title: Chromatin accessibility assay of Fetal Renal Pelvis; DS18431

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18431
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9991
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9990
****************
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: GSM817177_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18431.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis, Donor H-24078, Library DS18431 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.12597
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,273,429
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2728
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.277
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9871
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3688
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM817177_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18431.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis, Donor H-24078, Library DS18431 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.12660
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRP DNase 78 31
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24078 Library DS18431 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,273,429
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2728
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.277
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9871
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3688
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Fetal Kidney, renal, pelvis primary tissue, day 127; DS18431

value: Fetal Renal Pelvis

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

value: Primary Tissue

value: UW

value: fetal

value: day 127

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Lung, Left; DS18421

status: Public on Oct 15 2011

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18421
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9931
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9930
****************
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: GSM817175_UW.Fetal_Lung_Left.ChromatinAccessibility.H-24089.DS18421.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18421.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-24089, Library DS18421 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.12595
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,583,110
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4599
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.4468
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9937
IROC_PERCENTILE: 59
POISSON_SCORE: 0.518
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817175_UW.Fetal_Lung_Left.ChromatinAccessibility.H-24089.DS18421.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18421.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Left, Donor H-24089, Library DS18421 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.12658
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FLL DNase 89 21
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-24089 Library DS18421 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,583,110
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4599
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.4468
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9937
IROC_PERCENTILE: 59
POISSON_SCORE: 0.518
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal Lung, Left primary tissue, day 96; DS18421

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Lung, Left

tag: molecule

value: genomic DNA

tag: disease

value: day 96

value: Male

value: Chromatin Accessibility

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Kidney; DS16837

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS16837
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10034
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10033
****************
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: GSM817159_UW.Fetal_Kidney.ChromatinAccessibility.H-23663.DS16837.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16837.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-23663, Library DS16837 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.12579
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,761,487
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.348
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3436
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9892
IROC_PERCENTILE: 16
POISSON_SCORE: 0.4258
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817159_UW.Fetal_Kidney.ChromatinAccessibility.H-23663.DS16837.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS16837.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney, Donor H-23663, Library DS16837 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.12642
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FK DNase 63 37
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-23663 Library DS16837 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,761,487
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.348
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3436
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9892
IROC_PERCENTILE: 16
POISSON_SCORE: 0.4258
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Kidney primary tissue, day 105; DS16837

value: Fetal Kidney

value: day 105

value: Female


title: Chromatin accessibility assay of Fetal Skin; DS10987

description:
sample_term_id: UBERON_0002097
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS10987
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9797
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9796
****************
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: GSM817158_UW.Fetal_Skin.ChromatinAccessibility.H-22337.DS10987.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS10987.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Skin Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Skin, Donor H-22337, Library DS10987 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.12578
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,849,198
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.1494
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.1656
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9818
IROC_PERCENTILE: 5
POISSON_SCORE: 0.2339
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817158_UW.Fetal_Skin.ChromatinAccessibility.H-22337.DS10987.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS10987.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Skin Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Skin, Donor H-22337, Library DS10987 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.12641
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FSk DNase 37 87
BROWSER_TRACK_DESCRIPTION: UW Fetal Skin DNase Hypersensitivity Donor H-22337 Library DS10987 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,849,198
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.1494
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.1656
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9818
IROC_PERCENTILE: 5
POISSON_SCORE: 0.2339
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Skin primary tissue, day 82; DS10987

value: Fetal Skin

value: day 82


title: Actinomycin D-treated HL-60 cells, Biological Replicate 2, Technical Replicate 2

city: Singapore

first: Melissa

last: Fullwood

address: 8 College Road

country: Singapore

institute: A*STAR-Duke-NUS Neuroscience Research Partnership

data_processing: First, we aligned raw DNA sequences to the human genome to identify the origins of the DNA. Specifically, ABI SOLiD data was mapped to the human genome assembly hg19, using Batman (http://code.google.com/p/batman-aligner/, Tennakoon et al, manuscript in preparation). Batman is a Burrows-Wheeler-Transform-based (BWT) method that quickly maps short sequences to a reference genome. We sequenced the ends of the 180 bp DNA fragments, in numerous repeat experiments.  We predicted that randomly cleaved DNA would be less likely to be sequenced in many repeat experiments and thus, would distribute in a scattered or random manner across the genome. In contrast, the apoptotic cleaved DNA would be more clustered. Specifically, we performed ”peak-calling” (“peaks” indicate clusters of regions which were sequenced frequently) on the uniquely mapped reads with identical duplicates (which are likely the result of clonal PCR amplifications) merged using the MACS package frequently used for ChIP-Seq applications. Visual inspection of the data and preparation of screenshots was carried out through uploading tracks of the results to an in-house BASIC browser (Mulawadi et al., manuscript in preparation). Peaks within highly repetitive satellite regions as indicated by RepeatMasker (Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0.1996-2010 Program;  http://www.repeatmasker.org) were attributed to noise due to non-specific mapping and excluded from further analyses, as were peaks within ChrY, noise arising from HL-60, a female cell line. Peaks present in known copy number changes in HL-60 cells were not excluded from these analyses, but were flagged in the processed data.

source_name: HL-60 cells

growth_protocol: Apoptotic ladders were obtained from cells from the Merck Suicide-Track kit

extract_protocol: Apoptotic ladders were prepared with the Merck Suicide-Track kit. Selected DNA fragments were subjected to RNase ONE (Promega) digestion followed by Proteinase K treatment (Sigma). The 180 bp or 360 bp bands were excised following electrophoresis on 1.9% agarose gels and further purified using Qiaquick gel extraction kit (Qiagen). Standard ABI SoLiD library construction protocols were then followed. 50-base single-end sequencing was performed according to manufacturer’s protocols for the ABI SOLiD 3 system, using a bar-coded system.

treatment_protocol: 1 x 10^6 HL-60 cells were treated with 0.5 μg/ml Actinomycin D for 19h (Merck Suicide-Track kit information)

tag: cell line

tag: treatment

value: Actinomycin D


title: Chromatin accessibility assay of Fetal Kidney, Right; DS18463

description:
sample_term_id: UBERON_0004539
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18463
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10122
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10121
****************
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: GSM817180_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24089.DS18463.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18463.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Right, Donor H-24089, Library DS18463 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.12600
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,300,558
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2552
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.2627
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9882
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3615
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817180_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24089.DS18463.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18463.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Right, Donor H-24089, Library DS18463 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.12663
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FKR DNase 89 63
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Right DNase Hypersensitivity Donor H-24089 Library DS18463 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,300,558
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2552
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.2627
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9882
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3615
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, Right primary tissue, day 96; DS18463

value: Fetal Kidney, Right

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

value: Primary Tissue


title: Actinomycin D-treated HL-60 cells, Biological Replicate 2, Technical Replicate 1


title: Actinomycin D-treated HL-60 cells, Biological Replicate 1


title: Duke_DnaseSeq_Huh-7.5

status: Public on Oct 14 2011

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell description

value: hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

tag: replicate

value: Hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

value: align_on_cluster_bwa.pl v 1

tag: replicate description

value: tier 1


title: Chromatin accessibility assay of Fetal Muscle, Back; DS18377

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18377
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9880
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9879
****************
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: GSM817171_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24078.DS18377.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18377.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-24078, Library DS18377 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.12591
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,737,812
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.355
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.3438
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9919
IROC_PERCENTILE: 35
POISSON_SCORE: 0.4299
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM817171_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24078.DS18377.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18377.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-24078, Library DS18377 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.12654
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FMB DNase 78 77
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-24078 Library DS18377 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,737,812
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.355
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.3438
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9919
IROC_PERCENTILE: 35
POISSON_SCORE: 0.4299
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Back primary tissue, day 127; DS18377

value: Fetal Muscle, Back

value: genomic DNA

value: UW

value: fetal

value: day 127

value: Male

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Renal Cortex; DS18428

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18428
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10026
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10025
****************
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: GSM817176_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24078.DS18428.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18428.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex, Donor H-24078, Library DS18428 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.12596
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,424,828
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2456
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9873
IROC_PERCENTILE: 8
POISSON_SCORE: 0.3514
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM817176_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24078.DS18428.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18428.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex, Donor H-24078, Library DS18428 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.12659
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRC DNase 78 28
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24078 Library DS18428 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,424,828
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2456
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9873
IROC_PERCENTILE: 8
POISSON_SCORE: 0.3514
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Fetal Kidney, renal, cortex primary tissue, day 127; DS18428

value: Fetal Renal Cortex

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

value: Primary Tissue


title: Duke_DnaseSeq_Gliobla

source_name: Gliobla

value: DnaseSeq

value: DNaseI HS Sequencing

value: Gliobla/Input

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_H54,p-value cutoff:0.05

tag: cell organism

value: human

value: glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID:7252524)

value: cancer

value: ectoderm

value: U


title: Duke_DnaseSeq_GM19239

value: B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm

value: M

tag: treatment description

value: No special treatment or protocol applies

value: align_on_cluster_bwa.pl v 1

value: tier 1


title: Duke_DnaseSeq_8988T

value: DnaseSeq

value: DNaseI HS Sequencing

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

value: human pancreas adenocarcinoma (PA-TU-8988T), "established in 1985 from the liver metastasis of a primary pancreatic adenocarcinoma from a 64-year-old woman" - DSMZ

value: endoderm

value: F


title: Duke_DnaseSeq_Hepatocytes

source_name: Hepatocytes

value: primary hepatocytes, liver perfused by enzymes to generate single cell suspension

value: aligned to female and input was generic_female (should have been male),fseq v 1.84, iff_generic_female (should have been male),p-value cutoff:0.05, input was generic_female (should have been male),baseAlignCounts.pl v 1, input was generic_female (should have been male)

value: Primary Human Hepatocytes, liver perfused by enzymes to generate single cell suspension

value: normal

value: B

value: align_on_cluster_bwa.pl v 1, input was generic_female (should have been male)


title: Duke_DnaseSeq_T-47D

value: epithelial cell line derived from a mammary ductal carcinoma.

value: T-47D is a human epithelial cell line derived from an mammary ductal carcinoma.

value: cancer


title: Duke_DnaseSeq_Stellate

source_name: Stellate

value: hepatic stellate cells, liver that was perfused with collagenase and sellected for hepatic stellate cells by density gradient

value: Human Hepatic Stellate Cells, Liver that was perfused with collagenase and sellected for hepatic stellate cells by density gradient

value: align_on_cluster_bwa.pl v 1


title: Duke_DnaseSeq_GM12891

value: DnaseSeq

value: DNaseI HS Sequencing

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm

value: M

value: No special treatment or protocol applies

value: tier 1


title: Duke_DnaseSeq_GM18507

value: lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: Lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, Treatment:Epstein-Barr Virus transformed


title: Duke_DnaseSeq_HepG2

value: hepatocellular carcinoma

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_HepG2,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: liver carcinoma

value: cancer

value: endoderm


title: Duke_DnaseSeq_K562

value: DnaseSeq

value: DNaseI HS Sequencing

value: baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,p-value cutoff:0.05,fseq v 1.84, iff_K562

tag: cell

value: human

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: F

value: align_on_cluster_bwa.pl v 1


title: Duke_DnaseSeq_MCF-7_Hypoxia_LacAcid

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford)

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05

value: ectoderm

value: Hypoxia and Lactic acidosis:1% p02 and 10 mM Lactate, pH of 6.7 for 24 hours (Crawford)


title: Duke_DnaseSeq_HUVEC

source_name: HUVEC

value: HUVEC/Input

value: baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,p-value cutoff:0.05,fseq v 1.84, iff_HUVEC

value: umbilical vein endothelial cells

value: normal

value: mesoderm

value: U

value: No special treatment or protocol applies

value: tier 1


title: Duke_DnaseSeq_GM19240

value: DnaseSeq

value: DNaseI HS Sequencing

value: B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, Treatment:Epstein-Barr Virus transformed

value: unknown


title: Duke_DnaseSeq_HTR8svn

value: trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo

value: Blastula

value: F

value: align_on_cluster_bwa.pl v 1


title: Duke_DnaseSeq_A549

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: cancer

value: endoderm

value: M


title: Duke_DnaseSeq_GM19238

value: mesoderm

value: No special treatment or protocol applies


title: Duke_DnaseSeq_GM12878

value: DnaseSeq

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: baseAlignCounts.pl v 1,DNaseHS,fseq v 1.84, iff_GM12878,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: normal

value: tier 1


title: Duke_DnaseSeq_Osteobl

source_name: Osteobl

value: DNaseI HS Sequencing

value: osteoblasts (NHOst)

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

value: normal human osteoblasts (NHOst)

value: U


title: Duke_DnaseSeq_HeLa-S3

value: ectoderm

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_HelaS3,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: cervical carcinoma

value: F

value: align_on_cluster_bwa.pl v 1


title: Duke_DnaseSeq_Huh-7

value: hepatocellular carcinoma

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: Hepatocellular carcinoma

value: cancer

value: endoderm

value: M


title: Duke_DnaseSeq_HPDE6-E6E7

value: DnaseSeq

value: pancreatic duct cells immortalized with E6E7 gene of HPV

value: normal

value: Unknown

value: tier 1


title: Duke_DnaseSeq_Medullo

source_name: Medullo

value: DNaseI HS Sequencing

value: medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997)

value: aligned to female and input was generic_female (should have been male),fseq v 1.84, iff_generic_female (should have been male),p-value cutoff:0.05, input was generic_female (should have been male),baseAlignCounts.pl v 1, input was generic_female (should have been male)

value: Medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997)

value: U

value: No special treatment or protocol applies

value: align_on_cluster_bwa.pl v 1, input was generic_female (should have been male)


title: Duke_DnaseSeq_LNCaP

source_name: LNCaP

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: human

value: prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.)

value: align_on_cluster_bwa.pl v 1


title: BEAF-32_20HE_0hrs_ChIPSeq

city: Atlanta

first: Ashley

middle: M

last: Wood

state: GA

address: 1510 Clifton Rd. RRC 1071B

institute: Emory University

description: Chromatin IP against BEAF

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples and a p-value cutoff of 1e-10.

organism: Drosophila melanogaster

source_name: Kc cells

growth_protocol: Kc cells were maintained in HyClone CCM3 Serum-free media.

extract_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200-1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC.  Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC.  After washing and eluting from beads the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair ("End-It DNA End Repair Kit"  - Epicentre Cat# ER0720) and addition of 'A' base to 3' ends  (Klenow 3'-5'exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.

tag: chip antibody

tag: chip antibody supplier

value: Generated by the Corces lab. Bushey et al. 2009

tag: cell type

value: Kc167 Drosophila Embryonic Cell line

tag: ecdysone treatment


title: Duke_DnaseSeq_GM12892

tag: datatype

value: DnaseSeq

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm

value: F

tag: treatment


title: Duke_DnaseSeq_Chorion

source_name: Chorion

tag: datatype description

value: DNaseI HS Sequencing

tag: cell description

value: chorion cells (outermost of two fetal membranes), fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes.

value: extraembryonic mesoderm, trophectoderm

value: tier 1


title: Su(Hw)_20HE_0hrs_ChIPSeq

description: Chromatin IP against Su(Hw)

value: anti-Su(Hw)

value: Generated by the Corces lab. Gerasimova et al. 1995


title: Input_20HE_0hrs_ChIPSeq

description: Input DNA


title: Duke_DnaseSeq_MCF-7

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: cancer

value: ectoderm

value: No special treatment or protocol applies


title: BEAF-32_20HE_3hrs_ChIPSeq

description: Chromatin IP against BEAF after 3 hours of 5e-7 M  20HE treatment

value: Generated by the Corces lab. Bushey et al. 2009

value: Kc167 Drosophila Embryonic Cell line

value: 3 hours


title: Su(Hw)_20HE_48hrs_ChIPSeq

description: Chromatin IP against Su(Hw) after 48 hours of 5e-7 20HE treatment

value: 48 hours


title: dCTCF_20HE_3hrs_ChIPSeq

description: Chromatin IP against dCTCF after 3 hours of 5e-7 M  20HE treatment

value: anti-dCTCF

value: Generated by the Corces lab. Gerasimova et al. 2007


title: dCTCF_20HE_48hrs_ChIPSeq

description: Chromatin IP against dCTCF after 48 hours of 5e-7 20HE treatment


title: CP190_20HE_48hrs_ChIPSeq

description: Chromatin IP against CP190 after 48 hours of 5e-7 20HE treatment

value: Generated by the Corces lab. Pai et al. 2004


title: Input_20HE_0hrs_ChIPSeq2

description: Input DNA


title: dCTCF_20HE_0hrs_ChIPSeq

description: Chromatin IP against dCTCF


title: Su(Hw)_20HE_3hrs_ChIPSeq

description: Chromatin IP against Su(Hw) after 3 hours of 5e-7 M  20HE treatment


title: CP190_20HE_3hrs_ChIPSeq

description: Chromatin IP against CP190 after 3 hours of 5e-7 M  20HE treatment


title: BEAF-32_20HE_48hrs_ChIPSeq

description: Chromatin IP against BEAF after 48 hours of 5e-7 20HE treatment


title: Duke_DnaseSeq_H9ES

value: stem cell

tag: line

value: DnaseSeq

value: DNaseI HS Sequencing

value: embryonic stem cell (hESC) H9

value: baseAlignCounts.pl v 1,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

tag: replicate

value: human embryonic stem cell (hESC) H9

tag: cell karyotype

value: unknown

value: inner cell mass

value: F

value: align_on_cluster_bwa.pl v 1


title: CP190_20HE_0hrs_ChIPSeq

description: Chromatin IP against CP190


title: Duke_DnaseSeq_LNCaP_androgen

treatment_protocol: androgen

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05,1% ENCODE array platform validation tests

value: human

value: prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.)

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

value: androgen

value: 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford)

tag: replicate description

value: tier 1


title: Duke_DnaseSeq_Melano

source_name: Melano

value: DnaseSeq

value: DNaseI HS Sequencing

value: normal

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

value: epidermal melanocytes

value: ectoderm

value: U

tag: treatment description

value: No special treatment or protocol applies


title: Duke_DnaseSeq_NHEK

source_name: NHEK

value: baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,p-value cutoff:0.05,fseq v 1.84, iff_generic_female

tag: cell organism

value: epidermal keratinocytes

value: align_on_cluster_bwa.pl v 1


title: Duke_DnaseSeq_H1-hESC

growth_protocol: missing

value: human

value: embryonic stem cells

value: inner cell mass


title: Duke_DnaseSeq_HeLa-S3_IFNa4h

value: 4 hours of 500 U/ml Interferon alpha (Crawford)

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_HelaS3,p-value cutoff:0.05

value: cancer

value: F

value: Interferon alpha treatment - 4 hours with 500 U/ml (Crawford)


title: cyno_testes

city: shenzhen

first: zhiyong

last: huang

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

country: China

institute: BGI-Shenzhen, Shenzhen 518083, China

description: Sequenced reads were generated from testes in crab-eating macaque

library_source: transcriptomic

data_processing: use rheMac2 and crab-eating macaque genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.11 with default parameters except  -r 20 --mate-std-dev 20 --solexa1.3-quals

molecule: total RNA

organism: Macaca fascicularis

source_name: testes

extract_protocol: Total RNA was extracted using TRIzol Reagent For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 Î¼g total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3â dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200Â±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using a 1G Illumina Genome Analyzer and the paired-end sequencing module.

tag: species

value: crab-eating macaque

tag: tissue

value: testes


title: cyno_kidney

description: Sequenced reads were generated from kidney in crab-eating macaque

source_name: kidney

value: kidney


title: cyno_ileum

description: Sequenced reads were generated from ileum in crab-eating macaque

source_name: ileum

value: ileum


title: cyno_white_adipose

description: Sequenced reads were generated from white adipose in crab-eating macaque

source_name: white adipose

value: white adipose


title: cyno_brain

description: Sequenced reads were generated from brain in crab-eating macaque

source_name: brain

value: brain


title: rhesus_testes

description: Sequenced reads were generated from testes in Indian rhesus macaque

organism: Macaca mulatta

value: Indian rhesus macaque


title: rhesus_kidney

description: Sequenced reads were generated from kidney in Indian rhesus macaque


title: USC_ChipSeq_HepG2_Input_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: hepatocellular carcinoma

value: endoderm

value: M

value: No special treatment or protocol applies

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

value: remapped from hg18


title: rhesus_heart

description: Sequenced reads were generated from heart in Indian rhesus macaque

source_name: heart

value: heart


title: USC_ChipSeq_HCT-116_Input_UCDavis

tag: datatype

tag: datatype description

value: human

tag: cell description

value: colorectal carcinoma (PMID:7214343)

value: cancer

tag: treatment

tag: controlid

tag: labversion


title: Yale_ChipSeq_HeLa-S3_Input_std

value: Yale

value: Snyder - Yale University

value: cervical carcinoma

tag: cell karyotype

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: std

value: Standard input signal for most experiments.

tag: replicate


title: rhesus_brain

description: Sequenced reads were generated from brain in Indian rhesus macaque

tag: species

value: Indian rhesus macaque

tag: tissue

value: brain


title: gga lv M 1

status: Public on Oct 13 2011

city: Lausanne

first: Henrik

last: Kaessmann

address: Génopode

department: Center For Integrative Genomics

country: Switzerland

institute: University of Lausanne

description:
sample name: 554
Red Junglefowl

data_processing: for processed data, please refer to the original publication

molecule: polyA RNA

organism: Gallus gallus

source_name: Liver

extract_protocol: Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits as indicated. RNA quality was assessed using an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer's instructions. Briefly, polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded cDNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 250-300 bp fragments were excised and then PCR-amplified (15 cycles). After column-purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalyzers. Potential influences on RNA sequencing results due to different experimenters preparing the libraries were ruled out on the basis of RNA- Seq data comparisons of replicate libraries prepared by the different experimenters (i.e., expression levels derived from replicate libraries were highly correlated: rho > 0.99). The RNA-Seq libraries were each sequenced with 76 (101) cycles in at least one lane of the Illumina Genome Analyzer IIx platform according to the manufacturer's specifications. Technical replicates (i.e., sequencing the same library on different machines) were performed to rule out potential biases during the sequencing step (i.e., expression levels between technical replicates were highly correlated: rho > 0.98). After sequencing, we processed the fluorophore intensity files with the Ibis base caller (version 1.11), in addition to applying the standard Illumina base calling algorithms. As illustrated in Supplementary Note Table 1 and Supplementary Note Figure 1 for a small subset of samples, we found that Ibis significantly increased the number of usable reads and drastically reduced the error rate. This improvement was more pronounced for the sequencing runs processed with early versions of the Illumina pipeline, but remained noticeable even for the latest Illumina release (GA pipeline 1.60). All subsequent analyses were performed on the Ibis-called reads.

