
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6813
****************
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: GSM706072_UCSD.iPS_DF_19.11.H3K4me1.SK401.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.iPS-19.11_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the iPS DF 19.11 Cell Line, Library SK401 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.8297
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,918,857
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.2082
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3031
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9565
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4344
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706072_UCSD.iPS_DF_19.11.H3K4me1.SK401.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.iPS-19.11_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the iPS DF 19.11 Cell Line, Library SK401 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.8316
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 4
BROWSER_TRACK_NAME: iD19.11 H3K4me1 01
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Histone H3K4me1 Library SK401 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,918,857
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.2082
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3031
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9565
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4344
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K4me1.iPS-19.11_01.01

value: iPS DF 19.11 Cell Line

value: James Thompson Laboratory

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: Between 30 and 40


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in iPS 19.11 Cells; renlab.H3K4me3.iPS-19.11_01.01

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in iPS 19.11 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: SK227
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6826
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6813
****************
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: GSM706074_UCSD.iPS_DF_19.11.H3K4me3.SK227.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.iPS-19.11_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the iPS DF 19.11 Cell Line, Library SK227 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.8283
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,542,802
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
FINDPEAKS_SCORE: 0.5844
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.5843
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5731
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706074_UCSD.iPS_DF_19.11.H3K4me3.SK227.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.iPS-19.11_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the iPS DF 19.11 Cell Line, Library SK227 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.8302
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 4
BROWSER_TRACK_NAME: iD19.11 H3K4me3 27
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Histone H3K4me3 Library SK227 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,542,802
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
FINDPEAKS_SCORE: 0.5844
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.5843
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5731
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K4me3.iPS-19.11_01.01

value: mTeSR

value: Male

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: Millipore


title: Reference Epigenome: ChIP-Seq Input from iPS 6.9 Cells; renlab.Input.iPS-6.9_01.01

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from iPS 6.9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SKiPS6.9-1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6895
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6880
****************
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: GSM706083_UCSD.iPS_DF_6.9.Input.SKiPS6.9-1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.iPS-6.9_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS DF 6.9 Cell Line, Library SKiPS6.9-1 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.8282
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,724,896
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0453
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1863
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.7954
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3004
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706083_UCSD.iPS_DF_6.9.Input.SKiPS6.9-1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.iPS-6.9_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS DF 6.9 Cell Line, Library SKiPS6.9-1 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.8301
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 4
BROWSER_TRACK_NAME: iD6.9 Input 1
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line ChIP-Seq Input Library SKiPS6.9-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,724,896
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0453
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1863
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.7954
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3004
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.Input.iPS-6.9_01.01

value: iPS DF 6.9 Cell Line

value: genomic DNA

value: Cell Line

value: iPS 6.9

value: iPSC 6.9

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in iPS 19.11 Cells; renlab.H3K36me3.iPS-19.11_01.01

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in iPS 19.11 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK403
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6818
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6813
****************
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: Various levels of processed data files will be made available as this project proceeds.

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K36me3.iPS-19.11_01.01

value: iPS DF 19.11 Cell Line

value: James Thompson Laboratory

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Histone H3K36me3

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in iPS 6.9 Cells; renlab.H3K36me3.iPS-6.9_01.01

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in iPS 6.9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK400
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6883
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6880
****************
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: GSM706070_UCSD.iPS_DF_6.9.H3K36me3.SK400.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.iPS-6.9_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the iPS DF 6.9 Cell Line, Library SK400 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.8287
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,096,398
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.069
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.156
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9082
IROC_PERCENTILE: 29
POISSON_SCORE: 0.28
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706070_UCSD.iPS_DF_6.9.H3K36me3.SK400.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.iPS-6.9_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the iPS DF 6.9 Cell Line, Library SK400 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.8306
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 4
BROWSER_TRACK_NAME: iD6.9 H3K36me3 00
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line Histone H3K36me3 Library SK400 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,096,398
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.069
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.156
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9082
IROC_PERCENTILE: 29
POISSON_SCORE: 0.28
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K36me3.iPS-6.9_01.01

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: mTeSR

value: Male

value: Biorupter


title: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 6.9; methylC-seq_ff_ips_6_9_r1a

description:
Design description: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 6.9 derived from reprogramming of foreskin fibroblasts
Library name: methylC-seq_ff_ips_6_9_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6924
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6923
****************
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: GSM706057_UCSD.iPS_DF_6.9.Bisulfite-Seq.methylC-seq_ff_ips_6_9_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_6_9_r1a.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 6.9 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 6.9 Cell Line, Library methylC-seq_ff_ips_6_9_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.7647
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 4
BROWSER_TRACK_NAME: iD6.9 BS 1a
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line Bisulfite-Seq Library methylC-seq_ff_ips_6_9_r1a EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 600,114,864
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.19
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM706057_UCSD.iPS_DF_6.9.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_ff_ips_6_9_r1a-methylC-seq_ff_ips_6_9_r1b.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of iPS DF 6.9 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the iPS DF 6.9 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.7656
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 4
BROWSER_TRACK_NAME: iD6.9 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line Bisulfite-Seq Combined Libraries EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,058,102,841
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.19

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

SPECIAL NOTE: generated from combined data in GSM706057, GSM706058 (thus .wig files on these records are identical)

source_name: iPS cell line clone 6.9 derived from reprogramming of foreskin fibroblasts, biological replicate 1 (r1); methylC-seq_ff_ips_6_9_r1a

value: iPS DF 6.9 Cell Line

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: iPS DF 6.9

value: induced pluripotent stem cell

value: TeSR

value: Replicate 1

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: 16degC 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: >30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

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

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in iPS 6.9 Cells; renlab.H3K27me3.iPS-6.9_01.01

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in iPS 6.9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK275
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6881
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6880
****************
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: GSM706068_UCSD.iPS_DF_6.9.H3K27me3.SK275.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.iPS-6.9_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the iPS DF 6.9 Cell Line, Library SK275 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.8285
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,606,881
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.1477
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.2096
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9967
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2744
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706068_UCSD.iPS_DF_6.9.H3K27me3.SK275.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.iPS-6.9_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the iPS DF 6.9 Cell Line, Library SK275 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.8304
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 4
BROWSER_TRACK_NAME: iD6.9 H3K27me3 75
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line Histone H3K27me3 Library SK275 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,606,881
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.1477
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.2096
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9967
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2744
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K27me3.iPS-6.9_01.01

value: iPS DF 6.9 Cell Line

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: iPS 6.9

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: mTeSR

value: Male

value: iPSC 6.9

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore