description:
design description: Bisulfite-Seq analysis of foreskin keratinocyte from skin03 (A10341) using Illumina HiSeq 2000
library name: A10341
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 0.916 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 3 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 200-400 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 275-450 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.29
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 5
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
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: GSM1127056_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Bisulfite-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A10341-1-A10342-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Penis Foreskin Keratinocyte Primary Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.18772
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 9
BROWSER_TRACK_NAME: PFK BS 03 41
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Bisulfite-Seq Donor skin03 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 871,490,087
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.04
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1127056, GSM1127058 (thus .wig files on these records are identical)

value: Penis

value: Keratinocyte

value: primary cell culture

value: foreskin keratinocyte


status: Public on Sep 18 2013

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: Bisulfite-Seq analysis of breast myoepithelial cell from RM066 (A17783) using Illumina HiSeq 2000
library name: A17783
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 22 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 3.5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 150-300 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 263-500 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 99.94
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 16
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
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: GSM1127059_UCSF-UBC.Breast_Myoepithelial_Cells.Bisulfite-Seq.RM066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A17783-1-A12230-1-A12231-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Breast Myoepithelial Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Breast Myoepithelial Cells, Donor RM066 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.18769
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 9
BROWSER_TRACK_NAME: BMC BS 66 83
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Myoepithelial Cells Bisulfite-Seq Donor RM066 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 475,603,248
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.0
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1127059, GSM1127057, GSM1127054 (thus .wig files on these records are identical)

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: library construction protocol: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: female

tag: body site

value: Breast

tag: histological type

value: Myoepithelial cell

tag: is tumor

value: No

value: primary cell

value: breast myoepithelial cell


description:
design description: Bisulfite-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (A17784) using Illumina HiSeq 2000
library name: A17784
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 200-400 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 280-440 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 99.93
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
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: GSM1127055_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Bisulfite-Seq.HuFNSC02.A17784.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A17784-1-A13819-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.18770
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 9
BROWSER_TRACK_NAME: NGED BS 02 84
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Donor HuFNSC02 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 313,154,881
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.72
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Brain

value: Ganglionic eminence neurosphere culture

tag: cell type


description:
design description: Bisulfite-Seq analysis of foreskin keratinocyte from skin03 (A10342) using Illumina HiSeq 2000
library name: A10342
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 0.916 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 1 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 200-400 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 230-400 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.21
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 5
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
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: GSM1127058_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Bisulfite-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A10341-1-A10342-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Penis Foreskin Keratinocyte Primary Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.18772
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 9
BROWSER_TRACK_NAME: PFK BS 03 41
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Bisulfite-Seq Donor skin03 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 871,490,087
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.04
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1127056, GSM1127058 (thus .wig files on these records are identical)

value: male


description:
design description: Bisulfite-Seq analysis of breast myoepithelial cell from RM066 (A12231) using Illumina HiSeq 2000
library name: A12231
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 22 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 3.5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 150-300 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 211-459 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 99.2
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 16
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
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: GSM1127054_UCSF-UBC.Breast_Myoepithelial_Cells.Bisulfite-Seq.RM066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A17783-1-A12230-1-A12231-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Breast Myoepithelial Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Breast Myoepithelial Cells, Donor RM066 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.18769
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 9
BROWSER_TRACK_NAME: BMC BS 66 83
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Myoepithelial Cells Bisulfite-Seq Donor RM066 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 475,603,248
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.0
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1127059, GSM1127057, GSM1127054 (thus .wig files on these records are identical)


title: Whole Genome Shotgun Bisulfite Sequencing of Right Atrium Cells from Human STL003; methylC-seq_STL003RA-01c

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
Design description: Whole Genome Shotgun Bisulfite Sequencing of Right Atrium Cells from Human STL003
Library name: methylC-seq_STL003RA-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15852
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11888
****************
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: GSM1120334_UCSD.Right_Atrium.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003RA-01d-methylC-seq_STL003RA-01a-methylC-seq_STL003RA-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Right Atrium Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Right Atrium, Donor STL003 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.18762
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 9
BROWSER_TRACK_NAME: RA BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Right Atrium Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,302,897,809
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.18
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1120335, GSM1010987, GSM1120334 (thus .wig files on these records are identical)

source_name: Right Atrium tissue; methylC-seq_STL003RA-01c

extract_protocol: Library construction protocol: One µg of genomic DNA was extracted from frozen ground tissue 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 200 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: 25 µl 2x KAPA HiFi HotStart Uracil+ReadyMix, 2.5 µl Primer 1, 2.5 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 two independent libraries from the same biological sample.

tag: sample common name

value: Right Atrium

tag: sra sample accession

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian

value: DNA Methylation

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

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 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: >The adapter-ligated, bisulfite converted DNA was used in a 50 µl PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

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 Right Ventricle Cells from Human STL003; methylC-seq_STL003RV-01d

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL003
Library name: methylC-seq_STL003RV-01d
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15855
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12222
****************
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: GSM1120337_UCSD.Right_Ventricle.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003RV-01a-methylC-seq_STL003RV-01b-methylC-seq_STL003RV-01d-methylC-seq_STL003RV-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Right Ventricle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Right Ventricle, Donor STL003 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.18750
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 9
BROWSER_TRACK_NAME: RV BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,080,014,270
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.03
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010988, GSM1059433, GSM1120337, GSM1120336 (thus .wig files on these records are identical)

source_name: Right Ventricle tissue; methylC-seq_STL003RV-01d

value: Right Ventricle

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

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


title: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL003; methylC-seq_STL003GA-01d

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL003
Library name: methylC-seq_STL003GA-01d
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15851
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12180
****************
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: GSM1120333_UCSD.Gastric.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003GA-01a-methylC-seq_STL003GA-01d-methylC-seq_STL003GA-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Gastric Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Gastric, Donor STL003 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.18747
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 9
BROWSER_TRACK_NAME: Gastric BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,235,431,773
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.25
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010984, GSM1120333, GSM1120332 (thus .wig files on these records are identical)

value: Gastric

value: Male

value: Caucasian

value: DNA Methylation

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

value: Covaris S2

value: 200 bp, 3 cycles


title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003; methylC-seq_STL003AO-01d

description:
Design description: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003
Library name: methylC-seq_STL003AO-01d
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15845
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11864
****************
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: GSM1120327_UCSD.Aorta.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003AO-01a-methylC-seq_STL003AO-01f-methylC-seq_STL003AO-01e-methylC-seq_STL003AO-01c-methylC-seq_STL003AO-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Aorta Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Aorta, Donor STL003 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.18752
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 9
BROWSER_TRACK_NAME: Aorta BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,368,332,289
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.14
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM983648, GSM1120329, GSM1120328, GSM1120326, GSM1120327 (thus .wig files on these records are identical)

source_name: Aorta tissue; methylC-seq_STL003AO-01d

value: Aorta

value: 1 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: >The adapter-ligated, bisulfite converted DNA was used in a 50 µl PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix


title: Histone H3K27me3 ChIP-Seq of CD8 Primary Cells; Histone.DS22909

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS22909
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18607
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7035
****************
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: flow sorted CD8+ Cells, year 37; Histone.DS22909

extract_protocol: Library construction protocol: Single read - Illumina

value: FHCRC HEIMFELD

value: Primary Cell

value: CD8 Primary Cells

tag: markers

value: year 37

value: Hispanic

value: Histone H3K27me3

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Millipore


title: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL003; methylC-seq_STL003FT-01c

description:
Design description: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL003
Library name: methylC-seq_STL003FT-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15848
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11859
****************
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: GSM1120330_UCSD.Adipose_Tissue.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003FT-01d-methylC-seq_STL003FT-01a-methylC-seq_STL003FT-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Adipose Tissue Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Adipose Tissue, Donor STL003 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.18763
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 9
BROWSER_TRACK_NAME: AT BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Adipose Tissue Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 666,743,193
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.25
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1120331, GSM1010983, GSM1120330 (thus .wig files on these records are identical)

