description:
design description: H3K4me1 ChIP-Seq analysis of foreskin melanocyte from skin02 (A08743) using Illumina HiSeq 2000
library name: A08743
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: 20 ug
SIZE_FRACTION: 113-408 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 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: GSM941730_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me1.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08743-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12876
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,172,492
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.2015
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2822
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9604
IROC_PERCENTILE: 75
POISSON_SCORE: 0.4701
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM941730_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me1.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08743-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12900
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 7
BROWSER_TRACK_NAME: PFM H3K4me1 02 43
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin02 Library A08743 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,172,492
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.2015
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2822
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9604
IROC_PERCENTILE: 75
POISSON_SCORE: 0.4701
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.94

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


status: Public on Jun 04 2012

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: MeDIP-Seq analysis of foreskin fibroblast from skin02 (A09691) using Illumina HiSeq 2000
library name: A09691
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: 30 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 0.63 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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM941725_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MeDIP-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A09691-1-A08302-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12917
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 122,073,017
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4867
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5065
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9852
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5832
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM941725_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MeDIP-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A09691-1-A08302-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12920
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 7
BROWSER_TRACK_NAME: PFF MeDIP 02 91
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin02 Library A09691 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 122,073,017
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4867
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5065
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9852
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5832
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

molecule: genomic DNA

organism: Homo sapiens

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/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

tag: histological type

value: Fibroblast

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: foreskin fibroblast


description:
design description: MeDIP-Seq analysis of foreskin keratinocyte from skin02 (A09692) using Illumina HiSeq 2000
library name: A09692
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: 30 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 5 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 0.8 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: GSM941726_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MeDIP-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A09692-1-A08303-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12918
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 100,523,225
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4857
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.5104
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9844
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5778
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM941726_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MeDIP-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A09692-1-A08303-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12921
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 7
BROWSER_TRACK_NAME: PFK MeDIP 02 92
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin02 Library A09692 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 100,523,225
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4857
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.5104
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9844
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5778
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Keratinocyte

value: foreskin keratinocyte


description:
design description: MRE-Seq analysis of foreskin keratinocyte from skin02 (A08303) using Illumina HiSeq 2000
library name: A08303
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document '5xMRE-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: 5 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV
MRE_PROTOCOL_SIZE_FRACTION: 150-450 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: GSM941723_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08303-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12924
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 109,881,066
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 97.38
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM941723_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.MRE-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08303-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.12927
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 7
BROWSER_TRACK_NAME: PFK MRE 02 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin02 Library A08303 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 109,881,066
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 97.38
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

extract_protocol: library construction protocol: Refer to document '5xMRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)


title: MCF7 siGATA3

status: Public on Jun 05 2012

city: Columbus

first: rui

last: wang

state: OHIO

address: 212 Biomedical Research Tower,460 West 12th Ave

institute: Ohio State University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol as described in Trapnell et al, Nature Protocols  7, 562–578 (2012). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

source_name: Human breast adenocarcinoma cell-line MCF7

growth_protocol: Thawing Cells:  1. Thaw vial immediately in 37º C water bath. Keep O ring above the water surface to prevent contamination. Thaw content with slight  shake until only small ice is left in vial. It usually takes 1 min. Spray vial with 70% ethanol all over and wipe its surface with clean tissue in the hood.  2. Open the vial and transfer the content to a 15 ml Falcon tube already containing 5 ml of fresh medium.  3. Spin down at 1000 rpm or 200g for 3 to 5 mins at 4º C. Aspirate supernatant.  4. Resuspend cells in fresh medium and transfer to 150mm x 25mm tissue culture dish.  5. Check the cells under microscope.  6. Cells are cultured in CO2 incubator and medium is changed about every 3 days.  7. It usually takes 3 days or more for cells to recovery from freezing. After cell culture reaches  80-85%  confluence, subculture is conducted. Subculture ratio is about 1:3 or 1:4.  Passaging Cells:  1. Observe cells to see how confluent they are, whether the cells are alive, whether the cells are contaminated, and whether the cells have the correct morphology. After cell culture reaches 80 to 85% confluence, subculture is conducted  2. Remove media from dish  3. Wash 1x with 10 ml of PBS  4. Add 5 ml of Trypsin and trypsinize for 3 min at 37C. Whack hard – you should see the cells coming down. (Important: never overtrypsinize the cells, so work quickly)  5. Add 5 ml of media and use it to rinse the dish to detach the cells off (4 to 5 times)  6. Spin down at 1000rpm for 3 to 5 min at room temperature. Aspirate supernatant  7. Add 15 ml of media to 15ml tube containing cell pellet, and pipette up and down to mix  8. Add 15 ml of media to each new 150mm x 25mm tissue culture dish (we split 1 dish into 3 to 4 dishes)  9. Add 5mls of cell culturecontaining media to each tissue culture dish. Make sure the media covers the entire area of the dish. Put the cells into 37C with 5% CO2.

extract_protocol: RNA was extracted using Trizol Reagent (Life Technologies) following the suggested protocol; 2ug of each RNA sample was used with the Illumina TruSeq RNA Sample Prep Kit (Cat # RS-122-2001) to make RNA libraries following the Illumina TruSeq RNA Sample preparation Low-Throughput protocol. Briefly, RNA was fragmented, then first-strand cDNA was prepared using the kit supplied 1st Strand Master Mix and user-supplied Superscript III (Life Technologies, cat # 18080-051) followed by second strand cDNA synthesis. The Illumina protocol and reagents were used to complete the library preparation, with 12 cycles of PCR amplification.

treatment_protocol: 1. Low passage MCF7 cells were grown in DMEM supplemented with 10% FBS (no Pen/Step) to 85% confluency and passaged into 6-well dish at approximately 50% confluency  2. Cells were transfected with final concentration 50nM siRNA using Lipofectamine2000 according to the manufacturer's instructions (Invitrogen)  3. The media was replaced 12 hours post transfection and cells were grown for an additional 36 hours (hours posttransfection)

tag: cell line

tag: passage

tag: sirna

value: ON-TARGETplus Non-Targeting siRNA against GATA3

tag: treatment

value: GATA3 KD


description:
design description: H3K4me1 ChIP-Seq analysis of foreskin melanocyte from skin01 (A08383) using Illumina HiSeq 2000
library name: A08383
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: 10 ug
SIZE_FRACTION: 78-358 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 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: GSM941728_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me1.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08383-1-A08383-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Penis Foreskin Melanocyte 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.12875
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,390,230
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0265
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.1501
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.841
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3256
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM941728_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me1.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08383-1-A08383-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Penis Foreskin Melanocyte 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.12899
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 7
BROWSER_TRACK_NAME: PFM H3K4me1 01 83
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin01 Library A08383 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,390,230
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0265
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.1501
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.841
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3256
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

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: Melanocyte

value: foreskin melanocyte


description:
design description: H3K9me3 ChIP-Seq analysis of foreskin melanocyte from skin01 (A08385) using Illumina HiSeq 2000
library name: A08385
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: 10 ug
SIZE_FRACTION: 110-351 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: GSM941720_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K9me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08385-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Penis Foreskin Melanocyte 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.12886
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,401,260
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0593
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.136
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.8343
IROC_PERCENTILE: 67
POISSON_SCORE: 0.2906
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.69

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

ANALYSIS FILE NAME: GSM941720_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K9me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08385-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte 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.12910
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 7
BROWSER_TRACK_NAME: PFM H3K9me3 01 85
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin01 Library A08385 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,401,260
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0593
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.136
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.8343
IROC_PERCENTILE: 67
POISSON_SCORE: 0.2906
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.69

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


description:
design description: H3K36me3 ChIP-Seq analysis of cortex neural stem and progenitor cells from HuFNSC01 (A03273) using Illumina HiSeq 2000
library name: A03273
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: 114-314 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: 947467
****************
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: GSM941714_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.H3K36me3.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03273-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-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.12873
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,318,345
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.333
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.312
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9662
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5744
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM941714_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.H3K36me3.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03273-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-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.12897
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 7
BROWSER_TRACK_NAME: NCD H3K36me3 01 73
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K36me3 Donor HuFNSC01 Library A03273 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,318,345
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.333
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.312
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9662
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5744
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: female

value: Brain

value: Cortex neurosphere culture

value: cortex neural stem and progenitor cells


description:
design description: H3K27me3 ChIP-Seq analysis of cortex neural stem and progenitor cells from HuFNSC01 (A03272) using Illumina HiSeq 2000
library name: A03272
EXPERIMENT_TYPE: Histone H3K27me3
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: 74-314 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00241,A299-00242
****************
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: GSM941713_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.H3K27me3.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03272-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-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.12868
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,247,617
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.0875
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.1478
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9181
IROC_PERCENTILE: 71
POISSON_SCORE: 0.34
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM941713_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.H3K27me3.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03272-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-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.12892
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 7
BROWSER_TRACK_NAME: NCD H3K27me3 01 72
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K27me3 Donor HuFNSC01 Library A03272 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,247,617
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.0875
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.1478
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9181
IROC_PERCENTILE: 71
POISSON_SCORE: 0.34
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.96

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


description:
design description: H3K27me3 ChIP-Seq analysis of foreskin melanocyte from skin01 (A08386) using Illumina HiSeq 2000
library name: A08386
EXPERIMENT_TYPE: Histone H3K27me3
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: 10 ug
SIZE_FRACTION: 102-354 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00242
****************
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: GSM941721_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08386-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Penis Foreskin Melanocyte 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.12871
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,484,947
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.037
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1216
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8312
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3091
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM941721_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08386-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte 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.12895
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 7
BROWSER_TRACK_NAME: PFM H3K27me3 01 86
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin01 Library A08386 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,484,947
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.037
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1216
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8312
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3091
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.92

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


description:
design description: H3K36me3 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC01 (A03279) using Illumina HiSeq 2000
library name: A03279
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: 109-359 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: 947467
****************
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: GSM941716_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K36me3.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03279-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-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.12867
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 86,425,113
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.1413
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.1738
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9465
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4992
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM941716_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K36me3.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03279-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-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.12891
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 7
BROWSER_TRACK_NAME: NGED H3K36me3 01 79
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K36me3 Donor HuFNSC01 Library A03279 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 86,425,113
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.1413
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.1738
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9465
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4992
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Ganglionic eminence neurosphere culture


description:
design description: H3K27me3 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC01 (A03278) using Illumina HiSeq 2000
library name: A03278
EXPERIMENT_TYPE: Histone H3K27me3
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: 94-314 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00241
****************
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: GSM941715_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K27me3.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03278-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-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.12877
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 72,426,246
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.1002
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.131
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9423
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3766
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM941715_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K27me3.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03278-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-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.12901
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 7
BROWSER_TRACK_NAME: NGED H3K27me3 01 78
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 Donor HuFNSC01 Library A03278 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 72,426,246
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.1002
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.131
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9423
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3766
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.89

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


description:
design description: H3K4me1 ChIP-Seq analysis of foreskin fibroblast from skin02 (A08395) using Illumina HiSeq 2000
library name: A08395
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: 20 ug
SIZE_FRACTION: 104-354 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 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: GSM941717_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me1.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08395-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12882
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 72,061,575
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0369
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1535
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8799
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3994
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM941717_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me1.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08395-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12906
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 7
BROWSER_TRACK_NAME: PFF H3K4me1 02 95
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin02 Library A08395 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 72,061,575
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0369
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1535
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8799
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3994
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: male


description:
design description: H3K4me3 ChIP-Seq analysis of foreskin melanocyte from skin01 (A08384) using Illumina HiSeq 2000
library name: A08384
EXPERIMENT_TYPE: Histone H3K4me3
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: 10 ug
SIZE_FRACTION: 87-343 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM941719_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08384-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Penis Foreskin Melanocyte 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.12878
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,649,649
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.4096
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.4344
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4644
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM941719_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K4me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08384-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte 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.12902
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 7
BROWSER_TRACK_NAME: PFM H3K4me3 01 84
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin01 Library A08384 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,649,649
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.4096
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.4344
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4644
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: Penis


description:
design description: H3K4me3 ChIP-Seq analysis of foreskin fibroblast from skin02 (A08396) using Illumina HiSeq 2000
library name: A08396
EXPERIMENT_TYPE: Histone H3K4me3
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: 20 ug
SIZE_FRACTION: 74-284 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM941718_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08396-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12889
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 50,451,049
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.4212
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.4313
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.997
IROC_PERCENTILE: 25
POISSON_SCORE: 0.5081
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM941718_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08396-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12913
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 7
BROWSER_TRACK_NAME: PFF H3K4me3 02 96
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin02 Library A08396 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 50,451,049
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.4212
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.4313
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.997
IROC_PERCENTILE: 25
POISSON_SCORE: 0.5081
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Fibroblast


title: PA3_1.3

city: Lexington

first: Lisa

last: Vaillancourt

state: Kentucky

address: 201F Plant Science Building

department: Plant Pathology

institute: University of Kentucky

description: Penetrating appressoria, biological replicate 3, lane 1

data_processing: Aligned against Colletotrichum graminicola genome en genes (available via http://www.broadinstitute.org/annotation/genome/colletotrichum_group/MultiHome.html) using tophat for aligment and Bedtools for post processing.

organism: Colletotrichum graminicola

source_name: Pre-penetration appressoria, 24h

growth_protocol: Samples were produced as described in Mosquera et al. (The Plant Cell 21: 1273 (2009) with modifications.

extract_protocol: Illumina TruSeqTM RNA Sample Preparation Kit. Two µg of PolyA-enriched RNA per sample was processed, including chemical fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end-repair, 3’end adenylation, adapter ligation (including different barcoding indices) and PCR amplification. After quality control analysis, libraries were pooled (3 libraries per pool) followed by single-read sequencing (1-4 lanes/pool) with a read length of 76 bp (including 7 bp for the barcode adaptor) using the Illumina Genome Analyzer IIx, according to standard Illumina protocols.

tag: tissue type

value: fungus +  plant (samples that mapped to fungus only)


title: PA3_2.2

description: Penetrating appressoria, biological replicate 2, lane 2


title: PA3_2.3

description: Penetrating appressoria, biological replicate 3, lane 2


description:
design description: MRE-Seq analysis of foreskin fibroblast from skin02 (A08302) using Illumina HiSeq 2000
library name: A08302
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document '5xMRE-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: 5 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV
MRE_PROTOCOL_SIZE_FRACTION: 150-450 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: GSM941722_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MRE-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08302-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12923
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 81,999,316
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 96.61
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM941722_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.MRE-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08302-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12926
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 7
BROWSER_TRACK_NAME: PFF MRE 02 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin02 Library A08302 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 81,999,316
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 96.61
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

value: No

value: primary cell culture


title: PA3_1.1

description: Penetrating appressoria, biological replicate 1, lane 1


title: PA3_1.2

description: Penetrating appressoria, biological replicate 2, lane 1


title: DR1-control

city: Seoul

first: Jisun

last: Kim

address: Anam-Dong, Sungbuk-Gu

department: Environmental Science and Ecological Engineering

country: South Korea

institute: Korea university

description: control

data_processing:
Base-calling: CASAVA v1.6
Alignment: CLC Genomics Workbench 4.5
Generation of normalized abundance measurement: CLC Genomics Workbench 4.5
Genome_build: Acinetobacter oleivorans DR1 chromosome, complete genome RefSeq (NC_014259.1)
Supplementary_files_format_and_content: txt

organism: Acinetobacter oleivorans

source_name: stationary cells

extract_protocol: Total RNA was isolated from 5 ml of stationary cells, using the RNeasy Mini kit (QIAGEN, USA), according to the manufacturer’s instructions. The RNA was subjected to a subtractive Hyb-based rRNA removal process using the MICROBExpress Bacterial mRNA Enrichment Kit (Ambion). RNA sequencing was performed using the Illumina Genome Analyzer IIx to generate single-ended 36-bp reads.

tag: strain

tag: genotype

value: Wild type

tag: growth phase

value: exponential


title: DR1-nor4

description: treated with norfloxacin (4μg/ml) over a period of 15 min.


description:
design description: MRE-Seq analysis of foreskin melanocyte from skin02 (A08304) using Illumina HiSeq 2000
library name: A08304
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document '5xMRE-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: 5 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV
MRE_PROTOCOL_SIZE_FRACTION: 150-450 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: GSM941724_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MRE-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08304-1.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12922
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 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 76,385,499
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.47
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM941724_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.MRE-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08304-1.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12925
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 7
BROWSER_TRACK_NAME: PFM MRE 02 04
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin02 Library A08304 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 76,385,499
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 98.47
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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


title: BP2.3

description: Biotrophic hyphae, biological replicate 3

source_name: Biotrophic phase, 36h


title: PA2_2.3


title: PA2_1.3


title: NP2.2

description: Necrotrophic, biological replicate 2

source_name: Necrotrophic phase, 60h


title: NP2.3

description: Necrotrophic, biological replicate 3


title: BP2.2

description: Biotrophic hyphae, biological replicate 2


title: Switch, biological replicate 2

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

description: Switch, biological replicate 2

data_processing: Aligned against Colletotrichum higginsianum genome (Version 1, available via http://www.broadinstitute.org/annotation/genome/colletotrichum_group/MultiHome.html) using tophat for aligment and Bedtools for post processing.

organism: Colletotrichum higginsianum

source_name: Switch (necrotrophic phase)

growth_protocol: In vitro appressoria were produced as described by Kleemann et al. (Microbiology 154: 1204 (2008) and in planta samples as described by Takahara et al. (Plant Journal 59: 672 (2009).

extract_protocol: Illumina TruSeqTM RNA Sample Preparation Kit. Two µg of PolyA-enriched RNA per sample was processed, including chemical fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end-repair, 3’end adenylation, adapter ligation (including different barcoding indices) and PCR amplification. After quality control analysis, libraries were pooled (3 libraries per pool) followed by gel-based size selection and single-read sequencing (1-2 lanes/pool) with a read length of 100 bp (plus an additional 7 bp for the barcode adaptor) using the Illumina Genome Analyzer IIx, according to standard Illumina protocols.

tag: Stage

value: Switch (necrotrophic phase)


title: Switch, biological replicate 1

description: Switch, biological replicate 1


title: PA3_2.1

description: Penetrating appressoria, biological replicate 1, lane 2


title: Biotrophic hyphea, biological replicate 3

source_name: Biotrophic phase

value: Biotrophic phase


title: PA2_1.2


title: NP2.1

description: Necrotrophic, biological replicate 1


title: PA2_2.1


title: In vitro apressoria, biological replicate 2

source_name: In vitro apressoria

value: In vitro apressoria


title: Biotrophic hyphea, biological replicate 1


title: Biotrophic hyphea, biological replicate 2


title: In vitro apressoria, biological replicate 3


title: PA2_1.1


title: input_ChIP-Seq_3

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

country: Italy

institute: EMBL

description: Chromatin IP against sonicated genomic DNA

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the human 2006 (hg18) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates.
For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described.
As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out at a threshold of 1 per 7 million tags to remove possible sequencing and/or alignment artefacts.
Remaining tags were processed using a custom R pipeline, employing the ShortRead library.
Genome_build: hg18
Supplementary_files_format_and_content: The processed data files are provided in wig format. The wig files are fixed step and thus contain scores representing 50 nucleotides according to the binning method we used

source_name: Raji-cells

extract_protocol:
CTD mutants carry 48 consensus repeats (Con48), or have replaced Thr4 residues in all consensus repeats by alanine (Thr4/Ala) were induced for 24h and then treated with α-amanitin (2μg/ml) for 48h. Wild-type or stable-transfected Raji cells were crosslinked at room temperature with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 25 8.0, 50mM Hepes pH 7.8) in growth medium for 10min. The reaction was quenched with the addition of 250mM glycine for 5min. Cells were washed twice with cold DPBS and 5x107 cells/aliquot were pelleted. Final concentrations of 1x phosphatase inhibitors, 1x EDTA-free protease inhibitors  (Roche), 0.2mM PMSF and 1μg/ml pepstatin were added to all LB buffers. Centrifugations and lysis steps were carried out at 4°C. Each cell aliquot was lysed in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 1% NP-40, 0.5% Triton X-100) for 20min on a rotating wheel. Chromatin was collected by centrifugation for 5min at 1.350g and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 10mM Tris pH 8.0) for 20 minutes. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8.0, 0.5mM EGTA pH 8, 10mM Tris pH 8.0, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% Nlauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc.) sonicator for 14 cycles (30sec on, 30sec off, amplitude 40). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g for 20min a 50μl aliquot was taken to serve as input control. The input was combined with an equal volume of 2x elution buffer (100mM Tris pH 8.0, 20mM EDTA pH 8.0, 2% SDS) and incubated overnight at 65°C for 13-15h. SDS was diluted by the addition of an equal volume of TE (10mM Tris pH 8.0, 1mM EDTA pH 8.0), followed by 2h of RNase A (0.2μg/ml) and 2h of Proteinase K (0.2μg/ml) digestions at 37°C and 55°C, respectively. DNA was purified by two subsequent phenol:chloroform:isoamylalcohol (25:24:1, pH 8) extractions, followed by a PCR purification column (Qiagen). DNA was eluted using 50μl H2O and the concentration was measured on a Nanodrop 1000 (Thermo Scientific). To verify DNA fragmentation, 500ng were run on a 2% agarose gel.
EDTA-free protease inhibitors (Roche, France) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1µg/ml pepstatin. Phosphatase inhibitors (Roche, France) were added to a final concentration of 1x for Pol II phospho-serine ChIPs. Aliquots of 5x107 cells were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at 4°C. Chromatin was collected by centrifugation for 5 minutes at 4°C and 1.350g in a tabletop centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc, USA) sonicator for 14 cycles (30 seconds on, 30 seconds off, amplitude 40) with the tubes submerged in ice-cold sonication solution (500mM NaCl, 20% Ethanol). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g and 4°C for 20 minutes. For batch processing, supernatants were combined, mixed thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at -80°C until use and 50µl aliquots were taken to serve as input controls.  All experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G. For biological replicates, all steps were repeated using a biologically independent sample. Beads were washed 3x with 1ml and subsequently resuspended in 250µl of blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody, the beads were incubated at 4°C overnight on a rotating wheel. Unbound antibodies were removed through three further washes with 1ml of blocking solution. Beads were resuspended in 100µl of blocking solution, extracts were added and the mix was incubated overnight at 4°C on a rotating wheel.  EDTA-free protease inhibitors (Roche) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1µg/ml pepstatin. Phosphatase inhibitors (Roche) were added to a final concentration of 1x in the case of Pol II phospho-serine ChIPs. Beads were washed 8 times in RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 10 mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE+ (10mM Tris pH8, 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps at 65°C for 15 and 10 minutes in 110µl and 100µl of elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65°C overnight (13-15 hours) for crosslink reversal.

value: Raji-cells

tag: genotype/variation

value: Th4/Ala mutant

value: Burkitt's lymphoma

tag: ChIP


title: In vitro apressoria, biological replicate 1


title: PolII_HA_ChIP-Seq_2

description: Chromatin IP against PolII

extract_protocol: EDTA-free protease inhibitors (Roche, France) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1µg/ml pepstatin. Phosphatase inhibitors (Roche, France) were added to a final concentration of 1x for Pol II phospho-serine ChIPs. Aliquots of 5x107 cells were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at 4°C. Chromatin was collected by centrifugation for 5 minutes at 4°C and 1.350g in a tabletop centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc, USA) sonicator for 14 cycles (30 seconds on, 30 seconds off, amplitude 40) with the tubes submerged in ice-cold sonication solution (500mM NaCl, 20% Ethanol). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g and 4°C for 20 minutes. For batch processing, supernatants were combined, mixed thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at -80°C until use and 50µl aliquots were taken to serve as input controls.  All experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G. For biological replicates, all steps were repeated using a biologically independent sample. Beads were washed 3x with 1ml and subsequently resuspended in 250µl of blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody, the beads were incubated at 4°C overnight on a rotating wheel. Unbound antibodies were removed through three further washes with 1ml of blocking solution. Beads were resuspended in 100µl of blocking solution, extracts were added and the mix was incubated overnight at 4°C on a rotating wheel.  EDTA-free protease inhibitors (Roche) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1µg/ml pepstatin. Phosphatase inhibitors (Roche) were added to a final concentration of 1x in the case of Pol II phospho-serine ChIPs. Beads were washed 8 times in RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 10 mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE+ (10mM Tris pH8, 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps at 65°C for 15 and 10 minutes in 110µl and 100µl of elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65°C overnight (13-15 hours) for crosslink reversal.

value: Chromatin IP against PolII


title: Penetrating apressoria, biogical replicate 3

description: Penetrating apressoria, biological replicate 3

source_name: Penetrating apressoria

value: Penetrating apressoria


title: BP2.1

description: Biotrophic hyphae, biological replicate 1


title: PA2_2.2


title: input_ChIP-Seq_1

value: Wild-type

value: Chromatin IP against sonicated genomic DNA


title: PolII_Thr4P_ChIP-Seq

description: Chromatin IP against PolII phosphorylated at Thréonine 4


title: Switch, biological replicate 3

description: Switch, biological replicate 3


title: BP1

description: Biotrophic hyphae, lane 1


title: PolII_Ser2P_ChIP-Seq

description: Chromatin IP against PolII phosphorylated at Serine 2


title: Penetrating apressoria, biogical replicate 2

description: Penetrating apressoria, biological replicate 2


title: DSH_PA14_exp1

city: Milano

first: David

middle: Stephen

last: Horner

state: MI

address: Via Celoria 26

department: Molecular Biosciences and Biotechnology

institute: Università degli Studi di Milano

description: small RNA profiling

data_processing:
Adapters were trimmed using custom scripts written in Python. Reads were mapped to reference genomes [PAO1 genome build: NC_002516.1; PA14 genome build: NC_008463.1] using SEGEMEHL with default settings but reporting all equal best hits. WIG files prepared at single base resolution show log(coverage+1) for each genomic base on plus and minus strands of the reference genome sequences.
Genome Build:
DSH_PA14_exp1_plus.wig: NC_008463.1
DSH_PA14_exp1_minus.wig: NC_008463.1

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginoasa PA14 cDNA

growth_protocol: early stationary phase (A600 of about 2.6) cultures of P. aeruginosa strains PAO1  and PA14 grown at 37°C in 100 ml of Brain Heart Infusion (BHI) rich medium in 500-ml flasks vigorously shaken

extract_protocol:
Total RNA was extracted by RNeasy Kits (Qiagen) with modifications to enrich for small RNAs (<200 nt).
20 to 500 nt RNA was selected by PAGE and electroelution. RNA was first tagged at the 3’-end with 5'-monophosphate oligonucleotide adapters starting with three ribonucleotides followed by a sequence of 20 deoxyribonucleotides and terminally protected with an inverted dT.
RNase H-depletion of tRNA and 5S rRNA was performed essentially as described [PMCID 2665243] with some modifications. Size selection (40-520 nt for experiment 1(exp1) and 150-520 for experiment 2 (exp2)) were performed by PAGE/electroelution.  cDNA was generated using the SMARTer™ PCR cDNA Synthesis Kit (Clontech).
Amplicon libraries were prepared for 454 pyrosequencing by PCR amplification with primers tailored for 454-sequencing and including Roche Multiplex Identifiers (MID) for “barcoding”. Free primers, were removed and final size selection (130 to 610 nt) performed by PAGE/electroelution.

treatment_protocol: No additional treatments

tag: experiment

tag: size selection

value: 40-520 nt adapter ligated RNA


title: DSH_PA14_exp2

description: small RNA profiling

data_processing:
Adapters were trimmed using custom scripts written in Python. Reads were mapped to reference genomes [PAO1 genome build: NC_002516.1; PA14 genome build: NC_008463.1] using SEGEMEHL with default settings but reporting all equal best hits. WIG files prepared at single base resolution show log(coverage+1) for each genomic base on plus and minus strands of the reference genome sequences.
Genome Build:
DSH_PA14_exp2_plus.wig: NC_008463.1
DSH_PA14_exp2_minus.wig: NC_008463.1

value: 150-520 nt adapter ligated RNA


title: PA1_2

description: Penetrating appressoria, lane 2

value: fungus +  plant (samples that mapped to fungus only)


