description:
design description: RNA-Seq analysis of peripheral cd4 memory from TC014 (A01027) using Illumina Genome Analyzer IIx
library name: A01027
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: 15
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 8.8
RNA_PREPARATION_INITIAL_RNA_QNTY: N/A
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 219-440 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: GSM669618_UCSF-UBC.CD4_Memory_Primary_Cells.mRNA-Seq.TC014.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A01027-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on CD4 Memory Primary Cells, Donor TC014 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.6315
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 3

QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.9
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM669618_UCSF-UBC.CD4_Memory_Primary_Cells.mRNA-Seq.TC014.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A01027-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from CD4 Memory Primary Cells, Donor TC014 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.6322
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 3
BROWSER_TRACK_NAME: CD4M mRNA 14
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC CD4 Memory Primary Cells mRNA-Seq Donor TC014 Library A01027-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 7
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.9
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 100

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


status: Public on Mar 31 2011

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: MRE-Seq analysis of cortex neural stem and progenitor cells from HuFNSC01 (HS2774) using Illumina Genome Analyzer IIx
library name: HS2774
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: 155-391 bp
****************
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: GSM669600_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.MRE-Seq.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2774-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 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.6352
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 3

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.8
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM669600_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.MRE-Seq.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2774-1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 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.6359
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 3
BROWSER_TRACK_NAME: NCD MRE 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived MRE-Seq Donor HuFNSC01 Library HS2774-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.8
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100

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

molecule: genomic DNA

organism: Homo sapiens

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/)

tag: submitted sample id

tag: Sex

value: female

tag: body site

value: Brain

tag: histological type

value: Cortex neurosphere culture

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: cortex neural stem and progenitor cells


description:
design description: MRE-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (HS2780) using Illumina Genome Analyzer IIx
library name: HS2780
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: 155-372 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: GSM669603_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.MRE-Seq.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2780-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.6349
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 3

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.72
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 71

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

ANALYSIS FILE NAME: GSM669603_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.MRE-Seq.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2780-1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.6356
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 3
BROWSER_TRACK_NAME: NGED MRE 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived MRE-Seq Donor HuFNSC02 Library HS2780-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.72
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 71

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

value: Ganglionic eminence neurosphere culture


description:
design description: H3K36me3 ChIP-Seq analysis of breast luminal epithelial cell from RM080 (HS2795) using Illumina Genome Analyzer IIx
library name: HS2795
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 80-315 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 134025
****************
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: GSM669597_UCSF-UBC.Breast_Luminal_Epithelial_Cells.H3K36me3.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2795-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Breast Luminal Epithelial Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Breast Luminal Epithelial Cells, Donor RM080 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.6311
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 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.1946
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.2208
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9584
IROC_PERCENTILE: 42
POISSON_SCORE: 0.5045
POISSON_PERCENTILE: 62

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

ANALYSIS FILE NAME: GSM669597_UCSF-UBC.Breast_Luminal_Epithelial_Cells.H3K36me3.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2795-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM080 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.6653
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 3
BROWSER_TRACK_NAME: BLEC H3K36me3 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Luminal Epithelial Cells Histone H3K36me3 Donor RM080 Library HS2795-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.1946
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.2208
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9584
IROC_PERCENTILE: 42
POISSON_SCORE: 0.5045
POISSON_PERCENTILE: 62

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

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

value: Breast

value: Luminal epithelial cell

value: primary cell

value: breast luminal epithelial cell


description:
design description: H3K9me3 ChIP-Seq analysis of breast luminal epithelial cell from RM080 (HS2793) using Illumina Genome Analyzer IIx
library name: HS2793
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 80-300 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669596_UCSF-UBC.Breast_Luminal_Epithelial_Cells.H3K9me3.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2793-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Breast Luminal Epithelial Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Breast Luminal Epithelial Cells, Donor RM080 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.6307
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 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.0984
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.1878
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.816
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3925
POISSON_PERCENTILE: 81

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

ANALYSIS FILE NAME: GSM669596_UCSF-UBC.Breast_Luminal_Epithelial_Cells.H3K9me3.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2793-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM080 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.6649
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 3
BROWSER_TRACK_NAME: BLEC H3K9me3 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Luminal Epithelial Cells Histone H3K9me3 Donor RM080 Library HS2793-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.0984
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.1878
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.816
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3925
POISSON_PERCENTILE: 81