value: Adipose Tissue

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian

value: DNA Methylation

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

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 µg

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

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

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 Right Atrium Cells from Human STL003; methylC-seq_STL003RA-01d

description:
sample_term_id: UBERON_0002078
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Right Atrium Cells from Human STL003
Library name: methylC-seq_STL003RA-01d
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15853
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11888
****************
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: GSM1120335_UCSD.Right_Atrium.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003RA-01d-methylC-seq_STL003RA-01a-methylC-seq_STL003RA-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Right Atrium Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Right Atrium, Donor STL003 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.18762
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 9
BROWSER_TRACK_NAME: RA BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Right Atrium Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,302,897,809
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.18
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1120335, GSM1010987, GSM1120334 (thus .wig files on these records are identical)

source_name: Right Atrium tissue; methylC-seq_STL003RA-01d

value: Right Atrium

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: >The adapter-ligated, bisulfite converted DNA was used in a 50 µl PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix


title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003; methylC-seq_STL003AO-01f

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003
Library name: methylC-seq_STL003AO-01f
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15847
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11864
****************
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: GSM1120329_UCSD.Aorta.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003AO-01a-methylC-seq_STL003AO-01f-methylC-seq_STL003AO-01e-methylC-seq_STL003AO-01c-methylC-seq_STL003AO-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Aorta Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Aorta, Donor STL003 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.18752
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 9
BROWSER_TRACK_NAME: Aorta BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,368,332,289
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.14
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM983648, GSM1120329, GSM1120328, GSM1120326, GSM1120327 (thus .wig files on these records are identical)

source_name: Aorta tissue; methylC-seq_STL003AO-01f

value: Aorta

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian


title: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL003; methylC-seq_STL003RV-01c

description:
Design description: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL003
Library name: methylC-seq_STL003RV-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15854
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12222
****************
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: GSM1120336_UCSD.Right_Ventricle.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003RV-01a-methylC-seq_STL003RV-01b-methylC-seq_STL003RV-01d-methylC-seq_STL003RV-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Right Ventricle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Right Ventricle, Donor STL003 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.18750
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 9
BROWSER_TRACK_NAME: RV BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,080,014,270
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.03
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010988, GSM1059433, GSM1120337, GSM1120336 (thus .wig files on these records are identical)

source_name: Right Ventricle tissue; methylC-seq_STL003RV-01c

value: Right Ventricle

value: DNA Methylation

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

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 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 Aorta Cells from Human STL003; methylC-seq_STL003AO-01e

description:
Design description: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003
Library name: methylC-seq_STL003AO-01e
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15846
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11864
****************
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: GSM1120328_UCSD.Aorta.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003AO-01a-methylC-seq_STL003AO-01f-methylC-seq_STL003AO-01e-methylC-seq_STL003AO-01c-methylC-seq_STL003AO-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Aorta Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Aorta, Donor STL003 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.18752
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 9
BROWSER_TRACK_NAME: Aorta BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,368,332,289
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.14
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM983648, GSM1120329, GSM1120328, GSM1120326, GSM1120327 (thus .wig files on these records are identical)

source_name: Aorta tissue; methylC-seq_STL003AO-01e

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: >The adapter-ligated, bisulfite converted DNA was used in a 50 µl PCR reaction

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


description:
design description: Bisulfite-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC04 (A22476) using Illumina HiSeq 2000
library name: A22476
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 175-225 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 200-400 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.27
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 8
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
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: GSM1127121_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Bisulfite-Seq.HuFNSC04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22476-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.18771
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 9
BROWSER_TRACK_NAME: NGED BS 04 76
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Donor HuFNSC04 Library A22476 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 492,727,297
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.66
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Brain

value: Ganglionic eminence neurosphere culture

value: No

value: primary cell culture


title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003; methylC-seq_STL003AO-01c

