status: Public on May 17 2010

city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: H3K36me3 ChIP-Seq analysis of peripheral cd4 naive from TC001 (HS1989) using Illumina Genome Analyzer IIx
library name: HS1989
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 315-623 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 395432
****************
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: GSM543035_UCSF-UBC.CD4-Naive-Primary-Cells.H3K36me3.wig
ANALYSIS ALIAS: UCSF-UBC.CD4-Naive-Primary-Cells.H3K36me3
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells H3K36me3 Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K36me3 in CD4 Naive Primary Cells were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2824
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543035_UCSF-UBC.CD4_Naive_Primary_Cells.H3K36me3.TC001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1989-1_430RMAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4 Naive Primary Cells, Donor TC001 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4321
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2879
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3205
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9575
IROC_PERCENTILE: 44
POISSON_SCORE: 0.465
POISSON_PERCENTILE: 37

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

ANALYSIS FILE NAME: GSM543035_UCSF-UBC.CD4_Naive_Primary_Cells.H3K36me3.TC001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1989-1_430RMAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4 Naive Primary Cells, Donor TC001 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4370
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD4N H3K36me3 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD4 Naive Primary Cells Histone H3K36me3 Donor TC001 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2879
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3205
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9575
IROC_PERCENTILE: 44
POISSON_SCORE: 0.465
POISSON_PERCENTILE: 37

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

extract_protocol: library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Blood

tag: histological type

value: CD4 naive cell

tag: is tumor

value: No

value: primary cell


type: SRA

state: CA

country: USA

description:
design description: miRNA-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS1740) using Illumina Genome Analyzer IIx
library name: HS1740
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 8.9
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.0 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: transcriptomic

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

ANALYSIS FILE NAME: GSM543034_UCSF-UBC.Breast-vHMEC-Individual-2.smRNA-Seq.Run108066Lane7.wig
ANALYSIS ALIAS: UCSF-UBC.Breast-vHMEC-Individual-2.smRNA-Seq.Run108066Lane7
ANALYSIS TITLE: Raw Signal Density Graphs of Breast, vHMEC, Individual 2 smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Breast, vHMEC, Individual 2 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2823
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543034_UCSF-UBC.Breast_vHMEC.smRNA-Seq.RM035.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1740-1_430N8AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast vHMEC smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Breast vHMEC, Donor RM035 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5203
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 84.41
PERCENT_READS_MAPPING_TO_REPEATMASKER_RNA_REPEATS: 5.0

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

ANALYSIS FILE NAME: GSM543034_UCSF-UBC.Breast_vHMEC.smRNA-Seq.RM035.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1740-1_430N8AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Breast vHMEC, Donor RM035 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5205
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: Bv smRNA 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC smRNA-Seq Donor RM035 EA Release 2
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 84.41
PERCENT_READS_MAPPING_TO_REPEATMASKER_RNA_REPEATS: 5.0

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

ANALYSIS FILE NAME: GSM543034_UCSF-UBC.Breast_vHMEC.smRNA-Seq.RM035.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1740-1_430N8AAXX.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Breast vHMEC smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Breast vHMEC, Donor RM035 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5207
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 2
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 84.41
PERCENT_READS_MAPPING_TO_REPEATMASKER_RNA_REPEATS: 5.0

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

molecule: total RNA

organism: Homo sapiens

extract_protocol: library construction protocol: Refer to document 'miRNA3 - Plate Format miRNA Library Construction' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: female

value: Breast

value: Variant human mammary epithelial cell culture

value: primary cell culture

tag: cell type


description:
design description: MeDIP-Seq analysis of peripheral cd8 naive from TC003 (HS1774) using Illumina Genome Analyzer IIx
library name: HS1774
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 2 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: N/A ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80604
****************
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: GSM543027_UCSF-UBC.CD8-Naive-Primary-Cells.MeDIP-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.CD8-Naive-Primary-Cells.MeDIP-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings for DNA methylation assessment in CD8 Naive Primary Cells were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2827
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543027_UCSF-UBC.CD8_Naive_Primary_Cells.MeDIP-Seq.TC003.bed
ANALYSIS ALIAS: HS1774-1_612TYAAXX-HS1774-1_42TCVAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on CD8 Naive Primary Cells, Donor TC003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4244
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.3225
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3667
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9637
IROC_PERCENTILE: 70
POISSON_SCORE: 0.6804
POISSON_PERCENTILE: 41