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


description:
design description: H3K4me1 ChIP-Seq analysis of breast luminal epithelial cell from RM080 (HS2791) using Illumina Genome Analyzer IIx
library name: HS2791
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 2 ug
SIZE_FRACTION: 53-303 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 3.75 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-0011
****************
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: GSM669595_UCSF-UBC.Breast_Luminal_Epithelial_Cells.H3K4me1.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2791-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Breast Luminal Epithelial Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Breast Luminal Epithelial Cells, Donor RM080 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.6301
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 28
FINDPEAKS_SCORE: 0.3209
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.4115
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9699
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5061
POISSON_PERCENTILE: 46

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

ANALYSIS FILE NAME: GSM669595_UCSF-UBC.Breast_Luminal_Epithelial_Cells.H3K4me1.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2791-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM080 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.6643
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 3
BROWSER_TRACK_NAME: BLEC H3K4me1 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Luminal Epithelial Cells Histone H3K4me1 Donor RM080 Library HS2791-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 28
FINDPEAKS_SCORE: 0.3209
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.4115
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9699
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5061
POISSON_PERCENTILE: 46

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


description:
design description: H3K27me3 ChIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS2616) using Illumina Genome Analyzer IIx
library name: HS2616
EXPERIMENT_TYPE: Histone H3K27me3
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: 30 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: 4 ug
SIZE_FRACTION: 220-549 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 15 ul
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9733S
CHIP_ANTIBODY_LOT: 2
****************
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: GSM669594_UCSF-UBC.Breast_vHMEC.H3K27me3.RM035.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2616-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Breast vHMEC Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Breast vHMEC, Donor RM035, Library HS2616 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.6306
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 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 20
FINDPEAKS_SCORE: 0.121
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.21
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9148
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3151
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM669594_UCSF-UBC.Breast_vHMEC.H3K27me3.RM035.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2616-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Breast vHMEC, Donor RM035, Library HS2616 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.6648
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 3
BROWSER_TRACK_NAME: Bv H3K27me3 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast vHMEC Histone H3K27me3 Donor RM035 Library HS2616-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 20
FINDPEAKS_SCORE: 0.121
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.21
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9148
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3151
POISSON_PERCENTILE: 40

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

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/)

value: Variant human mammary epithelial cell culture


description:
design description: MeDIP-Seq analysis of cortex neural stem and progenitor cells from HuFNSC02 (HS2779) using Illumina Genome Analyzer IIx
library name: HS2779
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: 1 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
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: GSM669612_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.MeDIP-Seq.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2779-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC02 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.6332
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 3

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.2585
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.3754
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9538
IROC_PERCENTILE: 90
POISSON_SCORE: 0.4854
POISSON_PERCENTILE: 90

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

ANALYSIS FILE NAME: GSM669612_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.MeDIP-Seq.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2779-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC02 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.6342
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 3
BROWSER_TRACK_NAME: NCD MeDIP 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived MeDIP-Seq Donor HuFNSC02 Library HS2779-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.2585
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.3754
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9538
IROC_PERCENTILE: 90
POISSON_SCORE: 0.4854
POISSON_PERCENTILE: 90

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

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/)


description:
design description: MeDIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC01 (HS2777) using Illumina Genome Analyzer IIx
library name: HS2777
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: 1 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
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: GSM669611_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.MeDIP-Seq.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2777-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 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.6333
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 3

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.1089
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2684
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9012
IROC_PERCENTILE: 60
POISSON_SCORE: 0.4185
POISSON_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM669611_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.MeDIP-Seq.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2777-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 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.6343
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 3
BROWSER_TRACK_NAME: NGED MeDIP 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived MeDIP-Seq Donor HuFNSC01 Library HS2777-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.1089
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2684
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9012
IROC_PERCENTILE: 60
POISSON_SCORE: 0.4185
POISSON_PERCENTILE: 60

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


description:
design description: MRE-Seq analysis of peripheral cd4 memory from TC009 (HS2748) using Illumina Genome Analyzer IIx
library name: HS2748
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: 155-398 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: GSM669599_UCSF-UBC.CD4_Memory_Primary_Cells.MRE-Seq.TC009.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2748-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on CD4 Memory Primary Cells, Donor TC009 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.6354
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 3