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003
Library name: methylC-seq_STL003AO-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15844
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11864
****************
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: GSM1120326_UCSD.Aorta.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003AO-01a-methylC-seq_STL003AO-01f-methylC-seq_STL003AO-01e-methylC-seq_STL003AO-01c-methylC-seq_STL003AO-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Aorta Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Aorta, Donor STL003 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.18752
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 9
BROWSER_TRACK_NAME: Aorta BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,368,332,289
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.14
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM983648, GSM1120329, GSM1120328, GSM1120326, GSM1120327 (thus .wig files on these records are identical)

source_name: Aorta tissue; methylC-seq_STL003AO-01c

value: Aorta

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian

value: DNA Methylation

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

value: KAPA HiFi HotStart Uracil+ ReadyMix


title: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL003; methylC-seq_STL003FT-01d

description:
sample_term_id: UBERON_0001013
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL003
Library name: methylC-seq_STL003FT-01d
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15849
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11859
****************
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: GSM1120331_UCSD.Adipose_Tissue.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003FT-01d-methylC-seq_STL003FT-01a-methylC-seq_STL003FT-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Adipose Tissue Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Adipose Tissue, Donor STL003 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.18763
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 9
BROWSER_TRACK_NAME: AT BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Adipose Tissue Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 666,743,193
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.25
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1120331, GSM1010983, GSM1120330 (thus .wig files on these records are identical)

value: Adipose Tissue

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 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: >The adapter-ligated, bisulfite converted DNA was used in a 50 µl PCR reaction

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


title: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL003; methylC-seq_STL003AD-01d

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL003
Library name: methylC-seq_STL003AD-01d
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15843
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11638
****************
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: GSM1120325_UCSD.Adrenal_Gland.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003AD-01a-methylC-seq_STL003AD-01c-methylC-seq_STL003AD-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Adrenal Gland Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Adrenal Gland, Donor STL003 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.18751
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 9
BROWSER_TRACK_NAME: AG BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,008,110,717
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010981, GSM1120324, GSM1120325 (thus .wig files on these records are identical)

source_name: Adrenal Gland tissue; methylC-seq_STL003AD-01d

value: Adrenal Gland

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


description:
design description: Bisulfite-Seq analysis of cortex neural stem and progenitor cells from HuFNSC02 (A22475) using Illumina HiSeq 2000
library name: A22475
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 175-225 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 200-400 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.09
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 8
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
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: GSM1127118_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.Bisulfite-Seq.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22475-1.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Neurosphere Cultured Cells Cortex Derived Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC02 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.18767
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 9
BROWSER_TRACK_NAME: NCD BS 02 75
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Bisulfite-Seq Donor HuFNSC02 Library A22475 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 531,602,583
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.7
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: female

value: Brain

value: Cortex neurosphere culture

value: No

value: primary cell culture

value: cortex neural stem and progenitor cells


title: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL001; methylC-seq_STL001LV-01c

description:
Design description: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL001
Library name: methylC-seq_STL001LV-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15837
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11835
****************
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: GSM1120319_UCSD.Left_Ventricle.Bisulfite-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL001LV-01a-methylC-seq_STL001LV-01c-methylC-seq_STL001LV-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Left Ventricle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Left Ventricle, Donor STL001 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.18757
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 9
BROWSER_TRACK_NAME: LV BS 01
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Bisulfite-Seq Donor STL001 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,277,811,198
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.03
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

SPECIAL NOTE: generated from combined data in GSM1010978, GSM1120319, GSM1120320 (thus .wig files on these records are identical)

source_name: Left Ventricle tissue; methylC-seq_STL001LV-01c

value: Left Ventricle

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: DNA Methylation

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

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 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: KAPA HiFi HotStart Uracil+ ReadyMix


title: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL001; methylC-seq_STL001LV-01d