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

ANALYSIS FILE NAME: GSM543027_UCSF-UBC.CD8_Naive_Primary_Cells.MeDIP-Seq.TC003.wig
ANALYSIS ALIAS: HS1774-1_612TYAAXX-HS1774-1_42TCVAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from CD8 Naive Primary Cells, Donor TC003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4220
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD8N MeDIP 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD8 Naive Primary Cells MeDIP-Seq Donor TC003 EA Release 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.3225
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3667
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9637
IROC_PERCENTILE: 70
POISSON_SCORE: 0.6804
POISSON_PERCENTILE: 41

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

molecule: genomic DNA

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

value: CD8 naive cell


description:
design description: MeDIP-Seq analysis of peripheral mononuclear cell from TC003 (HS1772) using Illumina Genome Analyzer IIx
library name: HS1772
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 2 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: N/A ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80604
****************
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: GSM543025_UCSF-UBC.CD4-Naive-Primary-Cells.MeDIP-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.CD4-Naive-Primary-Cells.MeDIP-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings for DNA methylation assessment in CD4 Naive Primary Cells were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2825
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543025_UCSF-UBC.CD4_Naive_Primary_Cells.MeDIP-Seq.TC003.bed
ANALYSIS ALIAS: HS1772-1_612TYAAXX-HS1772-1_42TCVAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on CD4 Naive Primary Cells, Donor TC003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4260
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.1717
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.2893
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9355
IROC_PERCENTILE: 41
POISSON_SCORE: 0.6536
POISSON_PERCENTILE: 20

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

ANALYSIS FILE NAME: GSM543025_UCSF-UBC.CD4_Naive_Primary_Cells.MeDIP-Seq.TC003.wig
ANALYSIS ALIAS: HS1772-1_612TYAAXX-HS1772-1_42TCVAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from CD4 Naive Primary Cells, Donor TC003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4236
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD4N MeDIP 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD4 Naive Primary Cells MeDIP-Seq Donor TC003 EA Release 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.1717
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.2893
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9355
IROC_PERCENTILE: 41
POISSON_SCORE: 0.6536
POISSON_PERCENTILE: 20

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

value: Peripheral blood mononuclear cell


description:
design description: MeDIP-Seq analysis of breast myoepithelial cell from RM035 (HS1394) using Illumina Genome Analyzer IIx
library name: HS1394
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: N/A ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: N/A ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80604
****************
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: GSM543017_UCSF-UBC.Breast-Myoepithelial-Cells-Individual-2.MeDIP-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast-Myoepithelial-Cells-Individual-2.MeDIP-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of Breast, Myoepithelial Cells, Individual 2 MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings for DNA methylation assessment in Breast, Myoepithelial Cells, Individual 2 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2818
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543017_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM035.bed
ANALYSIS ALIAS: HS1394-1_42TE4AAXX-HS1394-1_42TEUAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Breast Myoepithelial Cells, Donor RM035 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4245
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.4689
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4554
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9828
IROC_PERCENTILE: 87
POISSON_SCORE: 0.7228
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM543017_UCSF-UBC.Breast_Myoepithelial_Cells.MeDIP-Seq.RM035.wig
ANALYSIS ALIAS: HS1394-1_42TE4AAXX-HS1394-1_42TEUAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Breast Myoepithelial Cells, Donor RM035 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4221
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC MeDIP 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells MeDIP-Seq Donor RM035 EA Release 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.4689
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4554
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9828
IROC_PERCENTILE: 87
POISSON_SCORE: 0.7228
POISSON_PERCENTILE: 100

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

value: Myoepithelial cell

value: breast myoepithelial cell


description:
design description: MeDIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS1768) using Illumina Genome Analyzer IIx
library name: HS1768
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: N/A ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80604
****************
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: GSM543021_UCSF-UBC.Breast-vHMEC-Individual-2.MeDIP-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast-vHMEC-Individual-2.MeDIP-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of Breast, vHMEC, Individual 2 MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings for DNA methylation assessment in Breast, vHMEC, Individual 2 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2821
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543021_UCSF-UBC.Breast_vHMEC.MeDIP-Seq.RM035.bed
ANALYSIS ALIAS: HS1768-1_612T0AAXX-HS1768-1_430L5AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast vHMEC MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Breast vHMEC, Donor RM035 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4249
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.4936
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.4648
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9868
IROC_PERCENTILE: 95
POISSON_SCORE: 0.7168
POISSON_PERCENTILE: 87

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

ANALYSIS FILE NAME: GSM543021_UCSF-UBC.Breast_vHMEC.MeDIP-Seq.RM035.wig
ANALYSIS ALIAS: HS1768-1_612T0AAXX-HS1768-1_430L5AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Breast vHMEC, Donor RM035 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4225
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: Bv MeDIP 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC MeDIP-Seq Donor RM035 EA Release 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.4936
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.4648
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9868
IROC_PERCENTILE: 95
POISSON_SCORE: 0.7168
POISSON_PERCENTILE: 87