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.57
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 14

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

ANALYSIS FILE NAME: GSM669599_UCSF-UBC.CD4_Memory_Primary_Cells.MRE-Seq.TC009.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2748-1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from CD4 Memory Primary Cells, Donor TC009 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.6361
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 3
BROWSER_TRACK_NAME: CD4M MRE 09
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC CD4 Memory Primary Cells MRE-Seq Donor TC009 Library HS2748-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.57
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 14

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

value: Blood

value: CD4 memory cell


description:
design description: H3K27me3 ChIP-Seq analysis of foreskin keratinocyte from skin01 (A02886) using Illumina Genome Analyzer IIx
library name: A02886
EXPERIMENT_TYPE: Histone H3K27me3
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: 5 ug
SIZE_FRACTION: 84-573 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9733
CHIP_ANTIBODY_LOT: 2
****************
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: GSM669592_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02886-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.6304
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 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 20
FINDPEAKS_SCORE: 0.0102
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0676
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.5027
IROC_PERCENTILE: 5
POISSON_SCORE: 0.161
POISSON_PERCENTILE: 20

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

ANALYSIS FILE NAME: GSM669592_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02886-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.6646
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 3
BROWSER_TRACK_NAME: PFK H3K27me3 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin01 Library A02886-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 20
FINDPEAKS_SCORE: 0.0102
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0676
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.5027
IROC_PERCENTILE: 5
POISSON_SCORE: 0.161
POISSON_PERCENTILE: 20

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

value: male

value: Penis

value: Keratinocyte

value: foreskin keratinocyte


description:
design description: H3K9ac ChIP-Seq analysis of foreskin keratinocyte from skin01 (A02884) using Illumina Genome Analyzer IIx
library name: A02884
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: 5 ug
SIZE_FRACTION: 128-501 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K9ac
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9649
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: GSM669590_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K9ac.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02884-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.6308
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 25
FINDPEAKS_SCORE: 0.6066
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5496
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9915
IROC_PERCENTILE: 44
POISSON_SCORE: 0.6811
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM669590_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K9ac.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02884-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.6650
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 3
BROWSER_TRACK_NAME: PFK H3K9ac 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9ac Donor skin01 Library A02884-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 25
FINDPEAKS_SCORE: 0.6066
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5496
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9915
IROC_PERCENTILE: 44
POISSON_SCORE: 0.6811
POISSON_PERCENTILE: 100

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


description:
design description: H3K4me3 ChIP-Seq analysis of foreskin keratinocyte from skin01 (A02883) using Illumina Genome Analyzer IIx
library name: A02883
EXPERIMENT_TYPE: Histone H3K4me3
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: 5 ug
SIZE_FRACTION: 146-407 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751
CHIP_ANTIBODY_LOT: 2
****************
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: GSM669589_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02883-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.6305
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 25
FINDPEAKS_SCORE: 0.731
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7346
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9748
IROC_PERCENTILE: 8
POISSON_SCORE: 0.7583
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM669589_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02883-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.6647
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 3
BROWSER_TRACK_NAME: PFK H3K4me3 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin01 Library A02883-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 25
FINDPEAKS_SCORE: 0.731
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7346
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9748
IROC_PERCENTILE: 8
POISSON_SCORE: 0.7583
POISSON_PERCENTILE: 100

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


description:
design description: H3K4me1 ChIP-Seq analysis of foreskin keratinocyte from skin01 (A02885) using Illumina Genome Analyzer IIx
library name: A02885
EXPERIMENT_TYPE: Histone H3K4me1
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: 5 ug
SIZE_FRACTION: 145-419 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.1 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAB-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669591_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me1.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02885-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.6303
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 28
FINDPEAKS_SCORE: 0.6114
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5729
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9966
IROC_PERCENTILE: 82
POISSON_SCORE: 0.6842
POISSON_PERCENTILE: 93

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

ANALYSIS FILE NAME: GSM669591_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K4me1.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A02885-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.6645
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 3
BROWSER_TRACK_NAME: PFK H3K4me1 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin01 Library A02885-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 28
FINDPEAKS_SCORE: 0.6114
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5729
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9966
IROC_PERCENTILE: 82
POISSON_SCORE: 0.6842
POISSON_PERCENTILE: 93