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL001
Library name: methylC-seq_STL001LV-01d
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15838
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11835
****************
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: GSM1120320_UCSD.Left_Ventricle.Bisulfite-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL001LV-01a-methylC-seq_STL001LV-01c-methylC-seq_STL001LV-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Left Ventricle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Left Ventricle, Donor STL001 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.18757
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 9
BROWSER_TRACK_NAME: LV BS 01
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Bisulfite-Seq Donor STL001 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,277,811,198
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.03
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

SPECIAL NOTE: generated from combined data in GSM1010978, GSM1120319, GSM1120320 (thus .wig files on these records are identical)

source_name: Left Ventricle tissue; methylC-seq_STL001LV-01d

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 µl PCR reaction

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 Thymus Cells from Human STL001; methylC-seq_STL001TH-01c

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Thymus Cells from Human STL001
Library name: methylC-seq_STL001TH-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15840
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13369
****************
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: GSM1120322_UCSD.Thymus.Bisulfite-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL001TH-01a-methylC-seq_STL001TH-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Thymus Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Thymus, Donor STL001 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.18749
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 9
BROWSER_TRACK_NAME: Thymus BS 01
BROWSER_TRACK_DESCRIPTION: UCSD Thymus Bisulfite-Seq Donor STL001 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,247,539,549
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.28
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010979, GSM1120322 (thus .wig files on these records are identical)

source_name: Thymus tissue; methylC-seq_STL001TH-01c

value: Thymus

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: DNA Methylation

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


title: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL003; methylC-seq_STL003AD-01c

description:
Design description: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL003
Library name: methylC-seq_STL003AD-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15842
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11638
****************
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: GSM1120324_UCSD.Adrenal_Gland.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003AD-01a-methylC-seq_STL003AD-01c-methylC-seq_STL003AD-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Adrenal Gland Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Adrenal Gland, Donor STL003 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.18751
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 9
BROWSER_TRACK_NAME: AG BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,008,110,717
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010981, GSM1120324, GSM1120325 (thus .wig files on these records are identical)

source_name: Adrenal Gland tissue; methylC-seq_STL003AD-01c

value: Adrenal Gland

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 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)


title: Whole Genome Shotgun Bisulfite Sequencing of Ovary Cells from Human STL002; methylC-seq_STL002OV-01c

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Ovary Cells from Human STL002
Library name: methylC-seq_STL002OV-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15841
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13360
****************
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: GSM1120323_UCSD.Ovary.Bisulfite-Seq.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL002OV-01a-methylC-seq_STL002OV-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Ovary Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Ovary, Donor STL002 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.18755
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 9
BROWSER_TRACK_NAME: Ovary BS 02
BROWSER_TRACK_DESCRIPTION: UCSD Ovary Bisulfite-Seq Donor STL002 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,339,301,372
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010980, GSM1120323 (thus .wig files on these records are identical)

source_name: Ovary tissue; methylC-seq_STL002OV-01c

value: Ovary

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

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: >The adapter-ligated, bisulfite converted DNA was used in a 50 µl PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

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


title: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL003; methylC-seq_STL003RV-01b

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL003
Library name: methylC-seq_STL003RV-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15089
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12222
****************
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: GSM1059433_UCSD.Right_Ventricle.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003RV-01a-methylC-seq_STL003RV-01b-methylC-seq_STL003RV-01d-methylC-seq_STL003RV-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Right Ventricle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Right Ventricle, Donor STL003 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.18750
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 9
BROWSER_TRACK_NAME: RV BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,080,014,270
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.03
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010988, GSM1059433, GSM1120337, GSM1120336 (thus .wig files on these records are identical)

source_name: Right Ventricle tissue; methylC-seq_STL003RV-01b

tag: sample alias

value: Right Ventricle

tag: molecule

value: genomic DNA

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian

value: DNA Methylation

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

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 µg

value: 25 µM


title: Chromatin accessibility assay of Fetal Kidney; DS17068

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17068
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.18637
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15174
****************
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: Fetal Kidney primary tissue, day 87; DS17068