tag: gender

value: Male

tag: age

value: ~1 year, adult

tag: extraction

value: Standard

tag: rin

tag: tissue source

value: Facility of Linkoping University, Sweden


title: gga ts M 1

description:
sample name: 557
Red Junglefowl

source_name: Testis


title: gga lv F 1

description:
sample name: 558
Red Junglefowl

value: Female


title: cyno_liver

description: Sequenced reads were generated from liver in crab-eating macaque

source_name: liver

value: crab-eating macaque

value: liver


title: rhesus_quadriceps

description: Sequenced reads were generated from quadriceps in Indian rhesus macaque

source_name: quadriceps

value: quadriceps


title: rhesus_liver

description: Sequenced reads were generated from liver in Indian rhesus macaque


title: gga ht F 1

description:
sample name: 560
Red Junglefowl

source_name: Heart


title: gga ts M 2

description:
sample name: 669
Red Junglefowl


title: gga ht M 1

description:
sample name: 556
Red Junglefowl


title: gga kd M 1

description:
sample name: 555
Red Junglefowl

source_name: Kidney


title: gga kd F 1

description:
sample name: 559
Red Junglefowl


title: gga br M 1

description:
sample name: 579
Red Junglefowl

source_name: Brain


title: gga cb M 1

description:
sample name: 576
Red Junglefowl

source_name: Cerebellum

value: Rneasy Lipid


title: mdo ts M 2

description: sample name: 397

organism: Monodelphis domestica

value: 4 months

value: RNeasy

value: Opossum colonies from the Museum of Natural History, Berlin, Germany


title: gga br F 1

description:
sample name: 577
Red Junglefowl


title: mdo ts M 1

description: sample name: 475

value: 6 months


title: mdo kd M 1

description: sample name: 516


title: mdo ht M 1

description: sample name: 515


title: mdo ht F 1

description: sample name: 513

value: 25 months


title: mdo cb M 1

description: sample name: 420


title: mdo br M 1

description: sample name: 603

value: miRNeasy


title: ppa ts M 1

description: sample name: Tatango_ts

organism: Pan paniscus

value: Lola ya Bonobo Sanctuary, Democratic Republic of Congo


title: ppa lv M 1

description: sample name: Tatango_lv


title: mdo lv M 1

description: sample name: 474


title: ppa kd M 1

description: sample name: Tatango_kd


title: ppa kd F 1

description: sample name: Lodja_kd


title: ppa lv F 1

description: sample name: Lodja_lv


title: ppa cb M 1

description: sample name: Tatango_cb


title: ppa br F 1

description:
sample name: Waola_br
Paired-end libraries, 101bp run

source_name: Brain, prefrontal cortex


title: ppa ht F 1

description: sample name: Lodja_ht


title: mdo kd F 1

description: sample name: 512


title: ppa cb F 1

description: sample name: Lodja_cb


title: ppa br F 2

description: sample name: Lodja_br


title: mdo br F 1

description: sample name: 459

value: 20 months


title: ptr kd F 1

description: sample name: Reba_kd

organism: Pan troglodytes

value: 44 years

value: Yerkes Regional Primate Center, USA


title: ptr ts M 1

description: sample name: Herman_ts

value: Male

value: 12 years

value: Biomedical Primate Research Center, Netherlands (BPRC)


title: ptr lv M 1

description: sample name: Herman_lv


title: ppa br M 1

description: sample name: Tatango_br


title: ptr kd M 1

description: sample name: Herman_kd


title: ptr cb M 1

description: sample name: Herman_cb


title: ptr lv F 1

description: sample name: Reba_lv

value: Female


title: ptr ht M 1

description: sample name: Herman_ht


title: mdo cb F 1

description: sample name: 458


title: oan ts M 2

description: sample name: 635

organism: Ornithorhynchus anatinus

value: adult

value: Standard

value: Captured in New South Wales, Australia (provided by Adelaide University)


title: ptr ht F 1

description: sample name: Reba_ht


title: ppa ht M 1

description: sample name: Tatango_ht


title: oan lv M 1

description: sample name: 471


title: oan lv F 1

description:
sample name: 486
not lactating


title: ptr br M 5

description:
sample name: C1_herman_br
Paired-end libraries, 101bp run


title: ptr br M 4

description:
sample name: C6_antoine_br
Paired-end libraries, 101bp run

value: 6.7 years


title: oan kd M 1

description: sample name: 479


title: ptr br M 2

description:
sample name: C3_big_male_zurich_br
Paired-end libraries, 101bp run

value: 35 years

value: RNeasy

value: Zoo Zurich, Switzerland


title: ptr br M 3

description:
sample name: C5_koos_br
Paired-end libraries, 101bp run

value: 12.1 years


title: oan kd F 1

description:
sample name: 548
not lactating


title: ptr br F 1

description: sample name: Reba_br


title: oan ht M 1

description: sample name: 478


title: ptr br M 1

description:
sample name: C2_Japie_br
Paired-end libraries, 101bp run

value: 12.3 years


title: oan cb M 1

description: sample name: 638


title: oan cb F 1

description:
sample name: 622
not lactating


title: ggo ts M 1

description: sample name: Matze_ts

organism: Gorilla gorilla

value: 51 years

value: Zoo Frankfurt, Germany


title: oan ts M 1

description: sample name: 472


title: ggo lv M 1

description: sample name: Matze_lv


title: ggo lv F 1

description: sample name: Gigi_lv

value: 50 years

value: Zoo Berlin, Germany


title: ggo kd M 1

description: sample name: Matze_kd

value: Male


title: oan br M 1

description: sample name: 542


title: oan br F 1

description:
sample name: 487
not lactating


title: ppy lv M 1

description: sample name: Gelar_lv

organism: Pongo pygmaeus

value: 21 years

value: Yerkes Regional Primate Center, USA


title: ggo kd F 1

description: sample name: Gigi_kd

value: Female


title: oan ht F 1

description:
sample name: 501
not lactating

value: adult


title: ggo ht M 1

description: sample name: Matze_ht


title: ppy kd M 1

description: sample name: Gelar_kd


title: ggo ht F 1

description: sample name: Gigi_ht


title: ppy kd F 1

description: sample name: Dunja_kd

value: 56 years

value: Zoo Leipzig, Germany


title: ggo cb M 1

description: sample name: Matze_cb


title: ggo cb F 1

description: sample name: Gigi_cb


title: ppy ht M 1

description: sample name: Gelar_ht


title: ppy ht F 1

description: sample name: Dunja_ht


title: ppy cb F 1

description: sample name: Dunja_cb


title: ptr cb F 1

description: sample name: Reba_cb

value: 44 years


title: ggo br F 1

description: sample name: Gigi_br


title: mml ts M 2

description: sample name: DPZ #7743

value: 9 years

value: Deutsches Primatenzentrum, Germany


title: mml ts M 1

description: sample name: 590

value: 8 years

value: Standard

value: Macaque facility in Souzhou, China


title: ppy br M 1

description:
sample name: Douglas
Paired-end libraries, 101bp run

value: 16 years

value: RNeasy

value: National Veterinary Institute, Uppsala, Sweden


title: Maize_waterlogging_0h

city: Cold Spring Harbor

first: Zhijie

last: Liu

state: New York

address: One Bungtown RD

institute: Cold Spring Harbor Labs

description: High-throughput sequencing of maize whole root without waterlogging

library_source: non-genomic

data_processing: Using perl scripts, raw reads from fastq files were trimmed of any 3' adapter sequence present. Identical trimmed sequences were collated into a single row, with occurrences (number of reads) tallied. Sequences reads less than 18 basepairs long after 3' adapter trimming and untrimed sequence reads were rejected.

organism: Zea mays

source_name: Maize whole root

growth_protocol: Maize line were sown in sand filled 3-inch pots (8 seeds per pot). The day/night temperatures during seedling development ranged from 25℃ to 33℃, that was the same as field temperature of maize seedling stage development.

extract_protocol: Total RNA from different tissues was extracted with TRIzol solution (Invitrogen). 100μg of total RNA were separated on 15% Acrylamide/8M Urea gel (Sequagel, National Diagnostic) along with 19 and 24nt RNA samples as marker. Small RNAs were extracted from the gel slices corresponding to 19 and 24nt RNA using high salt. Small RNAs were ligated with Modban (Linker 1 from IDT). Ligated samples were separated again on 15% Acrylamide/8M Urea gel. The gel fragments corresponding to 37-42nt were excised. Small RNA was purified from the gel fragments, and 5’ sequencing adaptors were added using T4 RNA ligase. This RNA was amplified using Superscript III Reverse transcriptase (Invitrogen) and PCR amplification (Phusion HF polymerase, NEB). Amplified cDNA were separated on 3% MetaPhor Agarose (VWR) and the bands corresponding to correct size (108-115nt) were cut and purified with QIAGENE gel purification kit and sent for Illumina sequencing.