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


description:
design description: MeDIP-Seq analysis of peripheral mononuclear cell from TC003 (HS1770) using Illumina Genome Analyzer IIx
library name: HS1770
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document "MeDIP-seq library construction protocol v2" by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document "MeDIP-seq library construction protocol v2" by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 2 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: N/A ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80604
****************
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: GSM543023_UCSF-UBC.Peripheral-Blood-Mononuclear-Primary-Cells.MeDIP-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.Peripheral-Blood-Mononuclear-Primary-Cells.MeDIP-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings for DNA methylation assessment in Peripheral Blood Mononuclear Primary Cells were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2829
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543023_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.MeDIP-Seq.TC003.bed
ANALYSIS ALIAS: HS1770-1_430L5AAXX-HS1770-1_600VGAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4267
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.3373
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.3758
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9629
IROC_PERCENTILE: 62
POISSON_SCORE: 0.6836
POISSON_PERCENTILE: 45

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

ANALYSIS FILE NAME: GSM543023_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.MeDIP-Seq.TC003.wig
ANALYSIS ALIAS: HS1770-1_430L5AAXX-HS1770-1_600VGAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4243
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: PBM MeDIP 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells MeDIP-Seq Donor TC003 EA Release 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.3373
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.3758
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9629
IROC_PERCENTILE: 62
POISSON_SCORE: 0.6836
POISSON_PERCENTILE: 45

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

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


title: XEN_H3K27me3_1

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description:
Chromatin IP against H3K27me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 2051KAAXX_5_NCBI-Build-36_ht10.wig.gz
unthresholded: 2051KAAXX_5_NCBI-Build-36_ht2.wig.gz

data_processing:
Reads were aligned to NCBI build 36 by standard protocols at UBC sequencing center.
Raw ChIP-sequencing data was processed using FindPeaks (version 2.1.4 (Fejes et al., 2008)) with a false discovery rate of 0.001, an average fragment size of 174bp and a minimum peak height of two. A Java program was written to read the output Wig files and generate a BED file that contained information on the maximum peak height of all thresholded K4me3 or K27me3 regions. Significant ChIP-sequencing peaks within +/- 1kb of the TSS for K4me3 and +/- 5kb of the TSS for K27me3 were included in the final dataset. All these data were imported as tables in to a MySQL database.processed using FindPeaks (version 2.1.4; Fejes 2008 Bioinformatics) with a false discovery rate of 0.001.

organism: Mus musculus

source_name: Extraembryonic endoderm stem cell

growth_protocol: Mouse ES cell lines, R1 (passages 12-15) and E14TG2a (passages 19-21), were cultured on gelatin-coated surfaces in standard ES cell media (DMEM supplemented with 15% FBS, 1mM sodium pyruvate, 50U/ml penicillin, 50mg/ml streptomycin, 50mM 2-mercaptoethanol, 0.1mM non-essential amino acids (NEAA), 2mM glutamax (all from Invitrogen) and 1000 U/ml LIF. TS cell lines, A4 (passages 6-15) and G3 (passages 7-14), were derived from E3.5 blastocysts obtained from ICR x B5/EGFPtg/tg matings as previously described (Tanaka). TS cells were maintained on gelatin-coated surfaces in RPMI (Sigma) supplemented with 20% FBS, 1mM sodium pyruvate, 50U/ml penicillin, 50mg/ml streptomycin, 50mM 2-mercaptoethanol, 2mM glutamax (all from Invitrogen), 25ng/ml FGF4 (R&D Systems) and 1mg/ml heparin (Sigma), with 70% of the media pre-conditioned by mitotically-inactivated embryonic fibroblasts. To induce TS cell differentiation, 1 x 105 cells / cm2 were plated in standard TS cell conditions for 24h, rinsed twice with PBS and cultured for six days in unconditioned TS cell media without FGF4 and heparin. Media was changed every two days. XEN cell lines, F3 (passages 7-12) and F4 (passages 7-14), were derived from E3.5 blastocysts obtained from ICR x B5/EGFPtg/tg matings as previously described (Kunath). XEN cells were maintained on gelatin-coated surfaces in TS cell media (70% pre-conditioned) without FGF4 or heparin. Protocols can be found at http://www.sickkids.ca/research/rossant/custom/stemCells.asp