title: DSH_PAO1_exp2

description: small RNA profiling

data_processing:
Adapters were trimmed using custom scripts written in Python. Reads were mapped to reference genomes [PAO1 genome build: NC_002516.1; PA14 genome build: NC_008463.1] using SEGEMEHL with default settings but reporting all equal best hits. WIG files prepared at single base resolution show log(coverage+1) for each genomic base on plus and minus strands of the reference genome sequences.
Genome Build:
DSH_PAO1_exp2_plus.wig: NC_002516.1
DSH_PAO1_exp2_minus.wig: NC_002516.1

source_name: Pseudomonas aeruginoasa PAO1 cDNA


title: Penetrating apressoria, biogical replicate 1

description: Penetrating apressoria, biological replicate 1


title: PA1_1

description: Penetrating appressoria, lane 1


title: PolII_N20_ChIPSeq

description: Chromatin IP against Total PolII

value: Chromatin IP against Total PolII


title: DSH_PAO1_exp1

description: small RNA profiling

data_processing:
Adapters were trimmed using custom scripts written in Python. Reads were mapped to reference genomes [PAO1 genome build: NC_002516.1; PA14 genome build: NC_008463.1] using SEGEMEHL with default settings but reporting all equal best hits. WIG files prepared at single base resolution show log(coverage+1) for each genomic base on plus and minus strands of the reference genome sequences.
Genome Build:
DSH_PAO1_exp1_plus.wig: NC_002516.1
DSH_PAO1_exp1_minus.wig: NC_002516.1


title: PolII_Ser5P_ChIPSeq

description: Chromatin IP against PolII phosphorylated at Serine 5


title: NP1

description: Biotrophic hyphae, lane 1


title: CbfA mutant_rep3

status: Public on Jun 03 2012

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
HCS v1.5.15.1
Reads were mapped to the Dictyostelium discoideum reference transcriptome downloaded from dictyBase (http://dictybase.org/; version: 2012-Jan-10) using the ELANDv2e (CASAVA v1.8)
RPKM values were calculated based on ELAND mapping output
Genome_build: http://dictybase.org/; version: 2012-Jan-10
Supplementary_files_format_and_content: txt format, RPKMs of all samples

molecule: polyA RNA

organism: Dictyostelium discoideum

source_name: CbfA mutant

growth_protocol: Cells grown in liquid medium (HL-5)

extract_protocol: Samples were processed using Illumina’s TruSeq™ RNA Sample Prep Kit v2 following the manufacturer’s instructions (RS-122-2001/2002)

treatment_protocol: Cells stored as dry pellets frozen at -80°C until RNA preparation

value: CbfA mutant


title: CbfA mutant expressing DdCbfA-CTD_rep2

source_name: CbfA mutant expressing DdCbfA-CTD

value: CbfA mutant expressing D. discoideum CbfA-CTD


title: CbfA mutant_rep1


title: CbfA mutant expressing PpCbfA-CTD_rep3

source_name: CbfA mutant expressing PpCbfA-CTD

value: CbfA mutant expressing Polysphondylium pallidum CbfA-CTD


title: Wild-type cells_rep1

source_name: Wild-type cells

value: wild type


title: CbfA mutant expressing PpCbfA-CTD_rep1


title: CbfA mutant expressing PpCbfA-CTD_rep2


title: CbfA mutant expressing DdCbfA-CTD_rep1


title: CbfA mutant_rep2


title: LNCaP_H3K36me3_T4hDHT_ChIPSeq

city: Lebanon

first: xiaoyang

last: zhang

address: 1 Medical Center Driver

institute: Dartmouth Medical School

data_processing: Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.

source_name: Prostate Cancer Cell Line

growth_protocol: LNCaP cells were maintained in RPMI (Invitrogen) supplemented with 10% FBS

extract_protocol: Library preparation for next-generation sequencing was performed according to manufacturer’s instruction starting with 5 ng of material (Illumina Inc.).

treatment_protocol: 100nM of DHT and 4 hours in red-free RPMI media.

tag: antibody

tag: vendor

value: Abcam

tag: catalog#

value: LNCap