title: ChIP-Seq analysis of H3K4me3 in human hiPS-20b cells; DNA_Lib 353

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 353
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8534
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9470
****************
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: GSM772844_BI.iPS-20b.H3K4me3.DNA_Lib_353.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 353-DNA_Lib 353-DNA_Lib 353-DNA_Lib 353.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the iPS-20b Cell Line, Library DNA_Lib 353, 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.10713
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,290,834
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5877
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.5896
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9973
IROC_PERCENTILE: 39
POISSON_SCORE: 0.6171
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

ANALYSIS FILE NAME: GSM772844_BI.iPS-20b.H3K4me3.DNA_Lib_353.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 353-DNA_Lib 353-DNA_Lib 353-DNA_Lib 353.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the iPS-20b Cell Line, Library DNA_Lib 353, 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.10977
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 5
BROWSER_TRACK_NAME: iPS20b H3K4me3 53
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K4me3 Library DNA_Lib 353 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,290,834
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5877
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.5896
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9973
IROC_PERCENTILE: 39
POISSON_SCORE: 0.6171
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

source_name: induced pleuripotent 20b stem cell line; DNA_Lib 353

value: induced pluripotent stem cells 20b

value: BioSam 174

value: iPS-20b Cell Line

value: genomic DNA

value: Protein A-Sepharose 4B

value: Millipore

value: Histone H3K4me3

value: Branson


title: ChIP-Seq analysis of H3K9ac in human hiPS-20b cells; DNA_Lib 352

status: Public on Dec 28 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 352
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8533
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9470
****************
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: GSM772843_BI.iPS-20b.H3K9ac.DNA_Lib_352.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 352-DNA_Lib 352-DNA_Lib 352-DNA_Lib 352.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the iPS-20b Cell Line, Library DNA_Lib 352, 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.10666
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,566,562
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2214
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.2641
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9968
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3297
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.81

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

ANALYSIS FILE NAME: GSM772843_BI.iPS-20b.H3K9ac.DNA_Lib_352.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 352-DNA_Lib 352-DNA_Lib 352-DNA_Lib 352.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the iPS-20b Cell Line, Library DNA_Lib 352, 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.10930
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 5
BROWSER_TRACK_NAME: iPS20b H3K9ac 52
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K9ac Library DNA_Lib 352 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,566,562
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2214
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.2641
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9968
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3297
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.81

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

molecule: genomic DNA

organism: Homo sapiens

source_name: induced pleuripotent 20b stem cell line; DNA_Lib 352

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

tag: lineage

value: induced pluripotent cells

tag: medium

value: 10% KOSR (Invitrogen)

tag: molecule

tag: disease

value: presumed normal

tag: passage

value: p14 and p15 mixed

tag: line

tag: batch

value: BioSAli 177

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K9ac


title: modmdg4_ChIPSeq_1 and 2

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

organism: Drosophila melanogaster

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No Treatment

tag: developmental stage

tag: antibody name

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog

tag: strain


title: Ubx_ChIPSeq_1

value: Ubx


title: ChIP-Seq analysis of H3K4me3 in human CD25- CD45RO+ mem cells; DNA_Lib 719

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 719
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8552
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9449
****************
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: GSM772862_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K4me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 719-DNA_Lib 719-DNA_Lib 719.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, 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.10755
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,840,450
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1284
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.1967
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9962
IROC_PERCENTILE: 30
POISSON_SCORE: 0.2303
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772862_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K4me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 719-DNA_Lib 719-DNA_Lib 719.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, 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.11019
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 5
BROWSER_TRACK_NAME: CCCM H3K4me3 62 19
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 719 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,840,450
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1284
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.1967
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9962
IROC_PERCENTILE: 30
POISSON_SCORE: 0.2303
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 719

value: BioSam 132

value: CD4+ CD25- CD45RO+ Memory Primary Cells

value: genomic DNA

tag: markers

value: CD4+ T cell

value: CD25- CD45RO+ mem

value: Primary Cell

value: Donor 62

value: Dana Farber

value: Protein A-Sepharose 4B

value: Millipore

value: Histone H3K4me3

value: Branson


title: Kc167_Ttk_ChIPSeq_1 and 2

value: Ttk


title: ChIP-Seq analysis of WCE in human hiPS-20b cells; DNA_Lib 350

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 350
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8531
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9470
****************
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: GSM772841_BI.iPS-20b.Input.DNA_Lib_350.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 350-DNA_Lib 350-DNA_Lib 350-DNA_Lib 350.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-20b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS-20b Cell Line, Library DNA_Lib 350, 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.10822
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,090,424
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0048
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.0106
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0545
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM772841_BI.iPS-20b.Input.DNA_Lib_350.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 350-DNA_Lib 350-DNA_Lib 350-DNA_Lib 350.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS-20b Cell Line, Library DNA_Lib 350, 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.11086
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 5
BROWSER_TRACK_NAME: iPS20b Input 50
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line ChIP-Seq Input Library DNA_Lib 350 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,090,424
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0048
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.0106
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0545
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: induced pleuripotent 20b stem cell line; DNA_Lib 350

value: induced pluripotent stem cells 20b

tag: sample alias

value: BioSam 174

value: iPS-20b Cell Line

value: induced pluripotent cells

value: 10% KOSR (Invitrogen)

value: presumed normal

value: p14 and p15 mixed

value: BioSAli 177

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: Ttk_ChIPSeq_1 and 2

value: Ttk

value: White Lab


title: ChIP-Seq analysis of H3K9me3 in human HUES64 cells; Lib EpiLabSPL Row 1724

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1724
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8017
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8178
****************
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: GSM772756_BI.HUES64.H3K9me3.Lib_EpiLabSPL_Row_1724.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1724.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the HUES64 Cell Line, Library Lib EpiLabSPL Row 1724, 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.10724
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,595,669
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1912
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.1982
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9416
IROC_PERCENTILE: 92
POISSON_SCORE: 0.4116
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772756_BI.HUES64.H3K9me3.Lib_EpiLabSPL_Row_1724.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1724.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib EpiLabSPL Row 1724, 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.10988
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 5
BROWSER_TRACK_NAME: HUES64 H3K9me3 24
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K9me3 Library Lib EpiLabSPL Row 1724 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,595,669
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1912
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.1982
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9416
IROC_PERCENTILE: 92
POISSON_SCORE: 0.4116
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1724

tag: sample common name

value: HUES64 Cell Line

value: embrionic stem cell

value: KSR

value: genomic DNA

value: ES cell HUES_64-2

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9me3

value: Bioruptor


title: WCE_Mxtx2_4.5hpf

city: Boston

first: Cong

last: Xu

address: 1 Blackfan Circle

institute: Harvard Medical School

data_processing:
WCE_MxtxControl_ZV8Embryo4.5.ylf; genome build: zv8
Counts: Sequence reads were obtained and mapped to the zebrafish Zv8 genome 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. Counts included.

organism: Danio rerio

source_name: 4.5hpf zebrafish embryos

growth_protocol: Embryos are grown in E3 fish water at 28 degree

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with Myc antibody (abcam, ab9132).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: tissue

value: embryos

value: TU

tag: chip antibody

value: WCE (none)

tag: binding site


title: WCE_Nanog-like_3.5hpf

data_processing:
WCE_NanogControl_ZV8Embryo3.5.ylf; genome build: zv8
Counts: Sequence reads were obtained and mapped to the zebrafish Zv8 genome 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. Counts included.

source_name: 3.5hpf zebrafish embryos

value: Nanog-like


title: WCE_Nanog-like_4.5hpf

data_processing:
WCE_NanogControl_ZV8Embryo4.5.ylf; genome build: zv8
Counts: Sequence reads were obtained and mapped to the zebrafish Zv8 genome 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. Counts included.


title: Dfd_INPUT_1

value: DFD, transgenic


title: Mxtx2_4.5hpf

data_processing:
Mxtx_ZV8Embryo4.5.ylf; genome build: zv8
Mxtx_ZV8Embryo4.5.WIG.gz; genome build: zv8
Counts: Sequence reads were obtained and mapped to the zebrafish Zv8 genome 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. Counts included.

value: Myc


title: ChIP-Seq analysis of H3K36me3 in human HUES64 cells; Lib EpiLabSPL Row 1721

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1721
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8012
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8178
****************
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: GSM772751_BI.HUES64.H3K36me3.Lib_EpiLabSPL_Row_1721.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1721.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the HUES64 Cell Line, Library Lib EpiLabSPL Row 1721, 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.10712
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,707,677
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3796
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.3344
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.994
IROC_PERCENTILE: 86
POISSON_SCORE: 0.5364
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772751_BI.HUES64.H3K36me3.Lib_EpiLabSPL_Row_1721.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1721.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib EpiLabSPL Row 1721, 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.10976
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 5
BROWSER_TRACK_NAME: HUES64 H3K36me3 21
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K36me3 Library Lib EpiLabSPL Row 1721 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,707,677
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3796
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.3344
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.994
IROC_PERCENTILE: 86
POISSON_SCORE: 0.5364
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1721

value: HUES64 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

tag: molecule

tag: disease

value: Cell Line

value: undifferentiated

value: Unknown

value: Histone H3K36me3


title: E16-24_TCF_ChIPSeq_1 and 2

value: TCF

value: White Lab


title: Nanog-like_3.5hpf

data_processing:
Nanog_ZV8Embryo3.5.ylf; genome build: zv8
Nanog_ZV8Embryo3.5.WIG.gz; genome build: zv8
Counts: Sequence reads were obtained and mapped to the zebrafish Zv8 genome 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. Counts included.


title: Nanog-like_4.5hpf

data_processing:
Nanog_ZV8Embryo4.5.ylf; genome build: zv8
Nanog_ZV8Embryo4.5.WIG.gz; genome build: zv8
Counts: Sequence reads were obtained and mapped to the zebrafish Zv8 genome 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. Counts included.


title: SuHw_INPUT_1


title: E16-24_INPUT_1


title: Dfd_ChIPSeq_1 and 2

value: Dfd


title: ChIP-Seq analysis of H3K9ac in human HUES64 cells; Lib EpiLabSPL Row 1723

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1723
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8010
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8178
****************
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: GSM772749_BI.HUES64.H3K9ac.Lib_EpiLabSPL_Row_1723.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1723.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the HUES64 Cell Line, Library Lib EpiLabSPL Row 1723, 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.10774
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,295,925
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1901
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.2321
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9974
IROC_PERCENTILE: 89
POISSON_SCORE: 0.2814
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772749_BI.HUES64.H3K9ac.Lib_EpiLabSPL_Row_1723.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1723.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib EpiLabSPL Row 1723, 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.11038
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 5
BROWSER_TRACK_NAME: HUES64 H3K9ac 23
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K9ac Library Lib EpiLabSPL Row 1723 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,295,925
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1901
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.2321
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9974
IROC_PERCENTILE: 89
POISSON_SCORE: 0.2814
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1723

value: genomic DNA

tag: passage

tag: line

tag: batch

value: ES cell HUES_64-2

tag: Sex

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: SuHw_ChIPSeq_1 and 2

tag: developmental stage

tag: antibody name

value: SuHw

tag: manufacturer

tag: lot/batch#


title: ChIP-Seq analysis of H3K9me3 in human mid frontal lobe cells; DNA_Lib 609

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 609
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8524
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9448
****************
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: GSM772834_BI.Brain_Mid_Frontal_Lobe.H3K9me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 609-DNA_Lib 609-DNA_Lib 609.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Mid Frontal Lobe, Donor 149, 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.10690
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,253,570
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0196
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.0903
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.6649
IROC_PERCENTILE: 12
POISSON_SCORE: 0.1952
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772834_BI.Brain_Mid_Frontal_Lobe.H3K9me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 609-DNA_Lib 609-DNA_Lib 609.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Mid Frontal Lobe, Donor 149, 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.10954
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 5
BROWSER_TRACK_NAME: BMFL H3K9me3 49 09
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K9me3 Donor 149 Library DNA_Lib 609 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,253,570
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0196
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.0903
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.6649
IROC_PERCENTILE: 12
POISSON_SCORE: 0.1952
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 609

tag: sample alias

value: Brain, Mid Frontal Lobe

value: Post-Mortem

value: no AD evident at demise

value: Mid Frontal Lobe

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K9me3

value: Branson


title: ChIP-Seq analysis of H3K27me3 in human mid frontal lobe cells; DNA_Lib 608

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 608
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8523
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9448
****************
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: GSM772833_BI.Brain_Mid_Frontal_Lobe.H3K27me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 608-DNA_Lib 608-DNA_Lib 608.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Brain Mid Frontal Lobe, Donor 149, 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.10821
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,065,996
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0168
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.0964
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.6697
IROC_PERCENTILE: 20
POISSON_SCORE: 0.2433
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772833_BI.Brain_Mid_Frontal_Lobe.H3K27me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 608-DNA_Lib 608-DNA_Lib 608.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Brain Mid Frontal Lobe, Donor 149, 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.11085
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 5
BROWSER_TRACK_NAME: BMFL H3K27me3 49 08
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K27me3 Donor 149 Library DNA_Lib 608 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,065,996
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0168
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.0964
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.6697
IROC_PERCENTILE: 20
POISSON_SCORE: 0.2433
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 608

tag: sample common name

value: genomic DNA

value: Protein A-Sepharose 4B

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K27ac in human anterior caudate cells; DNA_Lib 605