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


title: Snyder_PHA-4_GFP_YA_rep2 extraction5_seq5 aliquote 1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: eGFP;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

organism: Caenorhabditis elegans

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

tag: strain

value: OP37(official name :OP37 genotype :unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by :R. Waterston and S. Kim )

tag: developmental stage

value: Young Adult

tag: genotype

value: Hermaphrodite


title: Snyder_PHA-4_GFP_YA_rep2 extraction4_seq4 aliquote 1

value: unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG]


title: Snyder_PHA-4_GFP_YA_rep1 extraction7_seq7 aliquote 1

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180


title: Snyder_PHA-4_GFP_YA_rep2 extraction3_seq3 aliquote 1

description: channel ch1 is input DNA;

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180


title: Snyder_PHA-4_GFP_YA_rep1 extraction6_seq6 aliquote 1


description:
design description: MRE-Seq analysis of cortex neural stem and progenitor cells from HuFNSC02 (HS2778) using Illumina Genome Analyzer IIx
library name: HS2778
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: 139-395 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: GSM669602_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.MRE-Seq.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2778-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC02 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.6353
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 3

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.73
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 86

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

ANALYSIS FILE NAME: GSM669602_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.MRE-Seq.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2778-1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC02 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.6360
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 3
BROWSER_TRACK_NAME: NCD MRE 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived MRE-Seq Donor HuFNSC02 Library HS2778-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.73
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 86

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

value: female

value: Brain

value: Cortex neurosphere culture

value: No

value: primary cell culture

value: cortex neural stem and progenitor cells


title: Snyder_PHA-4_GFP_YA_rep2 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PHA-4_GFP_YA_rep2 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_EGL-5_GFP_L3_rep2 extraction9_seq9 aliquote 1

value: OP54(official name :OP54 genotype :unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by :R. Waterston and S. Kim )


description:
design description: H3K36me3 ChIP-Seq analysis of peripheral cd8 naive from TC001 (HS2387) using Illumina Genome Analyzer IIx
library name: HS2387
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: 80-271 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9763S
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: GSM669593_UCSF-UBC.CD8_Naive_Primary_Cells.H3K36me3.TC001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2387-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD8 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.6302
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 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.0464
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.1304
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.8437
IROC_PERCENTILE: 4
POISSON_SCORE: 0.2639
POISSON_PERCENTILE: 4

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

ANALYSIS FILE NAME: GSM669593_UCSF-UBC.CD8_Naive_Primary_Cells.H3K36me3.TC001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2387-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD8 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.6644
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 3
BROWSER_TRACK_NAME: CD8N H3K36me3 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC CD8 Naive Primary Cells Histone H3K36me3 Donor TC001 Library HS2387-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.0464
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.1304
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.8437
IROC_PERCENTILE: 4
POISSON_SCORE: 0.2639
POISSON_PERCENTILE: 4

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

value: Blood

value: CD8 naive cell

value: primary cell


title: Snyder_PHA-4_GFP_L2_rep1 extraction5_seq5 aliquote 1

description: channel ch1 is input DNA;

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS190


title: Snyder_EGL-5_GFP_L3_rep2 extraction8_seq8 aliquote 1

value: unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG]


title: Snyder_EGL-5_GFP_L3_rep1 extraction7_seq7 aliquote 1


title: Snyder_EGL-5_GFP_L3_rep2 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_EGL-5_GFP_L3_rep2 extraction5_seq5 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_EGL-5_GFP_L3_rep1 extraction6_seq6 aliquote 1


title: Snyder_EGL-5_GFP_L3_rep2 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_EGL-5_GFP_L3_rep2 extraction3_seq3 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PHA-4_GFP_L2_rep1 extraction3_seq3 aliquote 1


title: Snyder_EGL-5_GFP_L3_rep2 extraction4_seq4 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PES-1_GFP_L4_rep2 extraction7_seq7 aliquote 1