extract_protocol: Native (unfixed) ChIP to analyze histone modifications was performed as described (Umlauf et al., 2004). Briefly, 10-50 million cells were lysed in 0.2% (v/v) IGEPAL CA-630 (Sigma) for 10min on ice, nuclei were collected by centrifugation at 10000 x g for 20min at 4°C and suspended in digestion buffer at 1mg/ml. Chromatin aliquots (0.5mg in 500ul) were digested with 10U micrococcal nuclease (GE Healthcare) for 6-9min at 37°C and soluble chromatin recovered by overnight dialysis followed by centrifugation. Successful chromatin fractionation (sample contains predominantly mononucleosomes to tetranucleosomes) was verified by agarose gel electrophoresis. Fragmented chromatin (35ug per ChIP) was immunoprecipitated overnight at 4°C with 2-10ug of one of the following antibodies: H3K4me3 (Abcam, ab8580), H3K9me2 (Millipore, 07-212), H3K9me3 (Abcam, ab8898), H3K27me3 (Millipore, 07-449), 1ul H3K27me3 (Peters et al., 2003), H3K79me3 (Abcam, ab2621), H4K20me3 (Millipore, 07-463), H3K9 acetylation (Millipore, 07-352) or rabbit anti-mouse IgG (Jackson, 315-005-003). Protein A-Sepharose (100ul of 50% (v/v) slurry; GE Healthcare) was added to each sample and rotated for 4h at 4°C. Unbound material was removed, Sepharose beads washed in salt buffer (increasing sodium chloride concentration from 75-175mM) and chromatin eluted from the beads with two 15min incubations in 1% SDS at room temperature. DNA from bound, unbound and input samples was extracted by two rounds of phenol/chloroform and precipitated with isopropanol overnight at -20°C with 30ug glycogen (Roche) as carrier. Air-dried DNA pellets were reconstituted in TE buffer. 5 Throughout the procedure, all solutions were ice-cold and freshly supplemented with protease inhibitors (Mini Complete-EDTA free, Roche) and 5mM sodium butyrate.

tag: chip antibody


title: XEN_H3K27me3_2

description:
Chromatin IP against H3K27me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 2051KAAXX_7_NCBI-Build-36_ht10.wig.gz
unthresholded: 2051KAAXX_7_NCBI-Build-36_ht2.wig.gz


description:
design description: MeDIP-Seq analysis of breast progenitor enriched cell from RM035 (HS1395) using Illumina Genome Analyzer IIx
library name: HS1395
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: N/A ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: N/A ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80604
****************
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: GSM543019_UCSF-UBC.Breast-Stem-Cells-Individual-2.MeDIP-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast-Stem-Cells-Individual-2.MeDIP-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of Breast, Stem Cells, Individual 2 MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings for DNA methylation assessment in Breast, Stem Cells, Individual 2 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2820
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543019_UCSF-UBC.Breast_Stem_Cells.MeDIP-Seq.RM035.bed
ANALYSIS ALIAS: HS1395-1_42TE4AAXX-HS1395-1_42TEUAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Stem Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Breast Stem Cells, Donor RM035 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4259
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.5108
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4841
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9872
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7204
POISSON_PERCENTILE: 95

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

ANALYSIS FILE NAME: GSM543019_UCSF-UBC.Breast_Stem_Cells.MeDIP-Seq.RM035.wig
ANALYSIS ALIAS: HS1395-1_42TE4AAXX-HS1395-1_42TEUAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Stem Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Breast Stem Cells, Donor RM035 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4235
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BSC MeDIP 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Stem Cells MeDIP-Seq Donor RM035 EA Release 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.5108
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4841
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9872
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7204
POISSON_PERCENTILE: 95

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

value: Progenitor enriched cell

value: breast progenitor enriched cell


title: ESC_H3K4me3_1

description:
Chromatin IP against H3K4me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 201DDAAXX_2_NCBI-Build-36_ht8.wig.gz
unthresholded: 201DDAAXX_2_NCBI-Build-36_ht2.wig.gz

source_name: R1 embryonic stem cells


description:
design description: MRE-Seq analysis of peripheral cd8 naive from TC003 (HS1773) using Illumina Genome Analyzer IIx
library name: HS1773
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 144-400 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM543013_UCSF-UBC.CD8-Naive-Primary-Cells.MRE-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.CD8-Naive-Primary-Cells.MRE-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in CD8 Naive Primary Cells were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2828
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543013_UCSF-UBC.CD8_Naive_Primary_Cells.MRE-Seq.TC003.bed
ANALYSIS ALIAS: HS1773-1_42TCVAAXX-HS1773-1_430WUAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on CD8 Naive Primary Cells, Donor TC003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4212
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.39
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 85

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

ANALYSIS FILE NAME: GSM543013_UCSF-UBC.CD8_Naive_Primary_Cells.MRE-Seq.TC003.wig
ANALYSIS ALIAS: HS1773-1_42TCVAAXX-HS1773-1_430WUAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from CD8 Naive Primary Cells, Donor TC003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4184
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD8N MRE 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD8 Naive Primary Cells MRE-Seq Donor TC003 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.39
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 85