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 605
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8522
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9447
****************
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: GSM772832_BI.Brain_Anterior_Caudate.H3K27ac.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 605-DNA_Lib 605-DNA_Lib 605.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on Brain Anterior Caudate, Donor 149, 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.10759
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,285,811
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.2293
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.2884
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9733
IROC_PERCENTILE: 41
POISSON_SCORE: 0.4515
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772832_BI.Brain_Anterior_Caudate.H3K27ac.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 605-DNA_Lib 605-DNA_Lib 605.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from Brain Anterior Caudate, Donor 149, 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.11023
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 5
BROWSER_TRACK_NAME: BAC H3K27ac 49 05
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K27ac Donor 149 Library DNA_Lib 605 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,285,811
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.2293
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.2884
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9733
IROC_PERCENTILE: 41
POISSON_SCORE: 0.4515
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 605

value: Brain, Anterior Caudate

value: Post-Mortem

value: no AD evident at demise

value: Anterior Caudate

value: Abcam

value: Histone H3K27ac


title: TCF_INPUT_1

tag: strain


title: TCF_ChIPSeq_1 and 2

value: TCF

value: White Lab

tag: catalog


title: ChIP-Seq analysis of H3K4me1 in human anterior caudate cells; DNA_Lib 607

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 607
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8520
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9447
****************
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: GSM772830_BI.Brain_Anterior_Caudate.H3K4me1.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 607-DNA_Lib 607-DNA_Lib 607.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Anterior Caudate, Donor 149, 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.10820
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,077,138
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2172
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3027
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9562
IROC_PERCENTILE: 35
POISSON_SCORE: 0.4876
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772830_BI.Brain_Anterior_Caudate.H3K4me1.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 607-DNA_Lib 607-DNA_Lib 607.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Anterior Caudate, Donor 149, 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.11084
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 5
BROWSER_TRACK_NAME: BAC H3K4me1 49 07
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K4me1 Donor 149 Library DNA_Lib 607 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,077,138
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2172
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.3027
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9562
IROC_PERCENTILE: 35
POISSON_SCORE: 0.4876
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 607

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me3 in human anterior caudate cells; DNA_Lib 606

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 606
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8519
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9447
****************
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: GSM772829_BI.Brain_Anterior_Caudate.H3K4me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 606-DNA_Lib 606-DNA_Lib 606.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Anterior Caudate, Donor 149, 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.10816
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,650,026
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3706
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.4014
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9989
IROC_PERCENTILE: 48
POISSON_SCORE: 0.4321
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772829_BI.Brain_Anterior_Caudate.H3K4me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 606-DNA_Lib 606-DNA_Lib 606.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Anterior Caudate, Donor 149, 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.11080
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 5
BROWSER_TRACK_NAME: BAC H3K4me3 49 06
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K4me3 Donor 149 Library DNA_Lib 606 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,650,026
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3706
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.4014
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9989
IROC_PERCENTILE: 48
POISSON_SCORE: 0.4321
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 606

value: genomic DNA

value: Protein A-Sepharose 4B

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human anterior caudate cells; DNA_Lib 604

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 604
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8521
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9447
****************
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: GSM772831_BI.Brain_Anterior_Caudate.H3K9me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 604-DNA_Lib 604-DNA_Lib 604.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Anterior Caudate, Donor 149, 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.10632
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,566,033
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.061
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.1537
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.7558
IROC_PERCENTILE: 29
POISSON_SCORE: 0.2988
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772831_BI.Brain_Anterior_Caudate.H3K9me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 604-DNA_Lib 604-DNA_Lib 604.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Anterior Caudate, Donor 149, 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.10896
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 5
BROWSER_TRACK_NAME: BAC H3K9me3 49 04
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K9me3 Donor 149 Library DNA_Lib 604 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,566,033
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.061
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.1537
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.7558
IROC_PERCENTILE: 29
POISSON_SCORE: 0.2988
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 604

value: Brain, Anterior Caudate

value: Post-Mortem

value: no AD evident at demise

value: Anterior Caudate

value: Abcam

value: Histone H3K9me3


title: E0-8_Hth_ChIPSeq_1 and 2

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

value: Hth

value: White Lab


title: ChIP-Seq analysis of H3K36me3 in human anterior caudate cells; DNA_Lib 601

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 601
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8518
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9447
****************
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: GSM772828_BI.Brain_Anterior_Caudate.H3K36me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 601-DNA_Lib 601-DNA_Lib 601.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Anterior Caudate, Donor 149, 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.10839
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,734,946
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1545
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.2294
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9506
IROC_PERCENTILE: 57
POISSON_SCORE: 0.3969
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772828_BI.Brain_Anterior_Caudate.H3K36me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 601-DNA_Lib 601-DNA_Lib 601.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Anterior Caudate, Donor 149, 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.11103
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 5
BROWSER_TRACK_NAME: BAC H3K36me3 49 01
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K36me3 Donor 149 Library DNA_Lib 601 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,734,946
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1545
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.2294
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9506
IROC_PERCENTILE: 57
POISSON_SCORE: 0.3969
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 601

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K27me3 in human anterior caudate cells; DNA_Lib 603

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 603
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8517
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9447
****************
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: GSM772827_BI.Brain_Anterior_Caudate.H3K27me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 603-DNA_Lib 603-DNA_Lib 603.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Brain Anterior Caudate, Donor 149, 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.10638
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,829,357
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0197
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.1156
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.6784
IROC_PERCENTILE: 27
POISSON_SCORE: 0.2853
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.81

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

ANALYSIS FILE NAME: GSM772827_BI.Brain_Anterior_Caudate.H3K27me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 603-DNA_Lib 603-DNA_Lib 603.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Brain Anterior Caudate, Donor 149, 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.10902
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 5
BROWSER_TRACK_NAME: BAC H3K27me3 49 03
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K27me3 Donor 149 Library DNA_Lib 603 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,829,357
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0197
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.1156
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.6784
IROC_PERCENTILE: 27
POISSON_SCORE: 0.2853
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.81

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 603

value: genomic DNA

value: Protein A-Sepharose 4B

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Branson


title: E0-8_CG16778_ChIPSeq_1 and 2


title: USP_INPUT_1

value: USP, transgenic


title: ChIP-Seq analysis of WCE in human anterior caudate cells; DNA_Lib 602

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 602
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8516
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9447
****************
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: GSM772826_BI.Brain_Anterior_Caudate.Input.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 602-DNA_Lib 602-DNA_Lib 602.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Anterior Caudate ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Anterior Caudate, Donor 149, 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.10824
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,582,792
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0095
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0428
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772826_BI.Brain_Anterior_Caudate.Input.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 602-DNA_Lib 602-DNA_Lib 602.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Anterior Caudate, Donor 149, 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.11088
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 5
BROWSER_TRACK_NAME: BAC Input 49 02
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate ChIP-Seq Input Donor 149 Library DNA_Lib 602 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,582,792
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0095
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0428
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 602

value: Brain, Anterior Caudate

value: Post-Mortem

value: no AD evident at demise

value: Anterior Caudate

value: standard

value: ChIP-Seq Input

value: Input


title: FAIRE_ChIPSeq_1 and 2

source_name: CNS

value: CNS

value: FAIRE

value: White Lab


title: H3K36me3 TbetKO Th1

status: Public on Dec 27 2011

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

description: Chromatin IP against H3K36me3

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 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 200 bp (SICER) or 100 bp (CisGenome) to create summary windows.
Peaks: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958) for epigenetics modifcations and CisGenome ( Nature Biotechnology, 26: 1293-1300) for Tbet

organism: Mus musculus

source_name: primary CD4+ T cells from spleen and lymph nodes

growth_protocol: Control and STAT4-deficient or T-bet-deficient naïve CD4+CD44-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells were cultured with plate-bound anti-CD3 and anti-CD28 (10 ug/ml each), IL-12 (10 ng/ml) and anti-IL-4 (10 ug/ml) for 3 days, followed by IL-2 (50 U/ml) and IL-12 (10 ng/ml) for 4 days (Th1 conditions).

extract_protocol:
Cells were chemically cross linked by 1% formaldehyde (Tbet-ChIP-seq) or treated with MNase (histone-ChIP-seq). Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
DNase-seq: Cells were washed twice with PBS, pelleted and resuspended in ice-cold Buffer A (15mM Tris-Cl, pH 8.0, 15mM NaCl, 60mM KCl, 1mM EDTA, pH 8.0, 0.5mM EGTA, pH 8.0, 0.5mM spermidine). Nuclei were isolated by mixing with 2x lysis buffer (Buffer A containing 0.01% NP-40) and incubated on ice for 5 min. Nuclei was then pelleted and washed with Buffer A. DNaseI digestions (60-180 U/mL) were performed for 3 min at 37°C, then stop buffer (50mM Tris-Cl, pH 8.0, 100mM NaCl, 0.1% SDS, 100mM EDTA, pH 8.0, 10ug/mL RNase A) was added. Nuclei were incubated at 55°C for overnight and then proteinase K was added for 6 h at 55°C. DNA was purified by phenol chloroform extraction, then fragments of 100-500 bp were isolated by sucrose gradient centrifugation as described previously (Sabo et al., 2006). Purified DNA was made into a library for Illumina deep sequencing platform to perform DNase-seq. Briefly purified DNA was end repaired, ligated to the Illumina single read adaptors, amplified and further purified to the fraction of 220-250bp in size. The resulted libraries are sequenced using the Illumina Genome Analyser Iix. Only unique reads of 36 bp were mapped to the mouse genome (mm9) using SICER peak calling program (Wei et al., 2010).
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde (Tbet-ChIP-seq) or treated with MNase (histone-ChIP-seq). Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: After 7 day culture in vitro, cells were restimulated for 2hr with plate-bound anti-CD3 and anti-CD28 (10 ug/ml each) and IL-12 (10 ng/ml).