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: Fetal Kidney

value: UW

value: fetal

value: day 87

value: Chromatin Accessibility

value: Qiagen minElut


title: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL003; methylC-seq_STL003GA-01c

description:
Design description: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL003
Library name: methylC-seq_STL003GA-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15850
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12180
****************
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: GSM1120332_UCSD.Gastric.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003GA-01a-methylC-seq_STL003GA-01d-methylC-seq_STL003GA-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Gastric Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Gastric, Donor STL003 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.18747
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 9
BROWSER_TRACK_NAME: Gastric BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,235,431,773
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.25
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010984, GSM1120333, GSM1120332 (thus .wig files on these records are identical)

value: Gastric

value: Shin Lin, Stanford University

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

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: >The adapter-ligated, bisulfite converted DNA was used in a 50 µl PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

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


title: mRNA_P7_tumor

city: Berlin

first: Michal

middle: Ruth

last: Schweiger

address: Ihnestrasse 63-73

department: Lehrach

country: Germany

institute: Max Planck Institute For Molecular Genetics

description: total RNA

library_source: transcriptomic

data_processing:
Illumina Casava1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped hg19 whole genome using bwa 0.5.9-r16 with default parameters for the small RNA fraction experiments (Sample 1 – 24) and TopHat v1.3.3 with parameters -u -N --max-bundle-length 350000000 --max-bundle-frags 50000000 and using Ensembl v64 transcripts as template for all total RNA Seq experiments (Sample 25 – 36)
to obtain the .MirBase15.stat files mapped reads where counted for each miRNA if a read overlapped the miRNAs coordinates from miRbase 15 db by at least one base
to obtain the .geneExp.txt files, cuffdiff was called on the tophat pipeline output using the parameters  --max-bundle-frags 10000000 -L Benign,Tumor,Metastase -N -r
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each miRNA or gene

molecule: total RNA

source_name: colorectal biopsy, colon ascendens

extract_protocol:
RNA was harvested using Trizol reagent including a DNase digestion step with the RNase-free DNase set from Qiagen. For RNA sequencing rRNA substraction was performed with the RiboMinus™ Human/Mouse Transcriptome Isolation Kit SmallRNA.
cDNA library preparation, and sequencing was performed by Illumina’s DGE smallRNA sample and Illumina’s RNA-Seq prep kit following the manufacturer’s instructions with 2 ug of total RNA for the construction of mRNA sequencing libraries and 10 ug total RNA for the preparation of small RNA sequencing libraries.

tag: subject

tag: tissue

value: colorectal biopsy, colon ascendens

value: female

tag: disease state

value: tumor

tag: age

tag: microsatellite status

value: MSS


title: mRNA_P7_metastasis

description: total RNA

source_name: metastasis biopsy, lymph node

value: metastasis biopsy, lymph node

value: metastasis


title: mRNA_P5_metastasis

description: total RNA

value: MSI


title: mRNA_P5_tumor

description: total RNA

source_name: colorectal biopsy, colon

value: colorectal biopsy, colon


title: mRNA_P7_normal

description: total RNA

value: benign


title: mRNA_P4_normal

description: total RNA

source_name: colorectal biopsy, rectum/sigma

value: colorectal biopsy, rectum/sigma


title: mRNA_P5_normal

description: total RNA


title: mRNA_P4_metastasis

description: total RNA

source_name: metastasis biopsy, liver

value: metastasis biopsy, liver


title: mRNA_P4_tumor

description: total RNA


title: miRNA_P8_tumor

description: total RNA, small RNA fraction

source_name: colorectal biopsy, coecum

value: colorectal biopsy, coecum

value: male


title: mRNA_P3_normal

description: total RNA


title: miRNA_P8_metastasis

description: total RNA, small RNA fraction


title: mRNA_P3_metastasis

description: total RNA


title: miRNA_P8_normal

description: total RNA, small RNA fraction


title: miRNA_P7_normal

description: total RNA, small RNA fraction