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

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


title: XEN_H3K4me3_2

description:
Chromatin IP against H3K4me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 208GMAAXX_5_NCBI-Build-36_ht9.wig.gz
unthresholded: 208GMAAXX_5_NCBI-Build-36_ht2.wig.gz


title: TSC_H3K27me3_2

description:
Chromatin IP against H3K27me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 208GMAAXX_3_NCBI-Build-36_ht10.wig.gz
unthresholded: 208GMAAXX_3_NCBI-Build-36_ht2.wig.gz

source_name: Trophoblast stem cells


title: XEN_H3K4me3_1

description:
Chromatin IP against H3K4me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 20495AAXX_7_NCBI-Build-36_ht8.wig.gz
unthresholded: 20495AAXX_7_NCBI-Build-36_ht2.wig.gz


title: ESC_H3K27me3_1

description:
Chromatin IP against H3K27me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 201DDAAXX_3_NCBI-Build-36_ht9.wig.gz
unthresholded: 201DDAAXX_3_NCBI-Build-36_ht2.wig.gz


title: TSC_H3K27me3_1

description:
Chromatin IP against H3K27me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 20495AAXX_5_NCBI-Build-36_ht9.wig.gz
unthresholded: 20495AAXX_5_NCBI-Build-36_ht2.wig.gz


description:
design description: RNA-Seq analysis of breast myoepithelial cell from RM035 (HS1188) using Illumina Genome Analyzer II
library name: HS1188
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.40
RNA_PREPARATION_INITIAL_RNA_QNTY: 2500 ng
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 267-400 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM543031_UCSF-UBC.Breast-Myoepithelial-Cells-Individual-2.mRNA-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast-Myoepithelial-Cells-Individual-2.mRNA-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of Breast, Myoepithelial Cells, Individual 2 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast, Myoepithelial Cells, Individual 2 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2819
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543031_UCSF-UBC.Breast_Myoepithelial_Cells.mRNA-Seq.RM035.bed
ANALYSIS ALIAS: HS1188-1_6125LAAXX-HS1188-1_612EYAAXX-HS1188-1_31549AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Breast Myoepithelial Cells, Donor RM035 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4275
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 4
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.04
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM543031_UCSF-UBC.Breast_Myoepithelial_Cells.mRNA-Seq.RM035.wig
ANALYSIS ALIAS: HS1188-1_6125LAAXX-HS1188-1_612EYAAXX-HS1188-1_31549AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast Myoepithelial Cells, Donor RM035 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4270
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC mRNA 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells mRNA-Seq Donor RM035 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 4
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.04
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 50

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

extract_protocol: library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)


title: TSC_H3K4me3_2

description:
Chromatin IP against H3K4me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 208GMAAXX_4_NCBI-Build-36_ht9.wig.gz
unthresholded: 208GMAAXX_4_NCBI-Build-36_ht2.wig.gz


description:
design description: MRE-Seq analysis of peripheral mononuclear cell from TC003 (HS1769) using Illumina Genome Analyzer IIx
library name: HS1769
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 147-395 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM543009_UCSF-UBC.Peripheral-Blood-Mononuclear-Primary-Cells.MRE-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.Peripheral-Blood-Mononuclear-Primary-Cells.MRE-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in Peripheral Blood Mononuclear Primary Cells were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2830
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543009_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.MRE-Seq.TC003.bed
ANALYSIS ALIAS: HS1769-1_612T0AAXX-HS1769-1_430RMAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4196
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.99
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 64

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

ANALYSIS FILE NAME: GSM543009_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.MRE-Seq.TC003.wig
ANALYSIS ALIAS: HS1769-1_612T0AAXX-HS1769-1_430RMAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4168
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: PBM MRE 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells MRE-Seq Donor TC003 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.99
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 64

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


title: ESC_H3K27me3_2

description:
Chromatin IP against H3K27me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 208AJAAXX_5_NCBI-Build-36_ht10.wig.gz
unthresholded: 208AJAAXX_5_NCBI-Build-36_ht2.wig.gz


description:
design description: MRE-Seq analysis of peripheral mononuclear cell from TC003 (HS1771) using Illumina Genome Analyzer IIx
library name: HS1771
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 150-398 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM543011_UCSF-UBC.CD4-Naive-Primary-Cells.MRE-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.CD4-Naive-Primary-Cells.MRE-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in CD4 Naive Primary Cells were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2826
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543011_UCSF-UBC.CD4_Naive_Primary_Cells.MRE-Seq.TC003.bed
ANALYSIS ALIAS: HS1771-1_430L5AAXX-HS1771-1_42TCVAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on CD4 Naive Primary Cells, Donor TC003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4208
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 53