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS190

value: OP87(official name :OP87 genotype :unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PES-1::EGFP fusion protein is expressed in the correct pes-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PES-1 transcription factor. made_by :R. Waterston )


title: Snyder_PHA-4_GFP_L2_rep2 extraction1_seq1 aliquote 1


title: Snyder_PES-1_GFP_L4_rep2 extraction8_seq8 aliquote 1

value: unc-119(ed3) III; wgIs87 [unc-119(+) pes-1::TY1::EGFP::3xFLAG]


title: Snyder_PES-1_GFP_L4_rep2 extraction9_seq9 aliquote 1


title: Snyder_PHA-4_GFP_L2_rep1 extraction4_seq4 aliquote 1

description: channel ch1 is input DNA;

value: OP37(official name :OP37 genotype :unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by :R. Waterston and S. Kim )


title: Snyder_PHA-4_GFP_L2_rep2 extraction2_seq2 aliquote 1


title: Snyder_PES-1_GFP_L4_rep1 extraction5_seq5 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PES-1_GFP_L4_rep1 extraction6_seq6 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PES-1_GFP_L4_rep1 extraction4_seq4 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PES-1_GFP_L4_rep1 extraction2_seq2 aliquote 1


title: Snyder_PES-1_GFP_L4_rep1 extraction3_seq3 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ALR-1_GFP_L2_rep1 extraction4_seq4 aliquote 1

description: channel ch1 is input DNA;

value: OP200(official name :OP200 genotype :unc119(ed3);wgIs200(alr-1::TY1 EGFP FLAG C;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :his strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ALR-1::EGFP fusion protein is expressed in the correct alr-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALR-1 transcription factor. made_by :R. Waterston )


title: Snyder_ALR-1_GFP_L2_rep2 extraction1_seq1 aliquote 1

value: unc119(ed3);wgIs200(alr-1::TY1 EGFP FLAG C;unc119)

value: Hermaphrodite


title: Snyder_ALR-1_GFP_L2_rep1 extraction2_seq2 aliquote 1


title: Snyder_ALR-1_GFP_L2_rep1 extraction3_seq3 aliquote 1


title: Snyder_PES-1_GFP_L4_rep1 extraction1_seq1 aliquote 1


title: METSMITS145B-HH3-36h-lane5

status: Public on Mar 30 2011

city: St Louis

first: Federico

middle: E

last: Rey

state: MO

address: 4444 Forest Park Blvd

department: Pathology

institute: Washington University

description:
HH=high hydrogen (80%), high Formate concentration (44.1mM);
total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); in vitro modified MBC media, mid-log phase growth (60 hours), 80% hydrogen, 20% CO2 gasses at 30psi replensihed every 6 hours, formate concentration 44.1mM

library_source: transcriptomic

data_processing: After dividing sequence runs by barcode, we mapped the reads to the relevant genomes using the ssaha2 algorithm. Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32nt barcoded samples; 33 was the minimum score used for 36-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36nt there is a large fraction of the reads that map to multiple locations within a genome or across genomes. Reads that map non-uniquely were added to each gene in proportion to each geneâ€™s fraction of unique-match counts (e.g., a non-unique read that maps equally well to gene A with 18 unique reads and gene B with 2 unique reads will be scored as 0.9 count to gene A and 0.1 count to gene B). We added a pseudocount (i.e. added 1) to each gene count prior to normalization to account for differences in sampling depth, although clearly a more appropriate model-based approach to smooth lower expression values is needed in the future, particularly with mixed species samples where one or more species is clearly undersampled. Raw counts were normalized to reads/kb/million mapped reads. First column of counts files contains locus tag information.

molecule: total RNA

organism: Methanobrevibacter smithii

source_name: in vitro culture

growth_protocol: In vitro modified Methanobrevibacter complex medium MBC media, mid-log phase growth, 80% hydrogen, 20% CO2 gasses

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit. Briefly, cDNA was sonicated in a biorupter sonicator, cleaned up/concentrated through a Qiagen PCR column, and end-repaired. The blunt DNA was treated with Klenow fragment (exo minus) to add an A-overhang, and ligated to the relevant Illumina adapter sequence (either with our without a barcode).  Adaptered-DNA was then size-selected on a agarose gel and PCR amplified. The purified PCR was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: All samples were treated with RNAProtect (Qiagen) and immediately frozen at -80C.