treatment_protocol: Waterlogging treatment was given to eight two-week-old plants of each seedling by transferring to a container that was filled with water to 2-3 cm above the sand surface for subjecting these plants to short-term waterlogging (1h, 2h and 4h). For control treatment, plants were not subjected to waterlogging treatment and were allowed to grow in the same conditions. Just after the treatment, plants were removed from container, cleaned the roots and placed in liquid nitrogen for further biochemical and molecular studies.

tag: inbred

value: whole root

tag: time point

value: control


title: mml kd F 1

description: sample name: 599


title: ppy lv F 1

description: sample name: Dunja_lv


title: anterior trunk input DNA

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

institute: EPFL

description: input DNA

data_processing: Reads were mapped to the mm9 (NCBI m37, July 2007) Mouse genome assembly with bowtie version 0.12.5 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Duplicated reads (reads mapping at exactly the same genomic position in the same orientation) were removed as probable PCR artifacts. Genome coverage densities were calculated for each strand separately, then shifted downstream by 70 bp, averaged and normalized by the total number of mapped reads (times 10^-7). Enriched regions were detected using MACS version 1.4.0beta (Zhang et al., 2008) and selected for a p-value<0.001 and an FDR<0.05. Signal on chromosomes not containing Hox clusters was removed.

organism: Mus musculus

source_name: Anterior trunk cells

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Tissue samples were isolated in PBS supplemented with 10% Fetal Calf Serum and made single cell by collagenase treatment and applying a cell-strainer cap (BD Biosciences). Nuclei were sonicated to generate fragments with average length around 300 bp.

tag: strain

tag: cell type

value: anterior trunk cells

tag: chip antibody


title: mml ht F 1

description: sample name: 600


title: mml cb M 1

description: sample name: 589

value: Male


title: Pa2.2_miRNA_Seq

city: kunming

first: zhenghua

last: sun

address: jiaochangdong road 32#

institute: kunming institute of zoology.CAS

description: small RNA sequencing data of Pa2.2

data_processing: To obtain clean reads, the original 35nt reads from sequencing were filtered by trimming the 5' and 3' adaptors, getting rid of contaminant, too-small (<18nt) and low-quality reads.

source_name: embryonic stem cells

extract_protocol: Total RNA was extracted from each sample using the mirVana miRNA isolation kit (Ambion). According to the manufacturer's instructions (Illumina), small RNA fraction between 18â30 nt was isolated from total RNA by PAGE purification and ligated with a pair of adaptors to their 5' and 3' ends. Then the small RNA molecules were converted to cDNA by RT-PCR and amplified using the adaptor primers. The purified DNA was used directly for cluster generation and sequencing analysis by the Illumina Genome Analyzer

tag: cell line

value: stem cells

tag: origin

value: parthenogenetic activated blastocysts

tag: passage


title: mml lv F 1

description: sample name: 598

value: Female


title: mml br M 2

description:
sample name: DPZ#9050
Paired-end libraries, 101bp run

value: 7 years


title: mml cb F 1

description: sample name: 596


title: mml br M 1

description: sample name: 588


title: mml kd M 1

description: sample name: 592


title: H3K4me3 forebrain ChIPSeq

description: Chromatin IP against H3K4me3

source_name: Forebrain cells

value: forebrain cells

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

tag: chip antibody lot #


title: mmu ts M 2

description:
sample name: 675
Wild type mouse

value: adult

value: Captured in Catalonia, Spain


title: mml br F 1

description: sample name: 595

value: 8 years

value: Standard


title: H3K4me3 anterior trunk ChIPSeq

description: Chromatin IP against H3K4me3


title: hsa ts M 2

description: sample name: 71544_ts

value: National Disease Research Interchange, USA (NDRI)


title: mmu lv M 2

description:
sample name: 674
Wild type mouse


title: H3K27me3 forebrain ChIPSeq

description: Chromatin IP against H3K27me3


title: hsa ts M 1

description: sample name: 366

value: Commercial / AMS biotechnology


title: mmu ts M 1

description:
sample name: 495
C57BL/6 mouse

value: In house, C57BL7/6 colonies


title: hsa lv M 2

description: sample name: 10707_lv


title: Maize_waterlogging_4h

description: High-throughput sequencing of maize whole root under 4h waterlogging treatment

tag: tissue

value: whole root

tag: treatment

value: waterlogging


title: mmu lv F 1

description:
sample name: 497
C57BL/6 mouse

tag: gender

tag: age


title: hsa lv M 1

description: sample name: 521

tag: rin


title: Pa3_miRNA_Seq

description: small RNA sequencing data of Pa3


title: mmu kd M 2

description:
sample name: 673
Wild type mouse

tag: extraction

tag: tissue source


title: hsa kd M 2

description: sample name: 9498


title: H3K27me3 anterior trunk ChIPSeq

description: Chromatin IP against H3K27me3

value: anterior trunk cells


title: mmu kd M 1

description:
sample name: 587
C57BL/6 mouse

value: Male


title: hsa kd F 1

description: sample name: 873


title: mmu kd F 1

description:
sample name: 766
C57BL/6 mouse


title: mmu lv M 1

description:
sample name: 494
C57BL/6 mouse


title: hsa ht M 2

description: sample name: 47268_ht


title: hsa kd M 1

description: sample name: 614


title: hsa cb M 1

description: sample name: 288

value: Commercial / Ambion


title: gga cb F 1

description:
sample name: 578
Red Junglefowl

value: ~1 year, adult

value: Facility of Linkoping University, Sweden


title: hsa ht F 1

description: sample name: 872

value: Female


title: mmu cb F 1

description:
sample name: 583
C57BL/6 mouse

value: Rneasy Lipid


title: mmu ht M 2

description:
sample name: 672
Wild type mouse


title: hsa cb F 1

description: sample name: 871


title: mmu ht M 1

description:
sample name: 585
C57BL/6 mouse


title: mmu br M 2

description:
sample name: 670
Wild type mouse


title: hsa ht M 1

description: sample name: 362


title: mmu cb M 2

description:
sample name: 671
Wild type mouse


title: hsa br M 4

description:
sample name: H6_holland2_br
Paired-end libraries, 101bp run

value: Netherland Brain Bank, Netherlands


title: hsa br M 5

description: sample name: 520

source_name: Brain, temporal lobe


title: hsa br M 2

description: sample name: H5_holland1_br


title: mmu cb M 1

description:
sample name: 584
C57BL/6 mouse

value: adult


title: mmu br F 1

description:
sample name: 496
C57BL/6 mouse


title: mmu br M 1

description:
sample name: B6_br
C57BL/6 mouse; library generated from pool of brain RNAs extracted from 3 mice


title: mdo lv F 1

description: sample name: 511

value: 25 months

value: Opossum colonies from the Museum of Natural History, Berlin, Germany


title: hsa br M 1

description:
sample name: H3_holland3_br
Paired-end libraries, 101bp run


title: mmu ht F 1

description:
sample name: 776
C57BL/6 mouse

value: Standard


title: hsa br M 3

description: sample name: 290

source_name: Brain, frontal cortex


title: hsa br F 1

description:
sample name: 629
Note: This sample was originally provided as a "Female" sample to us and therefore labeled this way in the Brawand et al. paper and original GEO submission; however, detailed data analyses carried out in the meantime clearly show that this sample stems from a male individual.