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

ANALYSIS FILE NAME: GSM543011_UCSF-UBC.CD4_Naive_Primary_Cells.MRE-Seq.TC003.wig
ANALYSIS ALIAS: HS1771-1_430L5AAXX-HS1771-1_42TCVAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from CD4 Naive Primary Cells, Donor TC003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4180
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD4N MRE 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD4 Naive Primary Cells MRE-Seq Donor TC003 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 53

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


description:
design description: MRE-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS1673) using Illumina Genome Analyzer IIx
library name: HS1673
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 211-430 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM543007_UCSF-UBC.Breast-vHMEC-Individual-2.MRE-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast-vHMEC-Individual-2.MRE-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of Breast, vHMEC, Individual 2 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in Breast, vHMEC, Individual 2 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2822
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543007_UCSF-UBC.Breast_vHMEC.MRE-Seq.RM035.bed
ANALYSIS ALIAS: HS1673-1_42TCVAAXX-HS1673-1_430WUAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast vHMEC MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Breast vHMEC, Donor RM035 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4197
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.71
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 57

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

ANALYSIS FILE NAME: GSM543007_UCSF-UBC.Breast_vHMEC.MRE-Seq.RM035.wig
ANALYSIS ALIAS: HS1673-1_42TCVAAXX-HS1673-1_430WUAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Breast vHMEC, Donor RM035 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4169
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: Bv MRE 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC MRE-Seq Donor RM035 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.71
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 57

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


title: ESC_H3K4me3_2

description:
Chromatin IP against H3K4me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 208GMAAXX_6_NCBI-Build-36_ht9.wig.gz
unthresholded: 208GMAAXX_6_NCBI-Build-36_ht2.wig.gz


description:
design description: RNA-Seq analysis of breast luminal epithelial cell from RM035 (HS1187) using Illumina Genome Analyzer II
library name: HS1187
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.40
RNA_PREPARATION_INITIAL_RNA_QNTY: 10000 ng
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 267-400 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM543029_UCSF-UBC.Breast-Luminal-Epithelial-Cells-Individual-2.mRNA-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast-Luminal-Epithelial-Cells-Individual-2.mRNA-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of Breast, Luminal Epithelial Cells, Individual 2 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast, Luminal Epithelial Cells, Individual 2 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2817
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543029_UCSF-UBC.Breast_Luminal_Epithelial_Cells.mRNA-Seq.RM035.bed
ANALYSIS ALIAS: HS1187-1_31549AAXX-HS1187-1_6125LAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Luminal Epithelial Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Breast Luminal Epithelial Cells, Donor RM035 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4276
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 4
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.22
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM543029_UCSF-UBC.Breast_Luminal_Epithelial_Cells.mRNA-Seq.RM035.wig
ANALYSIS ALIAS: HS1187-1_31549AAXX-HS1187-1_6125LAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM035 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4271
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BLEC mRNA 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Luminal Epithelial Cells mRNA-Seq Donor RM035 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 4
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.22
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 75

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

value: Luminal epithelial cell

value: breast luminal epithelial cell


description:
design description: H3K9ac ChIP-Seq analysis of peripheral cd4 naive from TC001 (HS1987) using Illumina Genome Analyzer IIx
library name: HS1987
EXPERIMENT_TYPE: Histone H3K9ac
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 220-710 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K9ac
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9649S
CHIP_ANTIBODY_LOT: 1
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM543004_UCSF-UBC.CD4-Naive-Primary-Cells.H3K9ac.wig
ANALYSIS ALIAS: UCSF-UBC.CD4-Naive-Primary-Cells.H3K9ac
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells H3K9ac Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K9ac in CD4 Naive Primary Cells were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2831
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM543004_UCSF-UBC.CD4_Naive_Primary_Cells.H3K9ac.TC001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1987-1_430RMAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on CD4 Naive Primary Cells, Donor TC001 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4339
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1726
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.2771
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9908
IROC_PERCENTILE: 66
POISSON_SCORE: 0.36
POISSON_PERCENTILE: 49

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

ANALYSIS FILE NAME: GSM543004_UCSF-UBC.CD4_Naive_Primary_Cells.H3K9ac.TC001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1987-1_430RMAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from CD4 Naive Primary Cells, Donor TC001 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4388
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD4N H3K9ac 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD4 Naive Primary Cells Histone H3K9ac Donor TC001 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1726
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.2771
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9908
IROC_PERCENTILE: 66
POISSON_SCORE: 0.36
POISSON_PERCENTILE: 49

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

value: male


title: TSC_H3K4me3_1

description:
Chromatin IP against H3K4me3
To prepare samples for Illumima sequencing, the concentration of immunoprecipitated DNA was determined using Quant-iT PicoGreen dsDNA reagent (Invitrogen) and 100ng of each sample was sent to BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, where the service was performed.