value: B6.129S6-Tbx21<tm1Glm>/J (TbetKO)

tag: genetic background

tag: cell type

value: in vitro polarized T helper1 cells for 7 days

tag: passages

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition and restimulated with plate-bound CD3/28 +IL12 for 2 hrs

tag: chip antibody

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: Tbet WT Th1

description: Chromatin IP against T-bet

value: C57BL/6J (wild type)

value: T-bet

value: Santa Crus


title: H3K36me3 S4KO Th1

description: Chromatin IP against H3K36me3

value: C57BL6-STAT4<tm1> (STAT4KO)


title: H3K4me3 TbetKO Th1

description: Chromatin IP against H3K4me3


title: H3K4me3 WT Th1

description: Chromatin IP against H3K4me3


title: H3K36me3 WT Th1

description: Chromatin IP against H3K36me3


title: DHS WT naive

description: DHS for naïve

extract_protocol:
Cells were washed twice with PBS, pelleted and resuspended in ice-cold Buffer A (15mM Tris-Cl, pH 8.0, 15mM NaCl, 60mM KCl, 1mM EDTA, pH 8.0, 0.5mM EGTA, pH 8.0, 0.5mM spermidine). Nuclei were isolated by mixing with 2x lysis buffer (Buffer A containing 0.01% NP-40) and incubated on ice for 5 min. Nuclei was then pelleted and washed with Buffer A. DNaseI digestions (60-180 U/mL) were performed for 3 min at 37°C, then stop buffer (50mM Tris-Cl, pH 8.0, 100mM NaCl, 0.1% SDS, 100mM EDTA, pH 8.0, 10ug/mL RNase A) was added. Nuclei were incubated at 55°C for overnight and then proteinase K was added for 6 h at 55°C. DNA was purified by phenol chloroform extraction, then fragments of 100-500 bp were isolated by sucrose gradient centrifugation as described previously (Sabo et al., 2006). Purified DNA was made into a library for Illumina deep sequencing platform to perform DNase-seq. Briefly purified DNA was end repaired, ligated to the Illumina single read adaptors, amplified and further purified to the fraction of 220-250bp in size. The resulted libraries are sequenced using the Illumina Genome Analyser Iix. Only unique reads of 36 bp were mapped to the mouse genome (mm9) using SICER peak calling program (Wei et al., 2010).
DNase-seq: Cells were washed twice with PBS, pelleted and resuspended in ice-cold Buffer A (15mM Tris-Cl, pH 8.0, 15mM NaCl, 60mM KCl, 1mM EDTA, pH 8.0, 0.5mM EGTA, pH 8.0, 0.5mM spermidine). Nuclei were isolated by mixing with 2x lysis buffer (Buffer A containing 0.01% NP-40) and incubated on ice for 5 min. Nuclei was then pelleted and washed with Buffer A. DNaseI digestions (60-180 U/mL) were performed for 3 min at 37°C, then stop buffer (50mM Tris-Cl, pH 8.0, 100mM NaCl, 0.1% SDS, 100mM EDTA, pH 8.0, 10ug/mL RNase A) was added. Nuclei were incubated at 55°C for overnight and then proteinase K was added for 6 h at 55°C. DNA was purified by phenol chloroform extraction, then fragments of 100-500 bp were isolated by sucrose gradient centrifugation as described previously (Sabo et al., 2006). Purified DNA was made into a library for Illumina deep sequencing platform to perform DNase-seq. Briefly purified DNA was end repaired, ligated to the Illumina single read adaptors, amplified and further purified to the fraction of 220-250bp in size. The resulted libraries are sequenced using the Illumina Genome Analyser Iix. Only unique reads of 36 bp were mapped to the mouse genome (mm9) using SICER peak calling program (Wei et al., 2010).
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde (Tbet-ChIP-seq) or treated with MNase (histone-ChIP-seq). Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: freshly isolated naive CD4+ T cells

value: FACS sorted naive CD4+T cells

tag: treatment

value: 180 U/mL DNAseI


title: Dry seed Biological replicate 1

status: Public on Dec 22 2011

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole dry seeds

data_processing:
Raw: Original unprocessed and unfiltered data file from the Illumina sequencing pipeline.  The raw data was converted to the FASTQ format using custom perl scripts.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the FASTQ format.
Alignment: We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches.  The pre-processed reference genome consisted of sequences from the soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), and Phi-X174 reference genome (GenBank: J02482).  Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.