title: USC_ChipSeq_MCF-7_TCF7L2_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Rabbit monoclonal. Antibody Target:TCF7L2

tag: antibody targetdescription

value: TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following:Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note:there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4&search=TCF4

tag: antibody vendorname

value: Cell Signaling Technology

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate

tag: replicate description

value: tier 1


title: low_brain

status: Public on Oct 12 2011

description: Sequenced reads were generated from brain in 4 years old hypoxia-exposed naked mole rat

data_processing: Using naked mole rat genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -r 20 --mate-std-dev 10 -I 10000  --segment-mismatches 3  --segment-length 24 --solexa1.3-quals

organism: Heterocephalus glaber

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with oligo-dT-coupled beads from 20 Î¼g total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3â dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200Â±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: age

value: 4 years

tag: tissue

value: brain


title: USC_ChipSeq_HeLa-S3_TCF7L2_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: cervical carcinoma

tag: treatment


title: mixed

description: Sequenced reads were generated from mixture of 7 tissues of one naked mole rat

value: mixed

value: mixed 7 tissues


title: pup_brain

description: Sequenced reads were generated from brain in pupil naked mole rat

source_name: brain in pupil naked mole rat

value: new born


title: kidney20

description: Sequenced reads were generated from kidney in 20-year naked mole rat

source_name: kidney in 20-year naked mole rat

value: 20 years

value: kidney


title: kidney4

description: Sequenced reads were generated from kidney in 4-year naked mole rat

source_name: kidney in 4-year naked mole rat


title: brain4

description: Sequenced reads were generated from brain in 4-year naked mole rat

source_name: brain in 4-year naked mole rat


title: low_kidney

description: Sequenced reads were generated from kidney in 4 years old hypoxia-exposed naked mole rat


title: pup_kidney

description: Sequenced reads were generated from kidney in pupil naked mole rat

source_name: kidney in pupil naked mole rat


title: low_liver

description: Sequenced reads were generated from liver in 4 years old hypoxia-exposed naked mole rat

value: liver


title: brain20

description: Sequenced reads were generated from brain in 20-year naked mole rat

source_name: brain in 20-year naked mole rat


title: liver20

description: Sequenced reads were generated from liver in 20-year naked mole rat

source_name: liver in 20-year naked mole rat


title: pup_liver

description: Sequenced reads were generated from liver in pupil naked mole rat

source_name: liver in pupil naked mole rat


title: liver4

description: Sequenced reads were generated from liver in 4-year naked mole rat

source_name: liver in 4-year naked mole rat


title: ERa e2 5k LinDA rep1

status: Public on Oct 11 2011

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

country: France

institute: IGBMC

description: Chromatin IP against ER-alpha

data_processing: Sequenced reads were mapped to the mm9 mouse genome or to the hg19 human genome assembly for RXRα-RARγ and ERα-H3K4me3 profiling, respectively.

source_name: ERa e2 5k LinDA

growth_protocol: F9 teratocarcinoma stem cells were cultured in DMEM supplemented with 10% fetal calf serum (FCS) and 40 μg ml−1 gentamicin. Cells were seeded in gelatin-coated tissue-culture plates (0.1%) and ATRA was added to a final concentration of 1 μM. Human H3396 cells were grown in RPMI (with 25 mM HEPES) supplemented with 10% FCS and gentamicin. For induction, cells were maintained in estrogen (E2)-deficient conditions (charcoal-stripped serum, no phenol red) for 72 h; induction was with 10 nM E2 for 1 h.

extract_protocol: Immunoprecipitated chromatin was quantified using Qubit (Quant-It dsDNA HS Assay Kit; Invitrogen). 10ng of the ChIPed material was used for preparing the sequencing library (ChIP-seq DNA sample preparation kit, Illumina). F9 samples were sequenced with a GA2X sequencer (Illumina);  H3396 samples were sequenced on the HiSeq2000 (Illumina).

treatment_protocol: Cells were fixed with 1% para¬formaldehyde (Electron Microscopy Sciences) for 30 min at 25 °C. ChIPs were performed following standard conditions: chromatin sonication (200–500 bp length) and immunoprcipitation in lysis buffer (50 mM Tris-HCl (pH 8), 140 mM NaCl, 1m M EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) complemented with pro¬tease inhibitor cocktail (Roche); two washes with lysis buffer; two washes with lysis buffer containing 360 mM NaCl; two washes with washing buffer (10 mM Tris-HCl (pH 8), 250 mM LiCl, 0.5% NP-40, 1 mM EDTA and 0.5% Na-deoxycholate); two washes with TE buffer (10 mM Tris-HCl (pH 8) and 1 mM EDTA); elution at 65 °C; 15 min in elution buffer (50 mM Tris-HCl (pH 8), 10 mM EDTA, 1% SDS). The small-cell-number ChIPs were per¬formed following the original protocol described above except for the antibody amounts (anti-ERα, 2 μg for 2 million and 100,000 cells, 0.5 μg for 10,000 and 5,000 cells; anti-H3K4me3, 1 μg for 1 million cells, 0.25 μg for 10,000 cells). For reChIPs, the first antibody (anti-RXRa) was covalently linked to the sepharose–protein A (Sigma) using disuccinimidyl suberate. The covalently linked antibody beads were washed with ethanolamine (0.1 M), followed by gly¬cine (pH 2.8). Beads prewashed with 50 mM sodium borate (pH 8.2) and were incubated overnight at 4 °C as for regular ChIPs. After standard washing, elution was performed with 10 mM dithiotreitol (DTT) (30 min, 37 °C). Eluates from at least four ChIPs were combined, diluted at least 30 times with lysis buffer (containing protease inhibitors) and incubated overnight with the second antibody (anti-RARγ) and protein-A beads at 4 °C. The subsequent steps were performed as for regular ChIPs. reChIP-seq protocol is available in PROTOCOL EXCHANGE (2011) DOI 10.1038/protex.2011.256. LinDA amplification has been performed as described in Pattabhiraman et al. ((2011),  Nature Methods 8, 565-67). A detailed protocol has been submitted to Nature protocols (Pattabhiraman et al., Nature Protocols 2011, under revision).

tag: cell type

value: breast cancer cells

tag: cell line

tag: comment

value: chromatin IP against ER-alpha (Santa Cruz Biotech:HC20 )

tag: chip antibody

value: ER-alpha

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #

tag: amplification

value: 5k LinDA


title: ERa e2 5k LinDA rep2

description: Chromatin IP against ER-alpha


title: ERa e2 2M rep2

description: Chromatin IP against ER-alpha

source_name: ERa e2 2M


title: ERa e2 10k LinDA rep2

description: Chromatin IP against ER-alpha

source_name: ERa e2 10k LinDA

value: 10k LinDA


title: ERa e2 2M rep1

description: Chromatin IP against ER-alpha


title: ERa e2 10k LinDA rep1

description: Chromatin IP against ER-alpha


title: USC_ChipSeq_PANC-1_TCF7L2_UCDavis

value: ChipSeq

value: Chromatin IP Sequencing

value: human

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Rabbit monoclonal. Antibody Target:TCF7L2

tag: antibody targetdescription

value: TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following:Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note:there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4&search=TCF4

tag: antibody vendorname

value: Cell Signaling Technology

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate

tag: replicate description

value: tier 1


title: ERa e2 100k LinDA rep1

description: Chromatin IP against ER-alpha

source_name: ERa e2 100k LinDA

tag: cell type

value: breast cancer cells

tag: cell line

tag: comment

value: chromatin IP against ER-alpha (Santa Cruz Biotech:HC20 )

tag: chip antibody

value: ER-alpha

tag: chip antibody manufacturer

value: Santa Cruz

value: 100k LinDA

tag: treatment


title: ERa e2 100k LinDA rep2

description: Chromatin IP against ER-alpha

tag: chip antibody catalog #

tag: amplification


title: H3K4me3 e2 1k LinDA rep2

description: Chromatin IP against H3K4me3

source_name: H3K4me3 e2 1k LinDA

value: chromatin IP against H3K4me3 ( Abcam:AB1012 )

value: Abcam

value: 1k LinDA


title: H3K4me3 e2 1k LinDA rep1

description: Chromatin IP against H3K4me3


title: H3K4me3 e2 1M rep2

description: Chromatin IP against H3K4me3

source_name: H3K4me3 e2 1M


title: mRXRa(1)

description: Chromatin IP against RXRa

value: embryonal carcinoma cells

value: Chromatin IP against RXRa. In house polyclonal antibody generated by immunization of rabbits with the following peptide:mRXRa:PB105 (MDTKHFLPLDFSTQVNSSSLNSPTGRGC)]