tag: treatment

tag: genome accession

tag: sample type

value: rRNA depleted total RNA


title: METSMITS95D-HL2-36h-lane5

description:
HL=high hydrogen (80%), Low Formate concentration (2.8mM); 36h=36hours after innoculation
total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); in vitro modified MBC media, mid-log phase growth (36 hours), 80% hydrogen, 20% CO2 gasses at 30psi replensihed every 6 hours, formate concentration 2.8mM

tag: time

value: 36hours after innoculation


title: METSMITS96A-HH1-36h-lane7

description:
HH=high hydrogen (80%), high Formate concentration (44.1mM);
total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); in vitro modified MBC media, mid-log phase growth (36 hours), 80% hydrogen, 20% CO2 gasses at 30psi replensihed every 6 hours, formate concentration 44.1mM


title: METSMITS95D-HL3-36h-lane6

value: HL=high hydrogen (80%), Low Formate concentration (2.8mM)


title: METSMITS94C-HL1-36h-lane6


title: METSMITS94C-HL2-36h-lane7


title: METSMITS145B-HL2-36h-lane4

description:
HL=high hydrogen (80%), Low Formate concentration (2.8mM); 36h=36hours after innoculation
total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); in vitro modified MBC media, mid-log phase growth (60 hours), 80% hydrogen, 20% CO2 gasses at 30psi replensihed every 6 hours, formate concentration 2.8mM


title: METSMITS95D-HL1-36h-lane7


title: METSMITS96A-HH2-36h-lane2

value: HH=high hydrogen (80%), high Formate concentration (44.1mM)


title: METSMITS94C-HH3-36h-lane4


title: METSMITS146E-HH1-36h-lane7


title: METSMITS145B-HH3-36h-lane4


title: METSMITS96A-HL1-36h-lane7


title: Snyder_ALR-1_GFP_L2_rep1 extraction5_seq5 aliquote 1

description: channel ch1 is input DNA;


title: METSMITS146E-HL3-36h-lane7


title: METSMITS94C-HH2-36h-lane3


title: METSMITS146E-HL1-36h-lane7


title: METSMITS145B-HL3-36h-lane6


title: METSMITS146E-HL2-36h-lane5


title: METSMITS94C-HL1-36h-lane7


title: METSMITS145B-HL1-36h-lane7


title: METSMITS146E-HH3-36h-lane5


title: METSMITS146E-HH1-36h-lane8


title: METSMITS146E-HH2-36h-lane3


title: METSMITS95D-HH3-36h-lane4


title: METSMITS95D-HH3-36h-lane5


title: METSMITS95D-HH2-36h-lane2


title: METSMITS94C-HH2-36h-lane2


title: METSMITS94C-HL3-36h-lane3


title: METSMITS96A-HH1-36h-lane8


title: METSMITS94C-HL3-36h-lane2


title: METSMITS95D-HL1-36h-lane6


title: METSMITS96A-HL2-36h-lane8


title: METSMITS146E-HH3-36h-lane4

description:
HH=high hydrogen (80%), high Formate concentration (44.1mM); 36h=36hours after innoculation
total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); in vitro modified MBC media, mid-log phase growth (36 hours), 80% hydrogen, 20% CO2 gasses at 30psi replensihed every 6 hours, formate concentration 44.1mM


title: METSMITS145B-HH2-36h-lane3

description:
HH=high hydrogen (80%), high Formate concentration (44.1mM); 36h=36hours after innoculation
total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); in vitro modified MBC media, mid-log phase growth (60 hours), 80% hydrogen, 20% CO2 gasses at 30psi replensihed every 6 hours, formate concentration 44.1mM


title: METSMITS96A-HH3-36h-lane4


title: METSMITS95D-HL3-36h-lane7


title: Endogenous sRNAs from dormant buds of O. europaea (PicualxArbequina genetic cross)_dormant (adult) stage

city: Murcia

first: Livia

last: Donaire

state: Murcia

address: Campus de Espinardo

department: Plant Pathology

country: Spain

institute: Centro de Edafología y Biología Aplicada del Segura

description: Endogenous small RNAs from growing buds of O. europaea

data_processing: Raw sequences were parsed from FASTA formatted files and assigned to specific libraries. The adapter sequences in the raw reads were removed and non-redundant sequences were calculated using Perl scripts and bioperl libraries. A size range filter was used to removed the sRNAs sequences <18 nts and >25 nts.

organism: Olea europaea

source_name: Dormant lateral buds, Picual x Arbequina olive variety

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) and ~300 ug were used for construction of sRNAs libraries as described (Kasschau et al., 2007) with the following modifications. The 3’ adapter was replaced by a pre-activated 5’ adenylated oligo (5’ rAppCTGTAGGCACCATCAAT3ddC 3’) (Integrated DNA technologies) to avoid the circularization of sRNAs. The chimeric RNA/DNA oligonucleotide 5’ adapters were described previously (Kasschau et al., 2007). After each ligation step, sRNA was purified using 17% denaturing PAGE. The purified-ligated sRNA was reverse transcribed and the cDNA was amplified using Taq DNA polymerase (Perkin Elmer) and 3’ PCR FusionB and 5’ PCR FusionA primers (Kasschau et al., 2007). PCR primers contained the “A” and “B” tag sequences used by 454 Life Science during sequencing. DNA amplicons were gel-purified using 12% native polyacrylamide and eluted in 0.3 M NaCl as described (Donaire et al., 2008). Quantity and quality of DNA amplicons were measured using ND-1000 spectrophotometer (Nanodrop) and Experion Automated Electrophoresis System (BioRad), respectively. Same quantity of DNA amplicon from each library was pooled and sequenced by 454 Life Science technology (Lifesequencing).

tag: tissue

value: Lateral buds

value: Dormant


title: METSMITS96A-HL2-36h-lane7


title: Endogenous sRNAs from growing buds of O. europaea (PicualxArbequina genetic cross)_growing (juvenile) stage

source_name: Growing lateral buds, Picual x Arbequina olive variety

value: Growing


title: METSMITS145B-HL3-36h-lane7


title: METSMITS94C-HH3-36h-lane5


title: METSMITS146E-HH2-36h-lane2


title: METSMITS96A-HL3-36h-lane3


title: METSMITS96A-HH2-36h-lane3


title: METSMITS94C-HL2-36h-lane8


title: METSMITS145B-HL2-36h-lane5


title: METSMITS95D-HH1-36h-lane7


title: METSMITS94C-HH1-36h-lane7


title: METSMITS146E-HL2-36h-lane4


title: METSMITS145B-HH2-36h-lane2


title: METSMITS95D-HH1-36h-lane8


title: METSMITS146E-HL1-36h-lane6


title: METSMITS145B-HL1-36h-lane6


title: METSMITS146E-HL3-36h-lane6


title: METSMITS94C-HH1-36h-lane8


title: METSMITS95D-HL2-36h-lane4


title: METSMITS145B-HH1-36h-lane8


title: METSMITS96A-HH3-36h-lane5


title: METSMITS145B-HH1-36h-lane7


title: MsmPS-HH3-36h-lane5

organism: Methanobrevibacter smithii ATCC 35061

value: Methanobrevibacter smithii ATCC 35061


title: METSMITS96A-HL3-36h-lane2


title: MsmPS-HH2-36h-lane2


title: MsmPS-HH1-36h-lane8


title: MsmPS-HL2-36h-lane7

description:
HL=high hydrogen (80%), Low Formate concentration (2.8mM);
total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); in vitro modified MBC media, mid-log phase growth (36 hours), 80% hydrogen, 20% CO2 gasses at 30psi replensihed every 6 hours, formate concentration 2.8mM


title: MsmPS-HH1-36h-lane7


title: MsmPS-HH2-36h-lane3


title: Tet1_exp1 no KD

city: Boston

first: Hao

last: Wu

state: Massachusetts

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: Genetics

institute: Harvard Medical School/HHMI

description: Chromatin IP against Tet1 in WT mouse ES cells

data_processing:
Alignment: All sequencing reads were obtained and mapped to the mouse genome (NCBI build 36/mm8) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and reads were summed in sliding windows of 400 bp to create summary windows for visulization.
Peak detection:  Sequencing reads from two Tet1 ChIP-seq experiments were combined and Tet1 enriched regions were determined by the Model-based Analysis of ChIP-Seq (MACS, version 1.3.7.1) algorithm (http://liulab.dfci.harvard.edu/MACS/). Sequencing reads from IgG control experiments were used as negative controls in MACS. Only uniquely mapped reads were retained. Redundant reads were also filtered out. The statistical cutoff used for identifying Tet1 binding-sites was P-value<1e-08 and fold enrichment (over IgG control) >10.