organism: Glycine max

source_name: Dry soybean seeds

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Whole seeds containing globular (GLOB) stage, cotyledon (COT), early- (EM), mid- (MM), and late- (LM) maturation, pre-dormancy (PD1 and PD2) stage embryos were collected. Whole dry (DRY) seeds containing dormant embryos were also collected. For seedlings, seeds were sown on soil and after six days after imbibition, the whole seedlings and the cotyledons of seedling were manually collected.

extract_protocol: Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA  was isolated from the powder using the DNEASY Plant Mini kit (Qiagen, Valencia, CA) according to manufacturer’s instructions. Approximately one microgram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications.  We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion.  Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82


title: Early-maturation stage whole seed

description: Whole seeds 6.0 - 7.0 mm in length were collected

source_name: Soybean seeds containing early maturation (EM) stage embryos


title: Globular stage whole seed

description: Whole seeds 1.0 - 1.5 mm in length were collected.

source_name: Soybean seeds containing globular (GLOB) stage embryos


title: DHS WT Th1

description: DHS for Th1

value: 60 U/mL DNAseI


title: Control RNA-Seq rep1

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: RNAseq after non-targeting-RNAi; Replicate 1

library_source: transcriptomic

data_processing: RNA-seq analysis was done using TopHat v1.2.0 and Bowtie v0.12.7. Only uniquely mapping reads were used. Fly transcript annotations were from Ensembl 62. Differentially expressed genes after RNAi were called with an adjusted p-value < 0.001 and MA plots were determined by DEseq, v1.4.1. In order to avoid off-target RNAi, independent RNAi experiments, using two different dsRNA regions for each target, were treated as biological replicates for analysis of differential expression.

molecule: total RNA

source_name: Schneider's Drosophila Line 2

growth_protocol: S2 cells were grown in Schneider's media with 10% FBS at room temperature.

extract_protocol: Two micrograms of DNase-treated total RNA was depleted of Ribosomal RNA with the Ribo-Zero kit from Epicentre (catalog #RZH1046), followed by use of the TruSeq RNA Sample Prep Kit (catalog #FC-122-1001) following manufacturer instructions.

treatment_protocol: Drosophila RNAi was performed by feeding S2 cells with dsRNA prepared with the Megascript T7 dsRNA synthesis kit from Ambion (catalog #1626.) Cells at a density of 2e6 cells/ml were serum starved treated with 10 Âµg of dsRNA. Additional boosts of 10 Âµg dsRNA were added at 48 and 96 hours. Cells were harvested at 120 hours.

value: S2; Schneider's Drosophila Line 2;  Marco Blanchette's Lab

tag: cell line

tag: knockdown

value: control


title: E0-8_INPUT_1

tag: developmental stage


title: E0-8_CG16778_INPUT_1


title: Ice1-RNAi RNA-Seq rep1

description: RNAseq after Ice1-RNAi; Replicate 1


title: ELL-RNAi RNA-Seq rep1

description: RNAseq after ELL-RNAi; Replicate 1

value: ELL


title: Late-maturation stage whole seed biological replicate 1

description: Whole seeds 1.2 - 1.5 cm in length and have a fresh weight between 230 - 350 mg were collected.  The entire embryo is yellow including the axis and cotyledons.

source_name: Soybean seeds containing late-maturation (AA1) stage embryos


title: MEFp2_Input

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

country: Japan

institute: The University of Tokyo

description: input

data_processing: Bed files

source_name: Mouse embryonic fibroblast

extract_protocol: Cells on a plate were cross-linked with 1% formaldehyde for 10 min at room temperature and were prepared for ChIP. ChIP using anti-Ezh2 antibody (#39103, Active Motif, rabbit polyclonal) was performed. Briefly, crosslinked cell lysates underwent fragmentation by sonication and incubated with antibodies bound to protein A-sepharose bease (50% slurry) overnight at 4 ºC. The beads were washed several times and eluted with elution buffer (1%SDS, 0.1 M NaHCO3). The eluates were treated with 1.5 μg of pronase 2 hr at 42 ºC then incubated at 65 ºC over night to reverse the crosslinks. The ChIP’ed DNA was purified by phenol/chroloform treatment and precipitated with LiCl and 70% ethanol. Sample preparation for ChIP-sequencing was performed according to the manufacturer's instructions (Ilumina), and sequencing was performed using Solexa Giga sequencer. Briefly, size fractionated DNA was extracted and a single adenosine was added using Klenow exo– (3' and 5' exo minus; Illumina). Illumina adaptors were then added and DNA was subjected to 20 cycles of PCR according to manufacturer's instructions. We then purified DNA and performed cluster generation and 36 cycles of sequencing on the Illumina cluster station and 1G Analyzer following the manufacturer's instructions. Sequences were mapped to the Build #36 (mm8) reference mouse genome.

value: Mouse embryonic fibroblast

tag: passage

tag: antibody


title: RasV12_H3K4me3

description: Chromatin immunoprecipitation (ChIP)-Solexa analysis of H3K4me3 for oncogenic Ras-induced senescent MEF cells

value: infected with activated RasV12-expressing retrovirus


title: RasV12_H3K27me3

description: Chromatin immunoprecipitation (ChIP)-Solexa analysis of H3K27me3 for oncogenic Ras-induced senescent MEF cells


title: MEFp2_H3K27me3

description: Chromatin immunoprecipitation (ChIP)-Solexa analysis of H3K27me3 for MEF cells


title: MEFp2_H3K4me3

description: Chromatin immunoprecipitation (ChIP)-Solexa analysis of H3K4me3 for MEF cells


title: 3P-Seq 72 hpf

first: Igor

last: Ulitsky

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: 3P-Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html

data_processing: Reads were reverse complemented and aligned to the D. rerio genome (Zv9/danRer7) using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their 3' end within a terminal adenylate-run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. (GSE24924)

molecule: polyA RNA

source_name: whole embryo at 72 hours post fertilization

growth_protocol: Zebrafish embryos or adults grown under standard condition

treatment_protocol: Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS (137 mM NaCl, 2.7 mM KCl, 1.5 mM KH2PO4, 8 mM Na2HP04, pH 7.4) and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer, dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed, and pellets were rinsed twice with PBS, flash frozen in liquid nitrogen and stored at –80C.

tag: tissue

value: whole embryo

value: 72 hours post fertilization

tag: genotype

value: wt


title: RasV12_Input

description: input


title: H3K4me3 S4KO Th1

description: Chromatin IP against H3K4me3

tag: strain

value: in vitro polarized T helper1 cells for 7 days

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition and restimulated with plate-bound CD3/28 +IL12 for 2 hrs

value: Abcam


title: USP_ChIPSeq_1 and 2

tag: antibody name

value: USP

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog

value: USP, transgenic


title: Strand-specific RNA-Seq 72 hpf

description: poly(A)-selected RNA was amplified using RiboAmp Plus RNA Amplification kit, randomly fragmented by partial alkaline hydrolysis. Size-selected RNA fragments (25-45 nt) were used for library preparation. Libraries were prepared as in Guo et al, 2010 (GSE21992)

data_processing: Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie, allowing for up to one mismatch and up to 4 genomic matches.


title: Input Adult

description: ChIP-Seq was carried out as described in Guenther et al. 2010 (GSE22499)

source_name: mixed gender adults, input

treatment_protocol: For adult fish, anesthetized fish were homogenized in the TissueRuptor (Qiagen). Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed, and pellets were rinsed twice with PBS, flash frozen in liquid nitrogen and stored at –80C.

value: whole adult

value: mixed gender adults


title: Strand-specific RNA-Seq 24 hpf

source_name: whole embryo at 24 hours post fertilization

extract_protocol: poly(A)-selected RNA was amplified using RiboAmp Plus RNA Amplification kit, randomly fragmented by partial alkaline hydrolysis. Size-selected RNA fragments (25-45 nt) were used for library preparation. Libraries were prepared as in Guo et al, 2010 (GSE21992)

value: 24 hours post fertilization


title: Input 72 hpf (control for H3K36me3)

source_name: whole embryo at 72 hours post fertilization, input

extract_protocol: ChIP-Seq was carried out as described in Guenther et al. 2010 (GSE22499)


title: Input 24 hpf (control for H3K36me3)

source_name: whole embryo at 24 hours post fertilization, input


title: Input 72 hpf (control for H3K4me3)


title: Input 24 hpf (control for H3K4me3)


title: H3K36me3 IP Adult

data_processing: Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie, allowing for up to one mismatch and up to 4 genomic matches. Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), using the Input libraries to assess FDR

source_name: mixed gender adults, H3K36me3 ChIP

tag: antibody manufacturer

tag: antibody catalog #


title: H3K36me3 IP 72 hpf

source_name: whole embryo at 72 hours post fertilization, H3K36me3 ChIP


title: Ice1-RNAi RNA-Seq rep2

description: RNAseq after Ice1-RNAi; Replicate 2

tag: cell type

value: S2; Schneider's Drosophila Line 2;  Marco Blanchette's Lab


title: Control RNA-Seq rep2

description: RNAseq after non-targeting-RNAi; Replicate 2

value: control


title: 3P-Seq Adult

source_name: mixed gender adults