value: in-house polyclonal Ab against RXRa

value: in-house


title: mRXRa RARg reChIP LinDA

description: Chromatin IP against RXRa-RARg

source_name: mRXRa RARg reChIP LinDA

value: sequential Chromatin IP against RXRa and RARg. In house polyclonal antibodies generated by immunization of rabbits with the following peptides:mRXRa:PB105 (MDTKHFLPLDFSTQVNSSSLNSPTGRGC)]; mRARg:PB288 (CSKPGPHPKASSEDEAPGGQGKRGQSPQPD)]

value: in-house polyclonal Ab against RXRa and RAR

value: LinDA


title: H3K4me3 e2 10k LinDA rep2

description: Chromatin IP against H3K4me3

source_name: H3K4me3 e2 10k LinDA

value: 10k LinDA


title: RNA-PolII_24h-ATRA_ChIP-seq

description: Chromatin IP against RNA PolII

data_processing: The Illumina Pipeline v1.4.0 was used for primary data analysis (image processing: Firecrest; base calling: Bustard; alignment: Gerald) from which uniquely aligned reads with up to two mismatches relative to the mouse mm9 reference genome were kept.

source_name: embryonal carcinoma cells

growth_protocol: Embryonal carcinoma cells were cultured in Dubelccoâs modified Eagleâs medium supplemented with 10% foetal calf serum and 40ug/ml Gentamicin. Cells were seeded in gelatine-coated tissue culture plates (0.1%) and all-trans retinoic acid (ATRA) was added to the plates in a final concentration of 1x10-6 M at different time points.

extract_protocol: Immunoprecipitated chromatin was quantified using Qubit (Quant-It dsDNA HS Assay Kit; Invitrogen). 10ng of the ChIPed material was used for preparing the sequencing library (ChIP-seq DNA sample preparation kit, Illumina). 5 pmol of the library was used per flowcell in the Solexa 2G Genome analyzer (Illumina).

treatment_protocol: F9 cells induced into differentiation (ATRA treatment) at different time-points were fixed with 1% para-formaldehyde (Electron Microscopy Sciences) for 30 minutes at room temperature. ChIP assays for RARg, RXRa and RNA Polymerase II were performed following standard conditions.

value: F9 embryonal carcinoma cells

value: polyclonal anti-RNA-PolII (H-224)

tag: chip antibody supplier

value: Santa Cruz Biotechnology

tag: chip antibody catalog#


title: mouse_F9_WCE (input)

description: Input DNA


title: Mouse_TotalHeart_miRNA_FEMALE

city: Cambridge

first: Whitehead

last: Institute

state: MA

address: 9 Cambridge Center

department: Genome Technology Core

institute: Whitehead Institute

description: small RNA

data_processing: FASTQ files were created using standard Illumina pipeline. 3' adaptor was stripped off from the illumina reads and then aligned to known miRNA hairpin sequences (build: mm9). Total reads aligning to each hairpin were normalized between the 2 samples/replicates.

source_name: Mouse Heart

extract_protocol: Mice were housed under standard conditions. The Illumina/Solexa libraries were made as described in Grimson et al (Nature 445; 1193-1197; 2008) except the 3' ligation was performed separately with both commercially derived T4RNA ligase (GE Health Care) and with a mutant ligase (Rnl2(1-249)K->Q) and pooled prior to 5’ ligation.

tag: tissue

value: heart

tag: strain

tag: age

value: 6-8 weeks

tag: gender

value: Female


title: RNA-PolII_48h-ATRA_ChIP-seq

description: Chromatin IP against RNA PolII


title: H3K4me3 e2 1M rep1

description: Chromatin IP against H3K4me3

value: breast cancer cells

value: chromatin IP against H3K4me3 ( Abcam:AB1012 )


title: ppy br F 1

description: sample name: Dunja_br

source_name: Brain, prefrontal cortex

value: 56 years

tag: extraction

value: RNeasy

tag: rin

tag: tissue source

value: Zoo Leipzig, Germany


title: RNA-PolII_2h-ATRA_ChIP-seq

description: Chromatin IP against RNA PolII


title: RNA-PolII_48h-EtOH_ChIP-seq

description: Chromatin IP against RNA PolII


title: Mouse_TotalHeart_miRNA_MALE

description: small RNA

value: Male


title: RNA-PolII_6h-ATRA_ChIP-seq

description: Chromatin IP against RNA PolII


title: RARg_6h-ATRA_ChIP-seq

description: Chromatin IP against RARg

value: polyclonal anti-RARg

value: in-house antibody [generated by immunization of rabbits with the peptide mRARg:PB288 (CSKPGPHPKASSEDEAPGGQGKRGQSPQPD)]


title: RARg_24h-ATRA_ChIP-seq

description: Chromatin IP against RARg


title: RARg_48h-ATRA_ChIP-seq

description: Chromatin IP against RARg


title: mml ht M 1

description: sample name: 593

source_name: Heart

value: 8 years

value: Standard

value: Macaque facility in Souzhou, China


title: RARg_2h-ATRA_ChIP-seq

description: Chromatin IP against RARg

value: F9 embryonal carcinoma cells


title: Small RNAs from kidney tissue of transgenic mice expressing Mos inverted repeat (MosIR)

city: Prague 4

first: Radek

last: Malik

address: Videnska 1083

department: Dep. of Epigenetics Regulations

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

description:
Total small RNAs from kidney tissue of transgenic mice expressing an inverted repeat from mouse Moloney sarcoma oncogene (Mos) gene (MosIR).

Transgenic mice were generated by injecting linearized DNA into the male pronuclei of a C57BL/6 x BALB/c 1-cell embryo. Resulting mice were further crossed to C57BL/6 mice for at least 4 generations before being used in our experiments.

The pCag-EGFP_MosIR plasmid contains an inverted repeat from the mouse Mos (Moloney sarcoma oncogene) gene that is inserted into the 3'-UTR of the EGFP reporter gene, which is expressed using a promoter composed of the CMV enhancer and β-actin core promoter.

data_processing:
The sequencing and data processing were performed by Seqomics (Hungary). Reads of 18-30 nt length were mapped to the pCag-EGFP_MosIR plasmid allowing up to 1 mismatch.

Instrument Controller Software 3.5.0
Fluidics 1.12.4
Imager 1.9.20
Protocols 5P_v8.2.1
Scripts 5P_v8.3.0
Interlock FW 58.00
SETS 3.5r0.40.38126M

source_name: kidney tissue, MosIR

growth_protocol: Cell lines were grown under standard tissue culture conditions (DMEM + 10% FCS). Transgenic mice were maintained under NIH guidelines.

extract_protocol: Total small RNA was isolated using the mirPremier microRNA Isolation Kit (Sigma-Aldrich). Further sample processing and SOLid sequencing was performed by Seqomics Ltd. (Hungary). Briefly, adaptor was hybridized and ligated to each sample (10 ul 2x ligase buffer, 2 ul Adaptor mix A, 3 ul hybridization solution, 3 ul RNA sample, 2 ul ligation enzyme mix; incubate O.N. at 16°C). Adapter-ligated RNA was subjected to reverse transcription (4 ul 10x RT buffer, 2 ul dNTP mix, 1 ul ArrayScript RT, 13 ul water; incubate 30 min at 42°C ) followed by RNase H digestion (add 1 ul RNase H to 10 ul cDNA and incubate 30 min at 37°C). A 1 µL aliquot of cDNA library was used as a template for PCR using SOLiD PCR primers and AmpliTaq DNA polymerase. PCR products were run on a native polyacrylamide gel (1´ TBE, 6% 19:1 acrylimide:bisacrylamide). 105- to 150-nt products were excised, eluted, precipitaced and finally eluted into 20 µL nuclease-free water. Purified amplicons were sequenced using an ABI SOLiD 3 Plus instrument.

treatment_protocol: Cell lines were transiently transfected with 1 microgram of pCag-EGFP_MosIR plasmid (per well in 6-well plate) using TurboFect (Fermentas) trasnfection reagent.

tag: strain background

value: kidney

tag: expression

value: Mos inverted repeat


title: RARg_48h-EtOH_ChIP-seq

description: Chromatin IP against RARg

tag: cell line


title: Small RNAs from brain tissue of transgenic mice expressing Mos inverted repeat (MosIR)

description:
Total small RNAs from brain tissue of transgenic mice expressing an inverted repeat from the mouse Moloney sarcoma oncogene (Mos) gene (MosIR).