organism: Mus musculus

source_name: Mouse ES cells

growth_protocol: Mouse ES cells were maintained on gelatin-coated dishes in Glasgow Minimum Essential medium (GMEM; GIBCO), supplemented with 15% heat-inactivated fetal  bovine serum, 55 mM b-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of ESGRO (Chemicon) under feeder-free conditions.

extract_protocol: Mouse ES cells were crosslinked with 1% formaldehyde at room temperature for 10 min and sonicated to generate chromatin fragments of 200-500 bp. Chromatin fragments from 10-20 million cells were immunoprecipitated using 8 μg of the Tet1 antibody (affinity purified custom-made) or IgG control from two biologically independent samples. ChIP-seq library construction, and Illumina sequencing were performed according to Illumina's instructions.The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For Tet1 knockdown (KD), mouse ES cells were infected with lentiviruses expressing both the GFP reporter and short-hairpin RNA (shRNA) specific for Tet1 (Tet1 KD). Lentiviruses expressing GFP alone was used as a control (Con KD). Analyses were performed using control or  Tet1-depleted ES cells that were purified on the basis of GFP fluorescence by FACS 8 days after lentiviral transduction.

value: wild-type

tag: antibody manufacturer

value: custom

tag: antibody

value: Tet1 rabbit polyclonal antibodies

value: mouse ES cells

tag: knockdown


title: Tet1_exp2 mock KD

description: Chromatin IP against Tet1 in Con KD mouse ES cells

value: control KD

value: mock


title: Tet1_exp3 Tet1 KD

description: Chromatin IP against Tet1 in Tet1 KD mouse ES cells

value: Tet1 KD


title: MsmPS-HL3-36h-lane2


title: MsmPS-HL2-36h-lane8


title: IgG_exp1 no KD

description: Negative control in WT mouse ES cells

value: Rabbit IgG


title: MsmPS-HL1-36h-lane6


title: IgG_exp2 mock KD

description: Negative control in Con KD mouse ES cells


title: small intestine cDNA replicate D Biotin

status: Public on Mar 29 2011

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: RNA-Seq against polyadenylated RNA from small intestine

data_processing: Sequence reads were obtained using the Applied Biosystems Modular Analysis Pipeline (MOAP). Data is unfiltered and includes all identified beads.

source_name: small intestine total tissue

growth_protocol: small intestine and colon from 9-10 weeks old mice were prepared and frozen in liquid nitrogen.

extract_protocol: SMART cDNA synthesis and fragment library construction

value: Small Intestine

tag: extract protocol

tag: library selection

value: polyadenylated RNA


title: small intestine cDNA replicate B2 Biotin

value: SMART cDNA synthesis and fragment library construction


title: MsmPS-HL1-36h-lane7

value: HL=high hydrogen (80%), Low Formate concentration (2.8mM)

value: rRNA depleted total RNA


title: small intestine cDNA replicate B1 Biotin


title: METSMITS96A-HL1-36h-lane6

value: 36hours after innoculation


title: Tet1_exp4 Tet1 KD


title: MsmPS48hHH1

description:
HH=high hydrogen (80%), high Formate concentration (44.1mM);
total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); in vitro modified MBC media, stationary phase growth (48 hours), 80% hydrogen, 20% CO2 gasses at 30psi replensihed every 6 hours, formate concentration 44.1mM


title: colon B (Poly-A Enrichment)

description: RNA-Seq against polyadenylated RNA from colon

source_name: colon total tissue

extract_protocol: Whole Transcriptome Analysis Kit

value: Colon

value: Whole Transcriptome Analysis Kit


title: small intestine B (Poly-A Enrichment)


title: MsmPS48hHL2

description:
HL=high hydrogen (80%), Low Formate concentration (2.8mM);
total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); in vitro modified MBC media, stationary phase growth (48 hours), 80% hydrogen, 20% CO2 gasses at 30psi replensihed every 6 hours, formate concentration 2.8mM

value: Methanobrevibacter smithii ATCC 35061


title: colon A (Poly-A Enrichment)


title: METSMITS95D-HH2-36h-lane3

value: HH=high hydrogen (80%), high Formate concentration (44.1mM)


title: MsmPS-HH3-36h-lane4


title: small intestine cDNA replicate C Biotin


title: MsmPS48hHH2


title: MsmPS48hHL1