The wig processed data files are thresholded (FDR 0.0001) and unthresholded.
thresholded: 20495AAXX_6_NCBI-Build-36_ht8.wig.gz
unthresholded: 20495AAXX_6_NCBI-Build-36_ht2.wig.gz


title: Donor 2 biological replicate b

status: Public on May 16 2010

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

description: MNase treated chromatin

data_processing: Thirty-six base pair reads were aligned to the hg18 human genome assembly using Bowtie allowing for up to 2 mismatches and reads with multiple hits to genome (up to 100) were assigned to all matching regions with a weight of one over the number of hits. Wiggle files showing the average coverage were generated in 300bp windows.

source_name: Human sperm

extract_protocol: Libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina's instructions. After adapter ligation library fragments of ~250 bp were band isolated from an agarose gel. The DNA was PCR amplified with Illumina primers for 18 cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer 2 following the manufacturer's protocols.

treatment_protocol: Human spermatozoa were lysed in buffer I (0.3M Sucrose, 15mM Tris (pH 7.5), 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 0.5mM DTT) containing 0.5% deoxycholate and 0.25% NP-40 for 30 min on ice. Chromatin digestion was performed by micrococcal nuclease. Nucleosomal DNA was fractionated by polyacrylamide electroforesis. Control sample was prepared by sonication of human sperm chromatin that had been pretreated with detergents and DTT under the same conditions as used to generate mono-nucleosomal DNA by MNase treatment.

value: sperm


title: Donor 2 biological replicate a

description: MNase treated chromatin


title: Donor 3 biological replicate a

description: MNase treated chromatin


title: Sonicated control

description: Sonicated chromatin


title: Donor 3 biological replicate b

description: MNase treated chromatin


title: Donor 1 biological replicate a

description: MNase treated chromatin


title: Donor 1 biological replicate b

description: MNase treated chromatin


title: Sample control reads cerebellum ChIPseq

status: Public on May 13 2010

city: Cambridge

first: Kenzie

last: MacIsaac

state: MA

address: 77 Massachusetts Ave.

institute: MIT

description: sample control reads in cerebellum

data_processing:
Alignment: ChIP-seq analysis of immunoprecipitated DNA was carried out using the standard Illumina protocols and analysis pipeline.
BED files: Peak files, the enrichment of genomic regions for protein binding was assessed relative to a set of control reads obtained by sequencing unenriched whole-genome DNA. Bound regions were identified using the MACS algorithm with a calculated alignable genome size of 2.107 Gbp and an enrichment p-value cutoff of 1e-6.

source_name: cerebellum

growth_protocol: Tissue samples were harvested from male C57BL/6J. Animals were provided with water and chow without restriction. Murine preadipocyte 3T3-L1 cells were induced to differentiate to mature adipocytes using a standard protocol (Goldfine et al. Diabetes 2006)

extract_protocol: Hepatocytes were harvested by direct perfusion of the liver in anaesthetized animals using PBS, followed by crosslinking with a 1% formaldehyde solution. The liver was then removed and crosslinked for another 10 minutes followed by neutralization with glycine. This cellular material was homogenized, washed and passed through a sucrose gradient to enrich for hepatocytes. These were rinsed with 1X PBS, pelleted, and either used directly in ChIP experiments, or frozen in liquid nitrogen for later use. Mouse cerebella were harvested from male C57BL/6J mice and crosslinked, homogenized, and neutralized in a similar manner.  3T3-L1 cells were cross linked for ten minutes and then quenched with glycine.

tag: strain

tag: sample

value: cerebellum


title: Sample control reads liver ChIPseq

description: sample control reads in liver

source_name: liver hepatocytes

value: liver hepatocytes


title: CEBPa 3T3-L1 ChIPseq

description: Chromatin IP against C/EBPa

source_name: differentiated 3T3-L1 cells

value: fully differentiated 3T3-L1 cells

value: C/EBPalpha


title: E2F4 liver ChIPseq

description: Chromatin IP against E2F4

value: hepatocytes


title: FOXA1 liver ChIPseq

description: Chromatin IP against FOXA1


title: p300 3T3-L1 ChIPseq

description: Chromatin IP against p300


title: p300 liver ChIPseq

description: Chromatin IP against p300


title: FOXA2 liver ChIPseq

description: Chromatin IP against FOXA2


title: Sample control reads 3T3-L1 ChIPseq

description: sample reads in 3T3-L1


title: E2F4 3T3-L1 ChIPseq

description: Chromatin IP against E2F4


title: Normal PBMC Sample 1

city: New Delhi

first: Alok

last: Bhattacharya

state: New Delhi

address: New Mehrauli Road

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

description: PBMCs were isolated by ficoll gradient from the blood of normal volunteer

data_processing:
The raw sequence files, the untrimmed tag files and the trimmed tag files were provided by Illumina Inc, USA using the Illumina analysis pipeline.

Untrimmed tag files : Each file contains sequences (column2) with parts of the adaptor sequence:"TCGTATGCCGTCTTCTGCTTG" and their corresponding frequency (column1). The amount of the adaptor is variable and is dependent on the length of the sRNA.

Unique trimmed (adaptor sequence removed) sequence reads with their respective counts / frequency: Each file contains unique trimmed sequences (column1) with their corresponding frequency (column2). These sequences were generated by removal of the adaptor sequence. After the removal of the adaptor sequences the redundancy is removed to get a trimmed unique non-redundant file.  The numerical frequency of each sequence in these files gives a true indication of relative expression of the sequence transcripts. It also gives the researcher an indication of most common to most rare sequences in the dataset.

miRNA expression profile for the 4 samples: The trimmed files were then matched (using BLASTN) with the known Homo sapiens mature miRNAs from miRNA registry release 12 (866 mature miRNAs) to generate the expression profile.For making the samples comparable among each other, each transcript/sequence  (representing a known miRNA) frequency was divided by the total transcripts present in the corresponding sample and multiplied by 1000000.The total transcript is the sum of the frequencies of all the unique sequences / transcripts present in the trimmed file.This file contains a list of the known miRNAs found in all the 4 samples along with their respective frequencies and (Transcripts parts per million) TPM values.

source_name: Peripheral blood mononuclear cells (PBMC)

growth_protocol: Cells were grown in RPMI medium with 10% fetal bovine serum in 5% CO2 and passaged after every 2 days.

extract_protocol: Total RNA isolation was carried out from peripheral blood and cell lines using TRIzol® Reagent (Invitrogen) as per manufacturer’s instruction. RNA preparations were stored at -80C till further use. Small RNA (sRNA) population was isolated by separating 10 µg of total RNA on denaturing polyacrylamide gel electrophoresis (PAGE) and cutting a portion of the gel corresponding to the size 18-30 nucleotides based standard oligonucleotide markers. Adapter (5’) was ligated to sRNA population and  ligated RNAs (40-60 nt) were purified by running on urea PAGE. This was followed by 3’ adapter ligation and purification of adapter ligated RNAs (70-90 nt) in a similar manner. Modified sRNAs were reverse transcribed and then PCR amplified with adapter specific primers and the amplified cDNAs were finally purified on Urea PAGE to generate cDNA tag libraries for sequencing by illumina genome analyzer. The average number of sequencing reads was around 4.9 million.


title: Normal PBMC Sample 2

value: Peripheral blood mononuclear cells (PBMC)


title: HL60

description: HL60 cell line is derived from acute promyelogenous leukemia patient

source_name: Acute Promyelogenous Leukemia cell line

value: Acute Promyelogenous Leukemia cell line

tag: cell line


title: K562

description: K562 cell line is derived from a CML patient in terminal blast crisis and used as model for CML studies

source_name: Chronic Myelogenous Leukemia cell line

value: Chronic Myelogenous Leukemia cell line


title: Sirt1 cerebellum ChIPseq

description: Chromatin IP against Sirt1


title: U2OS_ERb_Doxy_nonspecificAntibodyIgG_rep1

status: Public on May 12 2010

city: Emeryville

first: Xiaoyue

last: Zhao

address: 5858 Horton St

institute: Bionovo Inc.

description: non-specific antibody IgG

data_processing: Alignment: Sequence reads were obtained and mapped to the human genomes (hg18) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

source_name: U2OS cells, ERb vector transfected with Doxycycline added

extract_protocol: Amplified ChIP DNA samples were prepared utilizing the ChIP-Seq DNA-Sample Prep Kit per manufacturers’ protocol (Illumina, San Diego), with the following modifications. Following gel purification and clean-up of the adapter ligated ChIP DNAs, PCR amplification was performed as described for 20 cycles. Final amplified ChIP DNA libraries were analyzed using the Experion capillary electrophoresis system and 1K DNA chips (Bio-Rad, Hercules).

value: IgG


title: U2OS_ERb_DoxyE2_nonspecificAntibodyIgG_rep1

description: non-specific antibody IgG

source_name: U2OS cells, ERb vector transfected with Doxycycline added and E2 treatment


title: U2OS_ERb_Doxy_specificAntibody_rep1

description: Chromatin IP against ERbeta

value: ER beta


title: CEBPa liver ChIPseq

description: Chromatin IP against C/EBPa