Transgenic mice were generated by injecting linearized DNA into the male pronuclei of a C57BL/6 x BALB/c 1-cell embryo. Resulting mice were further crossed to C57BL/6 mice for at least 4 generations before being used in our experiments.

The pCag-EGFP_MosIR plasmid contains an inverted repeat from the mouse Mos (Moloney sarcoma oncogene) gene that is inserted into the 3'-UTR of the EGFP reporter gene, which is expressed using a promoter composed of the CMV enhancer and β-actin core promoter.

source_name: brain tissue, MosIR

value: brain


title: rxra-ko_RXRa_48h-ATRA_ChIP-seq

description: Chromatin IP against RXRa

tag: chip antibody

value: polyclonal anti-RXRa

value: in-house antibody [generated by immunization of rabbits with the peptide mRXRa:PB105 (MDTKHFLPLDFSTQVNSSSLNSPTGRGC)]


title: RXRa_48h-ATRA_ChIP-seq

description: Chromatin IP against RXRa


title: Small RNAs from HeLa cells expressing Mos inverted repeat (MosIR)

description:
Total small RNAs from HeLa cells transfected with a plasmid expressing an inverted repeat from the mouse Moloney sarcoma oncogene (Mos) gene (MosIR).

The pCag-EGFP_MosIR plasmid contains an inverted repeat from the mouse Mos (Moloney sarcoma oncogene) gene that is inserted into the 3'-UTR of the EGFP reporter gene, which is expressed using a promoter composed of the CMV enhancer and β-actin core promoter.

source_name: HeLa cell line, MosIR

value: HeLa


title: H3K4me3 e2 10k LinDA rep1

description: Chromatin IP against H3K4me3

tag: cell type

value: breast cancer cells

tag: comment

value: chromatin IP against H3K4me3 ( Abcam:AB1012 )

tag: chip antibody manufacturer

value: Abcam

value: 10k LinDA


title: RXRa_24h-ATRA_ChIP-seq

description: Chromatin IP against RXRa


title: mRXRa 100xfold-diluted LinDA

description: Chromatin IP against RXRa

source_name: mRXRa 100xfold-diluted LinDA

value: embryonal carcinoma cells

value: Chromatin IP against RXRa. In house polyclonal antibody generated by immunization of rabbits with the following peptide:mRXRa:PB105 (MDTKHFLPLDFSTQVNSSSLNSPTGRGC)]

value: in-house polyclonal Ab against RXRa

value: in-house

tag: amplification

value: 100xfold-diluted LinDA


title: RXRa_6h-ATRA_ChIP-seq

description: Chromatin IP against RXRa

tag: chip antibody supplier


title: Small RNAs from HEK293 cells expressing Mos inverted repeat (MosIR)

description:
Total small RNAs from HEK293 cells transfected with a plasmid expressing an inverted repeat from the mouse Moloney sarcoma oncogene (Mos) gene (MosIR).

The pCag-EGFP_MosIR plasmid contains an inverted repeat from the mouse Mos (Moloney sarcoma oncogene) gene that is inserted into the 3'-UTR of the EGFP reporter gene, which is expressed using a promoter composed of the CMV enhancer and β-actin core promoter.

source_name: HEK293 cell line, MosIR


title: RXRa_2h-ATRA_ChIP-seq

description: Chromatin IP against RXRa


title: ECC1_Tn-RNA-seq_10pg_mRNA

status: Public on Oct 10 2011

city: Huntsville

first: Jason

last: Gertz

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

description: RNA-seq from poly(A) selected mRNA

data_processing: To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters: --phred64-quals -n 2 -k 1 -m 10 â-best.  The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.

growth_protocol: The human endometrial Â cancer cell line ECC-1 was grown in RPMI-1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone) and 1% penicillin-streptomycin (Invitrogen).

extract_protocol: Library construction protocols are indicated in the characteristics: Protocol

tag: protocol

value: Tn-RNA-seq

tag: mrna input

value: 10 pg


title: ECC1_Tn-RNA-seq_1pg_mRNA

description: RNA-seq from poly(A) selected mRNA

value: 1 pg


title: ECC1_Tn-RNA-seq_100pg_mRNA

description: RNA-seq from poly(A) selected mRNA


title: ECC1_Tn-RNA-seq_10ng_mRNA

description: RNA-seq from poly(A) selected mRNA

value: 10 ng


title: ECC1_Tn-RNA-seq_1ng_mRNA

description: RNA-seq from poly(A) selected mRNA

value: 1 ng


title: ECC1_Tn-RNA-seq_rep2

description: RNA-seq from poly(A) selected mRNA

value: 50 ng


title: ECC1_directional_Tn-RNA-seq_rep1

description: RNA-seq from poly(A) selected mRNA

value: Directional Tn-RNA-seq


title: ECC1_Tn-RNA-seq_500pg_mRNA

description: RNA-seq from poly(A) selected mRNA


title: ECC1_Tn-RNA-seq_rep1

description: RNA-seq from poly(A) selected mRNA


title: ECC1_Tn-RNA-seq_5ng_mRNA

description: RNA-seq from poly(A) selected mRNA

value: 5 ng


title: ECC1_standard_rep2

description: RNA-seq from poly(A) selected mRNA

value: Standard RNA-seq


title: UHR_directional_standard

description: RNA-seq from poly(A) selected mRNA

source_name: Universal human reference RNA (Agilent)

value: Directional RNA ligation


title: UHR_directional_Tn-RNA-seq

description: RNA-seq from poly(A) selected mRNA


title: K562_rep2

city: Santa Cruz

first: Jesse

last: Raab

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

data_processing: 3bp tag on 5' end was trimmed and reads were aligned with bowtie, and coverage of each restriction fragment in 1 MB region of chr17 (genome build hg18) was used to identify regions interacting at greater than the expected frequency for a given linear chromosome distance.

source_name: Erythroid Leukemia Cell line

growth_protocol: K562 cells were grown in Iscove's Modification of Dubelco's Media and were harvested at passage 8-11.

extract_protocol: Cells were crosslinked in 2% formaldehyde, digested with Csp6I and ligated with T4 DNA ligase and lysed for 15 minutes on ice in lysis buffer (10mM Tris ph8, 10mM NacL, 0.2%NP-40, Roche EDTA free protease inhibitor tablet). Nuclei were pelleted and counted and aliquoted in microfuge tubes at 1x10^7 nuclei per tube and snap frozen in liquid nitrogen and stored at -80. Bait regions were extended using a biotin tagged primer and Illumina adapters were ligated to the 3' end. Nested PCR was used to further amplify and add a second illumina adapter to the 5' end.

tag: passages

tag: library strategy

value: Chromosome Confirmation Capture


title: K562_rep1


title: CNC_INPUT_1

status: Public on Oct 07 2011

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.

source_name: WPP

growth_protocol: 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

value: WPP

tag: strain

value: iso1 (y; bw cn sp)


title: ECC1_directional_Tn-RNA-seq_rep2

description: RNA-seq from poly(A) selected mRNA


title: RXRa_48h-EtOH_ChIP-seq

description: Chromatin IP against RXRa

value: F9 embryonal carcinoma cells

value: polyclonal anti-RXRa

value: in-house antibody [generated by immunization of rabbits with the peptide mRXRa:PB105 (MDTKHFLPLDFSTQVNSSSLNSPTGRGC)]


title: CNC_ChIPSeq_1 and Seq2

tag: antibody name

value: CNC

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog