title: H3K4me3_ChIPSeq_Th1

description: Chromatin IP against H3K4me3


title: H3K9ac_ChIPSeq_Th2

status: Public on Aug 05 2011

type: SRA

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

description: Chromatin IP against H3K9ac

library_source: genomic

data_processing: A total of 170,000â250,000 clusters was generated per tile, and 36 cycles of the sequencing reactions were performed. Short-read sequences were aligned to the mouse genome sequences (mm9 from University of California, Santa Cruz Genome Browser; http://genome.ucsc.edu/) using the Eland program. Sequences allowing no more than two mismatches per sequence were used for the analysis.

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Splenic CD4 T cells were prepared using a magnetic cell sorter (AutoMACS; Miltenyi Biotec) yielding a purity of >98%. Where indicated, cells from C57BL/6 mice were stimulated with immobilized anti-TCR mAb (H57â597; 3 mg/ml) and anti-CD28 mAb under Th1- or Th2-culture conditions for 2 days in vitro.  Th1 conditions; 25 U/ml IL-2, 10 U/ml IL-12, and antiï¾IL-4 mAb.  Th2 conditions; 25 U/ml IL-2, 100 U/ml IL-4. After culturing under Th1- or Th2-culture conditions for 3 more days, the cells were harvested.

extract_protocol: For ChIP-Seq analysis, IP and input samples were prepared using ChIP-Seq Sample Prep kit (Illumina). Adaptor-ligated DNA fragments were size fractionated by 12% acrylamide gel, and the 170- to 250-bp fraction was recovered. DNA thus obtained was amplified by 18 cycles of PCR. One nanogram of DNA was used for the sequencing reaction of the Illumina GAIIx, according to the manufacturerâs instructions.

tag: strain

tag: tissue

value: spleen

tag: cell type

value: primary CD4 T cells

tag: culture condition

tag: chip antibody

tag: chip antibody vendor

value: Upstate

tag: chip antibody cat. & batch number


title: H3K27me3_ChIPSeq_Th1

description: Chromatin IP against H3K27me3


title: H3K9ac_ChIPSeq_Th1

description: Chromatin IP against H3K9ac


title: input DNA_Th2_2

description: control input DNA for H3K27me3-, H3K9ac-, and H3K4me3-ChIP (Th2) experiment

source_name: input DNA


title: Chromatin accessibility assay of Fetal Lung, Left; DS17154

status: Public on Aug 06 2011

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: DS17154
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8395
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8394
****************
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: GSM774211_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23758.DS17154.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17154.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-23758, Library DS17154 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.10379
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,912,012
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4904
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4782
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9928
IROC_PERCENTILE: 38
POISSON_SCORE: 0.5446
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM774211_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23758.DS17154.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17154.hg19.level.2.release.5
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-23758, Library DS17154 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.10332
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 5
BROWSER_TRACK_NAME: FLL DNase 58 54
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-23758 Library DS17154 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,912,012
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4904
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4782
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9928
IROC_PERCENTILE: 38
POISSON_SCORE: 0.5446
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

organism: Homo sapiens

source_name: Fetal Lung, Left primary tissue, day 107; DS17154

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: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 107

value: Female

value: Chromatin Accessibility

value: Qiagen minElut

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


title: input DNA_Th1_2

description: control input DNA for H3K27me3-, H3K9ac-, and H3K4me3-ChIP (Th1) experiment


title: GATA3_ChIPSeq_Th2

description: Chromatin IP against GATA3

value: Santa Cruz Biotechnology


title: Chromatin accessibility assay of Moblized CD3 Primary Cells; DS11148

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS11148
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8319
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8318
****************
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: GSM774201_UW.Mobilized_CD3_Primary_Cells.ChromatinAccessibility.RO_01508.DS11148.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS11148.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mobilized CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Mobilized CD3 Primary Cells, Donor RO 01508, Library DS11148 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.10359
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,338,752
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.1937
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.2076
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9981
IROC_PERCENTILE: 96
POISSON_SCORE: 0.1932
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM774201_UW.Mobilized_CD3_Primary_Cells.ChromatinAccessibility.RO_01508.DS11148.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS11148.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD3 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Mobilized CD3 Primary Cells, Donor RO 01508, Library DS11148 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.10312
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 5
BROWSER_TRACK_NAME: MCD3 DNase 08 48
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD3 Primary Cells DNase Hypersensitivity Donor RO 01508 Library DS11148 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,338,752
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.1937
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.2076
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9981
IROC_PERCENTILE: 96
POISSON_SCORE: 0.1932
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: flow sorted CD3+ Primary Cells, Mobilized, year 36; DS11148

value: Mobilized CD3 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 36

value: Male

value: Hispanic


title: input DNA_Th1_1

description: control input DNA for control_Ab- and GATA3-ChIP (Th1) experiments

value: spleen

value: primary CD4 T cells


title: GATA3_ChIPSeq_Th1

description: Chromatin IP against GATA3


title: control_Ab_ChIPSeq_Th2

description: Chromatin IP with control_Ab

value: Southern Biotech


title: H3K27me3_ChIPSeq_Th2

description: Chromatin IP against H3K27me3

value: Upstate


title: Chromatin accessibility assay of Fetal Lung, Left; DS17105

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: DS17105
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8400
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8399
****************
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: GSM774207_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23744.DS17105.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17105.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-23744, Library DS17105 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.10366
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,863,211
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.5121
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.5002
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9946
IROC_PERCENTILE: 64
POISSON_SCORE: 0.5533
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM774207_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23744.DS17105.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17105.hg19.level.2.release.5
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-23744, Library DS17105 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.10319
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 5
BROWSER_TRACK_NAME: FLL DNase 44 05
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-23744 Library DS17105 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,863,211
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.5121
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.5002
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9946
IROC_PERCENTILE: 64
POISSON_SCORE: 0.5533
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Lung, Left primary tissue, day 91; DS17105

value: Fetal Lung, Left

value: genomic DNA

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

value: Primary Tissue

value: UW

value: fetal

value: day 91


title: control_Ab_ChIPSeq_Th1

description: Chromatin IP with control_Ab


title: Chromatin accessibility assay of Mobilized CD34 Primary Cells; DS17112

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17112
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8370
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8369
****************
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: GSM774208_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01701.DS17112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17112.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Mobilized CD34 Primary Cells, Donor RO 01701, Library DS17112 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.10361
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,941,845
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4878
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.484
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9968
IROC_PERCENTILE: 91
POISSON_SCORE: 0.5367
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM774208_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01701.DS17112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17112.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Mobilized CD34 Primary Cells, Donor RO 01701, Library DS17112 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.10314
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 5
BROWSER_TRACK_NAME: MCD34 DNase 01 12
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01701 Library DS17112 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,941,845
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4878
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.484
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9968
IROC_PERCENTILE: 91
POISSON_SCORE: 0.5367
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION:

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

source_name: flow sorted CD34+ Cells, year 37; DS17112

value: Mobilized CD34 Primary Cells

value: CD34 Primary Cells

value: year 37

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 Lung, Right; DS17101

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17101
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8386
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8385
****************
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: GSM774206_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23744.DS17101.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17101.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-23744, Library DS17101 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.10365
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,459,164
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.578
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5603
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9957
IROC_PERCENTILE: 74
POISSON_SCORE: 0.6196
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774206_UW.Fetal_Lung_Right.ChromatinAccessibility.H-23744.DS17101.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17101.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Right, Donor H-23744, Library DS17101 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.10318
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 5
BROWSER_TRACK_NAME: FLR DNase 44 01
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-23744 Library DS17101 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,459,164
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.578
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5603
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9957
IROC_PERCENTILE: 74
POISSON_SCORE: 0.6196
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Lung, Right primary tissue, day 91; DS17101

value: Fetal Lung, Right

value: Female


title: RNAseq-Fusion

status: Public on Aug 04 2011

city: New York

first: Vladislav

middle: M

last: Sandler

state: NY

address: 1300 York Ave.

department: Genetic Medicine

institute: Weill Cornell Medical College

library_source: transcriptomic

data_processing:
Sequences were aligned against hg18 human genome using SOAP aligner. All reads mapping with two or fewer mismatches were retained.
SNPs were called using SOAPsnp tool, on aligned sequences

molecule: total RNA

source_name: RNAseq from RNA extracted from fused cells

growth_protocol: Two step liquid culture for differentiatioin of fused cells

extract_protocol:
Direct lysis of cells, RT, second strand synthesis, cDNA amplification, RNeasy column purification of a single colony of about 100 cells originating from a single fused cell. All molecules longer than 500 bp.
We constructed a cDNA library from total RNA from a single colony of hybrid cells (0.1-1ng) as described elsewhere (Kurimoto, Yabuta et al. 2007; Tang, Barbacioru et al. 2009) with some modifications. We modified primers used for reverse transcription and second strand cDNA synthesis to include a rare-cutter restriction site (BstU1) between unique sequences (UP1 and UP2) and poly (T) fragments of the primers. This allowed us to eliminate UP1 and UP2 anchor sequences from the cDNA library which reduced a number of non-specific reads in RNA-seq. UP1_BstU1 primer: ATA TGG ATC CGG CGC GCC GTC GAC CGC GTT TTT TTT TTT TTT TTT TTT TTT T; UP2_BstU2 primer: ATA TCT CGA GGG CGC GCC GGA TCC CGC GTT TTT TTT TTT TTT TTT TTT TTT T. We increased time of the reverse transcription to 1 hour. Second-strand synthesis was conducted in a two-cycle PCR reaction (95 °C for 2 min, 50 °C for 3 min, 72 °C for 6 min). cDNA amplification was conducted with UP1_BstU1 and UP1_BstU2 primers using 25-cycle PCR reaction (95 °C for 30 sec, 68 °C for 1 min, 72 °C for 6 min plus 6 sec for each consecutive cycle). Amplified cDNA was restricted with the BstU1 endonuclease and purified with Qiaquick PCR purification kit to remove UP1 and UP2 anchor sequences.  Kurimoto, K., Y. Yabuta, et al. (2007). "Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis." Nat Protoc 2(3): 739-752. Tang, F., C. Barbacioru, et al. (2009). "mRNA-Seq whole-transcriptome analysis of a single cell." Nat Methods 6(5): 377-382.

value: Differentiated fused HEF19 and FL24 cells


title: Vampire-DRG

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

state: CA

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Alignment files (*vs_bos.txt): blastx against Bos taurus genome build bt3.
Alignment file column headers are the standard blastx tabular output:
1. qseqid--Query Seq-id (sequencing read name) 2. sseqid--Subject Seq-id (RefSeq protein ID) 3. pident--Percentage of identical matches 4. length--Alignment length 5. mismatch--Number of mismatches 6. gapopen--Number of gap openings 7. qstart--Start of alignment in query (nucleotide coordinates) 8. qend--End of alignment in query (nucleotide coordinates) 9. sstart--Start of alignment in subject (amino acid coordinates) 10. send--End of alignment in subject (amino acid coordinates) 11. evalue--Expect value 12. bitscore--Bit score
.
Counts files (*bos_hits.txt): We used a custom script (described in the associated manuscript), that counts the number of reads whose best BlastX alignment is a hit on the RefSeq protein in question.

organism: Desmodus rotundus

source_name: Vampire bat DRG

extract_protocol: Paraformaldehyde fixation, trizol extraction, poly-(A)+ enrichment, cDNA synthesis, Illumina library generation from dsDNA

tag: bat type

value: Vampire

value: dorsal root ganglia (DRG)


title: Non-Pit-DRG

organism: Carollia brevicauda

source_name: Non-vampire bat DRG

value: Non-vampire


title: Non-Pit-TG

source_name: Non-vampire bat TG

value: trigeminal ganglia (TG)


title: Vampire-TG

source_name: Vampire bat TG


title: input DNA_Th2_1

description: control input DNA for control_Ab- and GATA3-ChIP (Th2) experiments

value: spleen

value: primary CD4 T cells


title: RT112.H3K27m3.ChIP-Seq

status: Public on Aug 03 2011

city: Gießen

first: Andreas

last: Gogol-Döring

address: Wiesenstraße 14

department: MNI

country: Germany

institute: Technische Hochschule MIttelhessen

data_processing: The sequencing reads (36bp) were mapped using Bowtie (Langmead et al) to the chromosomes of the human genome (NCBI build GRCh37/hg19, February 2009)  allowing up to two mismatches (command line argument -v 2). Only uniquely mapped reads were retained. If several reads were mapped to the same position and strand, we retained only one and discarded the rest.

source_name: Urinary bladder cancer cell line

growth_protocol: The bladder cancer cell lines grew in Dulbecco's medium with 10% fetal calf serum. We maintained NHU cells in keratinocyte serum-free medium containing bovine pituitary extract, epidermal growth factor (Invitrogen, Paisley, UK) and cholera toxin. NHU cells are non-immortalized and derived from histologically confirmed normal urothelium obtained from patients without a history of UCC, using standard methods (Southgate et al 1994).

extract_protocol: Cells were cross-linked with 1% formaldehyde in PBS for 10 min at room temperature. Glycine was added to the final concentration of 0.125M and the mixture incubated for 5 min to quench unreacted formaldehyde. Cross-linked cells were washed with PBS, lysed in 250ul SDS lysis buffer and sonicated (Bioruptor 200). Samples were pre-cleared with 15ul of protein G dynabeads (Invitrogen) and 50ul supernatant saved as total input control. Rotating samples were immunoprecipitated overnight at 4C. The chromatin-antibody complex was incubated with 20ul dynabeads protein G for 1h at 4C, before washing and DNA elution. Cross-links were reverted by overnight incubation with RNAse A at 65C before DNA purification using columns (Qiagen). Immunoprecipitated DNA ends were repaired using PNK and Klenow enzyme, adenosine was added to the 3' end of the fragments and the DNA was ligated with the adapters. Following ligation, the ChIP DNA was amplified for 17 cycles and fragments around 200-300bp isolated using electophoresis in an agarose gel. The purified DNA was used for cluster generation and sequencing analysis using the Solexa 1G Genome Analyzer according to manufacturer protocols

tag: cell line

value: bladder cancer


title: NHU.H3K9m3.ChIP-Seq

source_name: Normal urothelium cells

value: NHU

value: normal bladder

value: H3K9m3 (Millipore; 07-442)


title: NHU.H3K27m3.ChIP-Seq


title: EJ.H3K27m3.ChIP-Seq

growth_protocol: The bladder cancer cell lines grew in Dulbeccoâs medium with 10% fetal calf serum. We maintained NHU cells in keratinocyte serum-free medium containing bovine pituitary extract, epidermal growth factor (Invitrogen, Paisley, UK) and cholera toxin. NHU cells are non-immortalized and derived from histologically confirmed normal urothelium obtained from patients without a history of UCC, using standard methods (Southgate et al 1994).

value: EJ


title: RT112.H3K9m3.ChIP-Seq


title: EJ.H3K9m3.ChIP-Seq


title: retina_2 months_lane_1

city: Boston

first: Eric

last: Pierce

state: MA

address: 243 Charles Street

department: Ophthalmology

institute: Massachusetts Eye and Ear Infirmary

data_processing: 96 million 120bp paired-end sequence reads were obtained from the 4 channels of an Illumina flow cell. The reads were aligned to the mouse transcriptome and genome (mm9) using the RNA-Seq Unified Mapper (RUM).

source_name: neural retina

growth_protocol: Neural retina from five 2 month old C57BL/6J mice, mixed gender

extract_protocol: RNA-Seq using 5 ug total RNA;  insert size 350bp +/- 25bp

value: C57BL/6J - 129SvEvTac

value: neural retina

tag: age

value: 2 months


title: retina_2 months_lane_4


title: retina_2 months_lane_3


title: retina_2 months_lane_2


title: VCaP_sr_rep9

status: Public on Aug 02 2011

city: Ann Arbor

first: Matthew

last: Iyer

state: MI

address: 5316 CCGC 0940 1400 E. Medical Center Drive

department: Michigan Center for Translational Pathology

institute: University of Michigan

data_processing: Reads were aligned to the human genome (hg18, downloaded from UCSC) using TopHat v0.1.3.  Only uniquely aligned reads were considered "-g 1". In cases where insert size was not available, we assumed an insert of 200bp.  We used a insert size standard deviation of 20bp for all lanes.  In addition to standard human chromosomes, adapter sequences and human ribosomal sequences were included in the initial reference in order to filter out the corresponding reads in subsequent processing steps.

molecule: polyA RNA

source_name: prostate gland

extract_protocol: Messenger RNA (1 microgram) was fragmented at 70 °C for 2 min in a fragmentation buffer (Ambion) and converted to single- stranded cDNA using SuperScript II reverse transcriptase (Invitrogen), followed by second-strand cDNA synthesis using Escherichia coli DNA polymerase I (Invitrogen). The double- stranded cDNA was further processed by Illumina mRNA- sequencing Prep kit. Briefly, double-stranded cDNA was end repaired by using T4 DNA polymerase and T4 polynucleotide kinase, monoadenylated using a Klenow DNA polymerase I (3' to 5' exonucleotide activity), and ligated with adaptor oligo mix (Illumina) using T4 DNA ligase. The adaptor-ligated cDNA library was then fractioned on a 4% agarose gel, and a smear corresponding to 300 nt was excised, purified, and PCR amplified (15 cycles) by Pfu polymerase (Stratagene). The PCR product was again size selected on a 4% agarose gel by cutting out the library smear at 300 base pairs. The library was then purified with the Qiaquick Minelute PCR Purification Kit (Qiagen) and quantified with the Agilent DNA 1000 kit on the Agilent 2100 Bioanalyzer following the manufacturer’s instruc- tions. Library (10 nM) was used to prepare flowcells with 100,000–130,000 clusters per lane for analysis on the Illumina Genome Analyzer II.

tag: read type (single/paired-end)

tag: sample pool name

value: VCaP

tag: sample type

value: Cell Line

value: prostate cancer

tag: disease state

value: cancer

tag: patient id

tag: ets fusion status

value: ERG+

tag: tissue harvest site

tag: read length (bp)

tag: insert size (bp)

tag: insert size standard deviation (bp)


title: VCaP_sr_rep6

tag: tissue


title: VCaP_sr_rep7


title: VCaP_sr_rep10


title: VCaP_sr_rep5


title: VCaP_sr_rep8


title: VCaP_sr_rep4


title: VCaP_sr_rep2


title: VCaP_sr_rep3


title: ovary_C5_Piel-de-sapo

city: Espinardo

first: Daniel

last: Gonzalez-Ibeas

state: Murcia

address: Campus de Espinardo s/n

department: Biologia Estres y Patologia Vegetal

country: Spain

institute: CEBAS-CSIC

description:
small RNA sequencing
c5
ovary_C5_Piel-de-sapo
raw data file (original file name): FAI1VGH01.sff
raw data file (original file name): FAJ8I4S01.sff
Library strategy: BARCODE --> ATCGTAGCGGUCUGAUA

data_processing: sRNA sequences were parsed from FASTA formatted files containing 447,180 reads from two independent 454 sequencing runs and assigned to specific libraries through identification of the sRNA/adaptor boundaries and barcode analysis. Sequences were analyzed with standard Python scripts [74] and the BioPython library [75]. Known sRNAs were identified by sequence similarity to nucleic acids deposited in publicly available databases by using the Blast algorithm [76] version 2.2.19 and allowing up to 2 mismatches. Databases and sequences used were: transfer RNA database (version 2009) [77], Plant small nucleolar RNA database (v1.2) [78], SILVA (ribosomal RNA database, v100) [79], The Arabidopsis small RNA Project (ASRP) database [33], Rfam database 10.0 [80], miRBase: the microRNA database (release 16) [34], The Plant Repeat databases [81], chloroplast genome sequence of Cucumis melo (unpublished data), mithocondrial genome sequence of Arabidopsis thaliana (GenBank accession  Y08501), genome sequence of MNSV (GenBank accession AY122286.1), genome sequence of WMV (GenBank accession AY437609.1).

organism: Cucumis melo

source_name: ovary

growth_protocol: Plants were grown in a greenhouse at 16h/ligth/25-28C 8h/dark/18-20C

extract_protocol: Total RNA was extracted by using Trizol-Reagent and 300 ug were used for construction of sRNAs libraries. SRNAs were purified using 17% denaturing PAGE. Two adaptors were ligated to the 3' and 5' ends of melon sRNAs. The 3' adaptor was a pre-activated 5' adenylated oligo (5'rAppCTGTAGGCACCATCAAT3ddC 3') to avoid the circularization of sRNAs. 10 oligonucleotide 5' adaptor variants were used by modification of the four nucleotide identifier (barcode). After each ligation step, sRNA was purified using 17% denaturing PAGE. The purified ligated sRNA was reverse transcribed with SuperScript III Reverse Transcriptase and the cDNA was amplified by using AmpliTaq Gold DNA Polymerase and 3'PCR FusionB and 5' PCR FusionA primers. PCR primers contained the "A" and "B" tag sequences used by 454 technology during sequencing. DNA amplicons were gel-purified using 4% Metaphor agarose and isolated using a QIAEX II Gel Extraction Kit. Quantity and quality of DNA amplicons were measured using ND-1000 spectrophotometer and Experion Automated Electrophoresis System, respectively. The same amount of DNA amplicon from each library was pooled and sequenced by 454 Life Science technology.

value: ovary

tag: genotype/variation

value: Piel de sapo

tag: infection (physiological condition)

value: healthy

tag: treatment

value: no treatment


title: fruit_15dap_Piel-de-sapo

description:
small RNA sequencing
15d
fruit_15dap_Piel-de-sapo
raw data file (original file name): FAI1VGH01.sff
raw data file (original file name): FAJ8I4S01.sff
Library strategy: BARCODE --> ATCGTAGCGACCUGAUA

source_name: fruit

value: fruit


title: fruit_45dap_Piel-de-sapo

description:
small RNA sequencing
45d
fruit_45dap_Piel-de-sapo
raw data file (original file name): FAI1VGH01.sff
raw data file (original file name): FAJ8I4S01.sff
Library strategy: BARCODE --> ATCGTAGCGCACUGAUA


title: cotyledon_WMV_Tendral

description:
small RNA sequencing
Wt
cotyledon_WMV_Tendral
raw data file (original file name): FAI1VGH01.sff
raw data file (original file name): FAJ8I4S01.sff
Library strategy: BARCODE --> ATCGTAGGCCACUGAUA

source_name: cotyledon

value: cotyledon

value: Tendral

value: virus infected (WMV)

value: Virus infected samples were obtained from completely expanded cotyledons rubbed with carborundum (phi = 0.037 mm) and the corresponding viral inoculum (MNSV or WMV) in inoculation buffer (phosphate buffer 0.2M, pH = 8.0, beta-mercaptoethanol 0.1% (v/v), activated charcoal 0.03 g/ml).


title: ovary_C1_Piel-de-sapo

description:
small RNA sequencing
c1
ovary_C1_Piel-de-sapo
raw data file (original file name): FAI1VGH01.sff
raw data file (original file name): FAJ8I4S01.sff
Library strategy: BARCODE --> ATCGTAGCGUGCUGAUA


title: cotyledon_MNSVchimeric_Tendral

description:
small RNA sequencing
3'T
cotyledon_MNSVchimeric_Tendral
raw data file (original file name): FAI1VGH01.sff
raw data file (original file name): FAJ8I4S01.sff
Library strategy: BARCODE --> ATCGTAGACCGCUGAUA

value: virus infected (MNSV-chimeric)


title: cotyledon_WMV_TGR-1551

description:
small RNA sequencing
Cw
cotyledon_WMV_TGR-1551
raw data file (original file name): FAI1VGH01.sff
raw data file (original file name): FAJ8I4S01.sff
Library strategy: BARCODE --> ATCGTAGGCGUCUGAUA


title: cotyledon_MNSV_Tendral

description:
small RNA sequencing
Ta5
cotyledon_MNSV_Tendral
raw data file (original file name): FAI1VGH01.sff
raw data file (original file name): FAJ8I4S01.sff
Library strategy: BARCODE --> ATCGTAGACGCCUGAUA

value: virus infected (MNSV)


title: cotyledon_healthy_TGR-1551

description:
small RNA sequencing
Cwm
cotyledon_helathy_TGR-1551
raw data file (original file name): FAI1VGH01.sff
raw data file (original file name): FAJ8I4S01.sff
Library strategy: BARCODE --> ATCGTAGGCUGCUGAUA

value: mock inoculated

value: Mock inoculated cotyledons were rubbed only with carborundum (phi = 0.037 mm) and inoculation buffer (phosphate buffer 0.2M, pH = 8.0, beta-mercaptoethanol 0.1% (v/v), activated charcoal 0.03 g/ml).


title: VCaP_sr_rep1

value: VCaP

value: Cell Line


title: RWPE_sr_rep9

value: RWPE

value: benign

value: ETS-


title: RWPE_sr_rep7


title: RWPE_sr_rep5


title: RWPE_sr_rep6


title: RWPE_sr_rep1


title: RWPE_sr_rep4


title: RWPE_sr_rep2


title: LNCaP_sr_rep1

value: LNCaP

value: cancer


title: LNCaP_sr_rep6


title: PC3_sr_rep1


title: LNCaP_sr_rep7


title: LNCaP_sr_rep5


title: LNCaP_sr_rep2


title: cotyledon_healthy_Tendral

description:
small RNA sequencing
Wtm
cotyledon_halthy_Tendral
raw data file (original file name): FAI1VGH01.sff
raw data file (original file name): FAJ8I4S01.sff
Library strategy: BARCODE --> ATCGTAGGCACCUGAUA


title: LNCaP_sr_rep3


title: LNCaP_sr_rep4


title: PrEC_sr_rep1

value: PrEC


title: PrEC_sr_rep2


title: WPE1-NB26_pe_rep1

value: prostate cancer


title: PrSMC_pe_rep1

value: PrSMC


title: DU145_sr_rep3


title: DU145_sr_rep1


title: PrEC_pe_rep1


title: 22Rv1_sr_rep1


title: RWPE_sr_rep8


title: PC3_pe_rep1


title: PWR-1E_pe_rep1


title: NCI-H660_pe_rep1

value: ERG+


title: RWPE_sr_rep3


title: PrEC_pe_rep2


title: LNCaP-CDS2_pe_rep1

value: LNCaP CDS2

value: Lymph node


title: LNCaP-CDS-parent_pe_rep1

value: LNCaP CDS parent


title: WPMY-1_pe_rep1


title: LAPC-4_pe_rep1


title: DU145_pe_rep7

value: Metastatic Site


title: DU145_pe_rep5


title: CWR22_pe_rep1


title: DU145_pe_rep2


title: DU145_pe_rep1


title: CA-HPV-10_pe_rep1


title: DU145_pe_rep4


title: DU145_pe_rep3


title: 22Rv1_pe_rep1


title: C4-2B_pe_rep1


title: DU145_pe_rep6


title: LNCaP-CDS3_pe_rep1

value: LNCaP CDS3


title: Control DNA reads from K562

city: Bethesda

first: Mirit

middle: I

last: Aladjem

state: MD

address: 37 Convent Dr. Building 37, Room 5068D

department: DNA Replication Group

institute: National Cancer Institute

data_processing:
Illumina software pipeline (basecalls was done by using Illumina RTA 1.6 and RTA1.8. Alignment was done by using Illumina GAPipeline-1.4.0, CASAVA_v1.6.0, CASAVA-1.7.0 pipelines).
Genome_build: GRCh37 (hg19)

source_name: Cultured cancer cell line

growth_protocol: Cancer cells were grown in RPMI medium.

extract_protocol: Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit). The average and standard deviation of insert size of paired-end reads was as follows. For K562_NS_L2 and K562_NS_L3, 120 and 14, respectively. For K562_NS_L6 and K562_NS_L7, 129 and 11, respectively. For MCF7_NS, 106 and 10, respectively.

treatment_protocol: DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004.

tag: cell type

value: Chronic myeloid leukaemia

tag: read type

value: Single end


title: Nascent strands reads from MCF7

value: Breast carcinoma

tag: cell line

value: Paired end


title: Nascent DNA strands reads from K562


title: NucleosomalDNA_high_phosphate-normal

status: Public on Aug 01 2011

city: Singapore

first: Yuriy

middle: L

last: Orlov

address: 60 Biopolis Street

department: Computational Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description: nucleosomal DNA sequencing after sonication

data_processing: Alignment: Sequence reads were obtained and mapped to the yeast (sacSer1) genome using the Illumina Genome Analyzer II Pipeline. All reads mapping with two or fewer mismatches were retained. Nucleosome enriched/depleted regions were estimated by custom-made script. Control sequencing library was not used.

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast S. cerevisiae in log phase was grown in PNB medium with no phosphate for 3 hours and then shifted to various phosphate concentration (from 0 to 10 mM) for 80 minutes. The strain is PHO4-MYC::TRP1; CBF1-3HA::LEU2. In details: Overnight yeast culture in YPD (rich media). Dilute in YPD to log phase. Grow two more cycles. Wash the culture with water and then with YNB with no phosphate. Grow culture in YNB with no phosphate for 3 hours (Phosphate starvation). Shift yeast to YNB with various phosphate concentrations and grow for 80 minutes.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. After micrococcal nuclease treatment, reverse crosslink and gel purification mononucleosomes were isolated. The sequencing by Illumina Solexa following manufacturer protocol provided mononucleosomal maps in S. cerevisiae genome (Oct. 2003 SGD/sacSer1 genome release). Library fragments of ~200 bp 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. No antibody was used.

treatment_protocol: After growing in PNB medium with no phosphate for 3 hours yeast cells were treated by phosphate media  (0mM and 10 mM) for 80 minutes to prepare material for sequencing libraries. Micrococcal nuclease treatment, reverse crosslink following gel purification for mononucleosomal fragments.

value: normal cells


title: NucleosomalDNA_low_phosphate-starvation

value: cells after phosphate starvation


title: LNCaP-CDS1_pe_rep1

tag: read type (single/paired-end)

value: LNCaP CDS1

value: Cell Line


title: MDA-Pca-2b_pe_rep1

tag: sample pool name

value: MDA PCa 2b

value: cancer

value: ETS-


title: Control reads from MCF7


title: Spom Sap1ts genome-wide nucleosome data, cells grown in YES at restrictive temp 35C

first: Alex

last: Tsankov

address: 155 Bay State

institute: MIT

description:
mononuclesomal DNA
Mnase digested DNA and size selected for mononucleosomes (~150bp)
Illumina 1G Analyzer, 36bp read lengths
reference genome for wig file: Spom.fsa

data_processing:
Alignment: Sequence reads were mapped to the appropriate reference genome (fasta file attached) using BLAT. All reads mapping to a unique location in the genome with 4 or fewer mismatches were retained. *.read.zip files are tab delimited text files containing each uniques reads chromosomal coordinates. The files have 4 columns and the following headers: readChrom, readStart, readStop, onForwardStrand (1=forward strand or +, 0=reverse strand or -).
Read Extended Nucleosome Map: Each uniquely mapped read was then extended to a length of 100bp. To generate a genomic nucleosome occupancy landscape, we cumulatively summed all extended reads covering each base pair. The *.wig.zip files use the WIGGLE fixed_step format.
Genomes: The version of the species' genomic sequences used in this study are attached on the Series record as fasta files (*.fsa).

organism: Schizosaccharomyces pombe

source_name: in vivo cells

growth_protocol: Overnight cultures for each species were grown in 450ml of media at 220 RPM in a New Brunswick Scientific air-shaker at 30C or 35C until reaching mid log-phase.

extract_protocol:
Formaldehyde crosslink of cells, removal of cell wall with zymolase, shearing of DNA with MNase, reverse cross-linking and treatment with Protenase K. DNA was phenol:chloroform extracted, ethanol precipitated, and treated with DNase-free Rnase.  Isolation of mononucleosomal DNA using gel purification of DNA band ~150bp.
Libraries were prepared according to standard Illumina instructions. Briefly, DNA was end-repaired. The blunt, phosphorylated ends were treated with Klenow fragment (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 19 cycles and library fragments of ~300 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: Formaldehyde crosslink, shearing with MNase, isolation of mononucleosomal DNA using gel purification of DNA band ~150bp.

tag: strain

value: sap1ts, ENY1125 (h+ leu1-32 ura4-D18 sap1-48ts-3FLAG(kanMX6)) (Noguchi and   Noguchi)


title: Spom wildtype genome-wide nucleosome data, cells grown in YES at 30C


title: Spom wildtype genome-wide nucleosome data, cells grown in YES at restrictive temp 35C


title: DU145_sr_rep2

tag: sample type

tag: disease state


title: Spom wildtype genome-wide nucleosome data, cells grown in CM medium, 30C


title: Phytophthora phaseoli_plant-grown 6dpi - rep2

city: Newark

first: Sridhara

middle: G

last: Kunjeti

state: DE

address: 531, S. college Ave

department: Plant and Soil Sciences

institute: University of Delaware

description: P. phaseoli mycelium was harvested from the infected lima bean hypocotyl 6 days post inoculation rep 2

data_processing: The raw sequences from all the six *.fastq files were processed through velvet package to develop unique contigs (Pphaseoli-contigs.txt)

organism: Phytophthora phaseoli

source_name: Mycelium + Plant

extract_protocol: RNA was extracted from all the samples (plate-grown and plant-grown P. phaseoli race F) using Tri reagent (Ambion Inc., Austin, TX) according to manufacturerâs instructions. After nanodrop, total RNA from both the libraries (plate-grown and plant-grown P. phaseoli race F) were sent to NCGR for transcriptional analysis. At NCGR it was processed for mRNA-Seq according to Illumina manufacturerâs instructions (Illumina, San Diego, CA). Data was processed on one flow cell on an Illumina Genome Analyzer IIx (four lanes of plate-grown library and three lanes of plant-grown library)

value: Race F(PhyP18)

value: Infected lima bean hypocotyl

tag: time point

value: 6 days post inoculation


title: Phytophthora phaseoli_plant-grown 3dpi - rep1

description: P. phaseoli mycelium was harvested from the infected lima bean hypocotyl 3 days post inoculation rep 1

value: 3 days post inoculation


title: Phytophthora phaseoli_plate-grown_rep2

description: P. phaseoli grown on media plates rep 2

source_name: Mycelium

value: Plate-grown mycelium


title: Phytophthora phaseoli_plate-grown_rep1

description: P. phaseoli grown on media plates rep 1


title: Phytophthora phaseoli_plant-grown 6dpi - rep1

description: P. phaseoli mycelium was harvested from the infected lima bean hypocotyl 6 days post inoculation rep 1


title: Spom Sap1ts genome-wide nucleosome data, cells grown in YES at restrictive temp 35C, sample well-digested


title: DKO targeted BS-seq

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

description:
DNA methylation analysis using bisulfite sequencing
Library selection: Hybrid-selection

data_processing:
Alignment: The raw bisulfite sequencing reads were first converted to "unmethylated reads" via the conversion of all Cs to Ts in silico. The unmethylated, converted sequencing reads were then aligned to the two copies of in silico converted human reference genome (hg18) using SOAP2 (http://soap.genomics.org.cn/). The results of both mappings were combined, and any reads mapped against both copies of converted reference were resolved by identifying their strand based on the TCAG ratio and the mapping positions used accordingly
Methylation calculation: The methylation level [(# of methylated)/(# of methylated + # of unmethylated)] was calculated after measuring the amount of methylation (CG->CG) and unmethylation (CG->TG) in the CpG position. Only CpGs that are covered by at least 10 sequencing reads were included.

source_name: DNMT1, 3B double knockoutHCT116 colon cancer cell line

growth_protocol: Colon cancer cell lines were grown in RPMI1640 media supplemented with 10% FBS. HCT116 cells were kept in McCoy's 5A medium supplemented with 10% FBS.

extract_protocol: Illumina genomic library construction protocol, methylated adaptors were used.

value: Colon

tag: tumorgenecity

value: Unknown


title: 3BKO targeted BS-seq

source_name: DNMT3B knockout HCT116 colon cancer cell line


title: HCT116 targeted BS-seq

source_name: HCT116 colon cancer cell line

value: HCT116 colon cancer cell line

value: DNMT wild type

value: tumorgenic


title: MCF7-2 targeted BS-seq

source_name: MCF7 breast cancer cell line

growth_protocol: Breast cancer cell lines were grown in RPMI1640 media supplemented with 10% FBS.

extract_protocol: The genomic library was constructed using Illumina Paired-End DNA Sample Prep Kit according to Manufacturer's protocol. The methylated adaptors sets (part number ME-100-0010) were used instead of the pair-end adaptors came with the Sample prep kit.

value: Breast

value: MCF7 breast cancer cell line

tag: er status

value: ER+


title: MDA-MB-231 targeted BS-seq

source_name: MDA-MB-231 breast cancer cell line

value: MDA-MB-231 breast cancer cell line

value: ER-


title: MCF7-1 targeted BS-seq


title: C. albicans delta cbf1 genome-wide nucleosome data, cells grown in CM medium, 30C

description:
mononuclesomal DNA
Mnase digested DNA and size selected for mononucleosomes (~150bp)
Illumina 1G Analyzer, 36bp read lengths
reference genome for wig file: Calb.fsa

organism: Candida albicans

value: CBF1M5A (Biswas et al.) (delta cbf1::FRT/delta cbf1::URA3)


title: S. cerevisiae delta cbf1 genome-wide nucleosome data, cells grown in CM medium, 30C

description:
mononuclesomal DNA
Mnase digested DNA and size selected for mononucleosomes (~150bp)
Illumina 1G Analyzer, 36bp read lengths
reference genome for wig file: Scer.fsa

value: BY Cbf1D


title: Mitochondria PARE 5' end sequencing (rep2)

city: Sydney

first: Tim

middle: R.

last: Mercer

state: New South Wales

address: 384 Victoria Street Darlinghurst NSW 2010

country: Australia

institute: Garvan

description: Total RNA, no rRNA depletion

data_processing: Prior to alignment, sequenced reads were processed as follows; the adaptor sequence (5â was trimmed from the 3' end of reads and remaining adenine nucleotide stretches, resulting from polyA-tailing, were removed from the 5' end. All sequenced reads containing barcode sequences (5â-ATCACG-3â and 5â-CGATGT-3â - representing alternative technical replicates) were retain and pooled following removal of the barcode sequence. These reads were aligned the mitochondrial genome (hg19, chrM) with BowTie (Langmead et al., 2009) using default parameters and returning only unique aligning reads. Following alignment, the 5' terminal mononucleotide of sequenced reads was only retained since this corresponds to sites of RNA cleavage. These alignments were then converted to wiggle format for visualization on the UCSC genome browser.

source_name: 143B cells

growth_protocol: 143B osteosarcoma cells were cultured at 37C under humidified 95% air/5% CO2 in Dulbecco's modified Eagle's medium (DMEM, Invitrogen) containing glucose (4.5 g.l-1), 1 mM pyruvate, 2 mM glutamine, penicillin (100 U.ml-1), streptomycin sulfate (100 µg.ml-1) and 10 % fetal bovine serum (FBS).

extract_protocol: RNA was extracted from 143B mitochondria using the miRNeasy kit (Qiagen) and polyadenylated using a commercial poly(A)-tailing kit (Ambion). RNA was then ethanol precipitated and PARE libraries prepared as described, following a previously established methodology (German et al. 2009). Polyadenylated RNA was twice purified using oligo(dT) dynabeads (Dynal Biotech). An RNA adaptor (5'-GUUCAGAGUUCUACAGUCCGAC-3') was then ligated using T4 RNA ligase (Ambion) and RNA was extracted with phenol / chloroform, ethanol precipitated and purified with Oigo(dT) dynabeads. RNA was then reverse transcribed (SuperscriptII, Invitrogen) using the primer (5'-CGAGCACAGAATTAATACGACT(18)V-3') and amplified by PCR (Phusion DNA Polymerase, Finnzymes) using the primers (5'-GTTCAGAGTTCTACAGTCCGAC-3' goand 5'-CGAGCACAGAATTAATACGAC-3'). PCR conditions were 7 cycles of 98 °C for 20 s, 60 °C for 30 s and 72 °C for 3 min, followed by a 7 min incubation at 72C. Products were gel purified, cleaved with MmeI (New England Biolabs) and dephosphorylated (Calf Intestinal Alkaline Phospahatse, New England Biolabs). Samples were run on a 12% polyacrylamide gel and a 42 nt band excised. DNA was eluted from the gel overnight with 0.3 M NaCl, filtered through a Millex 0.45 µM column and ethanol precipitated. Products were then ligated using T4 DNA ligase (Promega) to double-stranded DNA adaptors (top 5'-P-TCGTATGCCGTCTTCTGCTTG-3', bottom NN: 3'-NNAGCATACGGCAGAAGACGAAC-5') that varied in the composition of an additional first 6 nucleotides (not in the given sequence) to enable barcoding of the separate tissue samples. Another 12% polyacrylamide gel was run and a 92 nt band excised and purified as above followed by PCR amplification using the following conditions : 25 cycles of 98 °C for 20 s, 60 °C for 30 s and 72 °C for 15s, followed by an incubation at 72C for 3 min. The product was run on a polyacrylamide gel and purified prior to high-throughput sequencing using the Illumina GAII platform.

treatment_protocol: Mitochondria were prepared from 2 x 107 143B cells grown overnight in 15 cm2 dishes. Cells in PBS were sedimented (150 g for 5 min at 4 °C), resuspended in 4 ml of ice-cold 10 mM NaCl, 1.5 mM MgCl2 and 10 mM Tris-HCl, pH 7.5. Cells were allowed to swell for 5 min on ice and briefly homogenised with a 7 ml glass homogenizer. The sucrose concentration was then adjusted to 250 mM by adding 2 M sucrose in 10 mM Tris-HCl and 1 mM EDTA, pH 7.6 (T10E20 buffer). The nuclei from this suspension were sedimented (1,300 g for 3 min at 4 °C), and the centrifugation step was repeated for the supernatant once more. Mitochondria were sedimented from the supernatant by centrifugation (15,000 g for 15 min at 4 °C). The mitochondrial suspension was layered on a discontinuous sucrose gradient (1.0 and 1.7 M) in T10E20 buffer and centrifuged at 70,000 g for 40 min at 4C. The mitochondrial fraction was recovered from the interface between the two sucrose cushions, diluted with 400 µl of 250 mM sucrose in T10E20 buffer and washed once in the same solution. The final mitochondrial pellet was resuspended in 100 µl of 250 mM sucrose in T10E20 buffer and protein concentration as determined by the bicinchoninic acid (BCA) assay using bovine serum albumin (BSA) as a standard.

tag: subcellular

value: Mitochondria

value: 143B cells


title: HeLa30-100_XRN1/2

status: Public on Jul 31 2011

city: Copenhagen E

first: Eivind

last: Valen

state: Select

address: Ole Maaloes Vej 4

department: Dep. of Biology

country: Denmark

institute: University of Copenhagen

description: XRN1&2 knockdown

data_processing: mapping to hg18 using Bowtie

source_name: HeLa S2

growth_protocol: DMEM-Glutamax (Invitrogen) supplemented with 10% (v/v) FBS, 37°C

extract_protocol: Trizol extraction, size-selection on polyacrylamide gel

tag: sirna treatment

tag: immunoprecipitation

tag: rna size range & source

value: 30-100nt/whole cell


title: HeLa30-100_RRP40

description: RRP40 knockdown


title: HeLa30-100

description: Whole cell RNA

value: control


title: HeLa18-30_AGO1/2_RRP40

description: IP against AGO 1 & 2, RRP40 knockdown

value: 18-30nt/whole cell


title: Phytophthora phaseoli_plant-grown 3dpi - rep2

description: P. phaseoli mycelium was harvested from the infected lima bean hypocotyl 3 days post inoculation rep 2

value: Race F(PhyP18)

tag: tissue

value: Infected lima bean hypocotyl

value: 3 days post inoculation


title: 1KO targeted BS-seq

source_name: DNMT1 knockout HCT116 colon cancer cell line

value: Colon

tag: genotype/variation

value: Unknown


title: HeLa18-30_AGO1/2

description: IP against AGO 1 & 2


title: MCF10A targeted BS-seq

source_name: MCF10A importalized breast epithelial cell line

value: Breast

value: non-tumorgenic


title: Input

city: La Jolla

first: Yin

middle: Chun

last: Lin

address: 9500 Gilman Drive

department: Division of Biological Sciences

institute: UCSD

description:
Rag2-/-; thymocyte; DN3
Chromatin IP control of untreated Rag2-/- thymocytes.

data_processing:
Fastq files were generated by CASAVA.
Alignment: Reads were aligned to the mouse mm8 genome (NCBI Build 36) using Bowtie.  Only reads that mapped to a single, unique position were used for downstream analysis.
Custom HOMER software was used for downstream analysis (HOMER, available at http://biowhat.ucsd.edu/homer/).

source_name: Rag2-/- thymocytes, input

extract_protocol: Lysates were clarified from sonicated cells, and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. 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 (minus exo) 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, ChIP DNA was PCR-amplified with Illumina primers for 18 cycles, and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size selected from an 8% polyacrylamide gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: Thymocytes were isolated from either untreated Rag2-/- mice or Rag2-/- mice injected with anti-CD3e antibody 2 days after injection.

tag: genetic background

tag: genotype

tag: cell type

value: thymocyte

tag: treatment

tag: chip antibody


title: H3K4me1, Day 2

description:
Rag2-/-; anti-CD3e; day2; thymocyte;DN4
Chromatin IP against H3K4me1 of Rag2-/- thymocytes treated with anti-CD3e Ab.

source_name: Rag2-/- thymocytes, anti-CD3e Ab injection, H3K4me1 ChIP

value: anti-CD3e Ab injection

tag: treatment duration

value: 2 days

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog #

tag: chip antibody lot #


title: H3K4me1, Day 0

description:
Rag2-/-; thymocyte; DN3
Chromatin IP against H3K4me1 of untreated Rag2-/- thymocytes.

source_name: Rag2-/- thymocytes, H3K4me1 ChIP


title: E2A, Day 2

description:
Rag2-/-; anti-CD3e; day2; thymocyte;DN4
Chromatin IP against E2A of Rag2-/- thymocytes treated with anti-CD3e Ab.

source_name: Rag2-/- thymocytes, anti-CD3e Ab injection, E2A ChIP

value: Santa Cruz Biotechnology


title: HeLa12-20_N

description: Nuclear RNA


title: HeLa18-30

description: Whole cell RNA


title: HeLa18-30_N

description: Nuclear RNA


title: HeLa18-30_XRN1/2

description: XRN1&2 knockdown


title: E2A, Day 0

description:
Rag2-/-; thymocyte; DN3
Chromatin IP against E2A of untreated Rag2-/- thymocytes.

source_name: Rag2-/- thymocytes, E2A ChIP


title: LICR_ChipSeq_Lung_Input

status: Public on Jul 30 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

source_name: Lung

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

value: Lung

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

value: M

tag: antibody

value: Input

tag: antibody description

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

tag: age

tag: age description

value: Adult 8 weeks

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

value: Lung/Input/std

tag: labversion

tag: replicate

tag: replicate description

value: tier 1

tag: softwareversion

value: ELAND

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Kidney_Input

source_name: Kidney

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: cell

value: Kidney

value: Kidney/Input/std


title: LICR_ChipSeq_Heart_Input

source_name: Heart

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: Heart

tag: cell organism

tag: cell description

tag: cell sex

tag: antibody

tag: antibody description

value: Heart/Input/std


title: LICR_ChipSeq_Liver_Input

source_name: Liver

value: ChipSeq

value: ChIP-Seq

value: Liver

value: mouse

tag: age

tag: age description

tag: control

tag: control description

tag: controlid

value: Liver/Input/std


title: HeLa18-30_RRP40

description: RRP40 knockdown

tag: sirna treatment

tag: immunoprecipitation

tag: rna size range & source

value: 18-30nt/whole cell


title: LICR_ChipSeq_MEF_H3K4me3

source_name: MEF

tag: lab

tag: lab description

value: MEF

value: Mouse Embryonic Fibroblast

value: M

tag: antibody antibodydescription

value: rabbit polyclonal

tag: antibody targetdescription

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

value: Adult 8 weeks

value: std

value: Standard input signal for most experiments.

value: MEF/Input/std

tag: labversion

tag: replicate

tag: replicate description

tag: softwareversion

tag: strain

tag: strain description


title: LICR_ChipSeq_Heart_H3K4me1

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

tag: datatype description

value: tissue

tag: cell organism

value: heart

tag: Sex

tag: antibody

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

value: Abcam

tag: age

tag: age description

tag: control

tag: control description

value: heart/Input/std

value: tier 1

value: ELAND

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Cortex_H3K4me3

source_name: Cortex

tag: lab

tag: lab description

value: ChipSeq

value: ChIP-Seq

tag: cell

value: Cortex

value: mouse

tag: cell description

tag: cell sex

value: M

tag: antibody antibodydescription

value: rabbit polyclonal

tag: antibody targetdescription

tag: antibody vendorname

tag: controlid

value: Cortex/Input/std


title: LICR_ChipSeq_BoneMarrow_H3K4me1

source_name: BoneMarrow

value: LICR-m

tag: datatype

tag: datatype description

value: BoneMarrow

value: Bone Marrow

tag: antibody vendorid

value: Adult 8 weeks

value: std

value: Standard input signal for most experiments.

value: BoneMarrow/Input/std

tag: labversion

tag: replicate

tag: replicate description

tag: softwareversion

tag: strain

tag: strain description


title: LICR_ChipSeq_MEF_Input

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

value: MEF

tag: cell organism

value: Mouse Embryonic Fibroblast

tag: antibody

value: Input

tag: antibody description

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

tag: age

tag: age description

tag: control

tag: control description

value: MEF/Input/std

value: tier 1


title: Genotype 8×5 grown at 25°C

city: Los Angeles

first: Jason

last: Curole

address: 3616 Trousdale Pkwy.

department: Biological Sciences

institute: University of Southern California

data_processing: identical tags were condensed into a set of unique tags and a count equivalent to the number of times a tag was observed was assigned to each unique tag.  Counts were analyzed using a linear model.

organism: Magallana gigas

source_name: larvae

growth_protocol: Animals were grown in seawater and fed ad-libitum

extract_protocol:
Animals homogenized in RNA extraction buffer, RNA extracted with Qiagen Rneasy Kit
Digital Gene Expression: poly-A selected, DpnII digest and sequenced on Illumina Genome Analyzer according to manufacturer's instructions

tag: Genotype 8X5, 25°C


title: LICR_ChipSeq_MEF_H3K4me1

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

value: mouse

tag: cell description

tag: cell sex

value: M

tag: antibody antibodydescription

tag: antibody targetdescription

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: controlid

value: ELAND

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Kidney_H3K4me1

tag: lab

value: LICR-m

tag: lab description

value: Kidney

tag: cell organism

tag: antibody

value: rabbit polyclonal

value: Adult 8 weeks

value: std

value: Standard input signal for most experiments.

value: Kidney/Input/std

tag: labversion

tag: replicate

tag: replicate description

tag: softwareversion

tag: strain

tag: strain description


title: LICR_ChipSeq_Cortex_H3K4me1

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

tag: datatype description

tag: cell

value: Cortex

tag: cell description

tag: age

tag: age description

tag: control

tag: control description

value: Cortex/Input/std


title: Genotype 5×8 grown at 20°C

tag: Genotype 5X8, 20°C


title: LICR_ChipSeq_Cerebellum_H3K4me3

source_name: Cerebellum

value: tissue

value: cerebellum

tag: lab

tag: lab description

value: ChipSeq

value: ChIP-Seq

value: Cerebellum

tag: cell organism

tag: cell sex

tag: antibody antibodydescription

tag: antibody targetdescription

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: controlid

value: Cerebellum/Input/std

value: tier 1


title: LICR_ChipSeq_BoneMarrow_H3K4me3

value: LICR-m

tag: datatype

tag: datatype description

value: BoneMarrow

value: mouse

value: Bone Marrow

value: M

tag: antibody

value: rabbit polyclonal

value: BoneMarrow/Input/std

tag: labversion

tag: replicate

tag: replicate description

tag: softwareversion

value: ELAND

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Cortex_Input

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: cell

value: Cortex

tag: cell description

value: Input

tag: antibody description

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

tag: age

tag: age description

value: Adult 8 weeks

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

value: Cortex/Input/std


title: LICR_ChipSeq_BoneMarrow_Input

value: LICR-m

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell organism

tag: cell sex

tag: controlid

value: tier 1


title: LICR_ChipSeq_Lung_H3K4me1

value: Lung

value: mouse

value: M

tag: antibody

tag: antibody antibodydescription

tag: antibody targetdescription

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: Lung/Input/std

tag: labversion

tag: replicate

tag: replicate description

tag: softwareversion


title: LICR_ChipSeq_Kidney_H3K4me3

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: cell

value: Kidney

tag: cell description

value: rabbit polyclonal

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

value: Millipore

tag: age

tag: age description

value: Kidney/Input/std

value: ELAND

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Lung_H3K4me3

value: LICR-m

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell organism

tag: cell sex

tag: antibody

value: Adult 8 weeks

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid


title: LICR_ChipSeq_Liver_H3K4me3

value: ChIP-Seq

value: Liver

value: mouse

value: M

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

value: Liver/Input/std

tag: labversion

tag: replicate

tag: replicate description

value: tier 1

tag: softwareversion


title: LICR_ChipSeq_Heart_H3K4me3

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: cell

value: Heart

tag: cell description

value: rabbit polyclonal

tag: age

tag: age description

value: Heart/Input/std

tag: strain

tag: strain description


title: Genotype 8×5 grown at 15°C

tag: Genotype 8X5, 15°C


title: LICR_ChipSeq_Liver_H3K4me1

tag: datatype

tag: datatype description

value: tissue

tag: cell organism

value: liver

tag: Sex

tag: antibody

tag: antibody antibodydescription

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

value: Abcam

tag: control

tag: control description

tag: controlid

value: liver/Input/std

value: ELAND


title: LICR_ChipSeq_Cerebellum_H3K4me1

tag: lab

value: LICR-m

tag: lab description

value: ChipSeq

value: Cerebellum

tag: cell sex

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

value: Adult 8 weeks

value: std

value: Standard input signal for most experiments.

value: Cerebellum/Input/std

tag: labversion

tag: replicate

tag: replicate description

tag: softwareversion

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_ES-Bruce4_H3K4me1

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

tag: datatype description

value: ChIP-Seq

tag: line

tag: cell organism

value: mouse

value: mouse embryonic stem cells

value: M

tag: age

tag: age description

value: Embryonic day 0 (stem cell)

value: 12/23/09 SOLEXA2 Lane 4

value: tier 1

tag: strain

tag: strain description


title: Genotype 5×8 grown at 25°C

tag: Genotype 5X8, 25°C


title: Genotype 5×8 grown at 15°C

tag: Genotype 5X8, 15°C


title: LICR_ChipSeq_Spleen_Input_adult-8wks

source_name: Spleen

tag: lab

tag: lab description

tag: cell

value: Spleen

tag: cell description

tag: cell sex

tag: antibody

value: Input

tag: antibody description

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

tag: control

tag: control description

tag: controlid

value: Spleen/Input/std

value: ELAND


title: LICR_ChipSeq_Spleen_H3K4me3_adult-8wks

value: LICR-m

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell organism

tag: antibody antibodydescription

value: rabbit polyclonal

tag: antibody targetdescription

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

value: Adult 8 weeks

value: std

tag: labversion

tag: replicate

tag: replicate description

tag: softwareversion

value: Bowtie


title: Genotype 8×5 grown at 20°C

tag: Genotype 8X5, 20°C


title: LICR_ChipSeq_Spleen_H3K4me1_adult-8wks

tag: lab

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

value: ChIP-Seq

value: tissue

value: mouse

tag: Sex

value: M

tag: antibody

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

value: Abcam

tag: age

tag: age description

value: Standard input signal for most experiments.

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: CSHL_RnaSeq_HUVEC_cell_longNonPolyA (superseded by GSE78600)

status: Public on Jul 29 2011

description:
****************************
GSM767856 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78600
****************************

source_name: HUVEC

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: rnaextract

value: longNonPolyA

tag: rnaextract description

value: Poly(A)- RNA longer than 200 nt

tag: biorep

tag: labexpid

value: iIDR

tag: readtype

tag: readtype description

value: Paired 76 nt directed reads

tag: spikeinpool

tag: localization description

value: Whole cell

value: Paired 76 n.t. directed reads

value: tier 1


title: CSHL_RnaSeq_HUVEC_nucleus_longNonPolyA (superseded by GSE78601)

description:
****************************
GSM767857 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78601
****************************

molecule: nuclear RNA

tag: labversion

tag: replicate

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA

tag: replicate description

value: tier 3


title: CSHL_RnaSeq_BJ_cell_longNonPolyA (superseded by GSE90243)

description:
****************************
GSM767855 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90243
****************************

source_name: BJ

tag: cell description

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID:9916803)


title: CSHL_RnaSeq_A549_cell_longNonPolyA (superseded by GSE90242)

description:
****************************
GSM767854 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90242
****************************

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


title: CSHL_RnaSeq_GM12878_cytosol_longNonPolyA (superseded by GSE90244)

description:
****************************
GSM767852 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90244
****************************

molecule: cytoplasmic RNA

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


title: LICR_ChipSeq_Cerebellum_Input

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: ChIP-Seq

tag: cell

value: Cerebellum

tag: cell organism

value: mouse

tag: cell sex

value: M

tag: antibody

value: Input

tag: antibody description

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

tag: age

tag: age description

value: Adult 8 weeks

tag: control

value: std

tag: control description

tag: controlid

value: Cerebellum/Input/std

tag: softwareversion

value: ELAND


title: CSHL_RnaSeq_HepG2_nucleus_longNonPolyA (superseded by GSE90248)

description:
****************************
GSM767850 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90248
****************************

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

value: hepatocellular carcinoma

tag: rnaextract

value: longNonPolyA

tag: rnaextract description

value: Poly(A)- RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Paired 76 nt directed reads

tag: spikeinpool

value: Paired 76 n.t. directed reads

value: tier 1


title: CSHL_RnaSeq_GM12878_nucleus_longNonPolyA (superseded by GSE90245)

description:
****************************
GSM767853 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90245
****************************

tag: cell description

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

tag: replicate

tag: replicate description


title: CSHL_RnaSeq_MCF-7_cell_longNonPolyA (superseded by GSE90241)

description:
****************************
GSM767851 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90241
****************************

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


title: CSHL_RnaSeq_H1-hESC_nucleus_longNonPolyA (superseded by GSE90253)

description:
****************************
GSM767841 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90253
****************************

growth_protocol: missing

tag: localization

value: nucleus

tag: localization description

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA

value: tier 2


title: CSHL_RnaSeq_H1-hESC_cytosol_longNonPolyA (superseded by GSE90252)

description:
****************************
GSM767842 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90252
****************************

value: cytosol

value: The fluid between the cells outer membrane and the nucleus


title: CSHL_RnaSeq_K562_cytosol_longNonPolyA (superseded by GSE90249)

description:
****************************
GSM767849 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90249
****************************


title: CSHL_RnaSeq_HeLa-S3_cell_longNonPolyA (superseded by GSE90247)

description:
****************************
GSM767847 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90247
****************************

tag: cell lineage

value: ectoderm


title: CSHL_RnaSeq_NHEK_cytosol_longNonPolyA (superseded by GSE78602)

description:
****************************
GSM767843 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78602
****************************

source_name: NHEK

value: RnaSeq

tag: cell sex

value: F

value: tier 3


title: CSHL_RnaSeq_NHEK_nucleus_longNonPolyA (superseded by GSE78603)

description:
****************************
GSM767846 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78603
****************************

tag: datatype

value: Sequencing analysis of RNA expression

value: longNonPolyA


title: K562-PRAME

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description: Chromatin IP with PRAME serum

data_processing: Reads (35 bp) were aligned to the human reference genome HG18 with eland and non-uniquely mappable reads were discarded. The number of Preimmune ChIP-seq reads was normalized to the slightly lower number of PRAME ChIP-seq reads. ChIP-seq reads were directionally extended to the length of the fragments used for sequencing, the number of overlapping sequence reads was determined for each base pair in the genome, averaged over a 10 bp window for visualization in the UCSC genome browser (Wiggle processed file). Peaks were called using MACS. Normalized expression values (NE) for RefSeq genes were computed from RNA-seq data with the Genomatix Region Miner tools.

source_name: Chromatin IP with PRAME serum

growth_protocol: K562 cells were cultured in standard conditions with RPMI medium with 10% FBS and antibiotics

extract_protocol: Cells were fixed in 1% formaldehyde for 15 minutes, chromatin extracted and sheared using a Bioruptor (Diagenode), immunoprecipitated using the antibodies indicated, purified and sequenced using Illumina Genome Analyzer.

tag: cell line

tag: antibody

value: PRAME (V27/S6)


title: CSHL_RnaSeq_HepG2_cytosol_longNonPolyA (superseded by GSE90256)

description:
****************************
GSM767840 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90256
****************************

tag: datatype description

value: hepatocellular carcinoma

tag: rnaextract

tag: rnaextract description

value: Poly(A)- RNA longer than 200 nt

value: iIDR

value: Paired 76 nt directed reads


title: K562-NFYA

description: Chromatin IP with NFYA Ab

source_name: Chromatin IP with NFYA Ab

value: NFYA (Santa Cruz H-209 sc-10779, Lot D2408)


title: CSHL_RnaSeq_HeLa-S3_nucleus_longNonPolyA (superseded by GSE90246)

description:
****************************
GSM767848 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90246
****************************

tag: biorep

tag: labexpid

tag: labversion

value: Paired 76 n.t. directed reads

value: tier 1


title: CSHL_RnaSeq_K562_nucleus_longNonPolyA (superseded by GSE90250)

description:
****************************
GSM767844 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90250
****************************

tag: readtype

tag: readtype description

tag: spikeinpool

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: CSHL_RnaSeq_HUVEC_cytosol_longNonPolyA

value: cytosol

tag: replicate

tag: replicate description


title: LICR_ChipSeq_ES-Bruce4_Input

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: ChIP-Seq

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: mouse embryonic stem cells

value: M

value: Input

tag: antibody description

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

tag: age

tag: age description

value: Embryonic day 0 (stem cell)

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: softwareversion

value: ELAND

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: K562-NFYB

description: Chromatin IP with NFYB Ab

source_name: Chromatin IP with NFYB Ab

tag: cell line

tag: antibody

value: NFYB (Diagenode pAb-007-100, Lot TF-0010)


title: K562-Preimmune

description: Chromatin IP with preimmune serum (control for PRAME ChIP)

value: preimmune serum (preV27)


title: mRNA_D21

city: Shantou

first: Zeng-Ming

last: Yang

address: 263 Daxue Road

department: Biology

country: China

institute: Shantou University

description: mRNA tag sequencing of the endometrium on day 21 of menstral cycle

data_processing: A computational pipeline was used to process the raw sequencing data. The fast format data were transformed into fasta format using fq_all2std.pl (http://maq.sourceforge.net/fq_all2std.pl). All reads without perfect matches to the most proximal 8 nt of the adaptor sequence (5'-UCGUAUGCCGUCUUCUGCUUGU-3') were first removed using an in-house perl script. Then adaptor-clean reads containing ambiguous bases were filtered out. Redundant reads were merged and the count number was calculated for each unique/non-redundant sequence. The processed files were provided with 2 columns. The first column holds the unique/non-redundant sequence.The second is the count number for the corresponding sequence.

organism: Macaca mulatta

growth_protocol: Healthy and mature female rhesus monkeys (Macaca mulatta) were housed singly in a controlled environment with a 12 h light/12 h dark cycle at the Fuzhou Non-human Primate Research Center (Fujian, China). This study design was approved by the Institutional Animal Care and Use Committee of Xiamen University (XMUEA-0080).

extract_protocol: mRNAs were isolated through binding to a magnetic oligo(dT) beads. First strand cDNA was synthesized using the binding mRNA as a template, and followed by the synthesis of the second strand of cDNA. After cDNAs were digested with DpnII, the double stranded cDNA fragment attached to the oligo(dT) bead was collected and ligated to a GEX DpnII adapter 1 at the site of DpnII cleavage. The sequence for MmeI was included in GEX DpnII adapter 1. After purification, products coupled with oligo(dT) bead were digested with MmeI to create a 16 bp tag, followed by ligating to a GEX adapter 2 at the site of MmeI cleavage. After PCR amplification, the purified DNA fragments were used directly for sequencing using the Illumina Cluster Station in Shenzhen Huada Gene Sci-Tech Company.

treatment_protocol: All female rhesus monkeys were evaluated daily by visual examination of the perineum for menses, with the onset of menses defined as day 1 of the menstrual cycle. Female rhesus monkeys showing at least two consecutive menstrual cycles of approximately 28 days were chosen for the study. Estrogen measurement was performed to calculate ovulation and period dates as a double check (26). Endometrial tissues were collected on day 15 (pre-receptive phase, n=3) and day 21 (receptive phase, n=3) of menstrual cycle by hysterectomy. Samples were flash-frozen in liquid nitrogen and stored at -80 °C for further analysis.

tag: tissue

value: endometrium

tag: menstral cycle day


title: mRNA_D15

description: mRNA tag sequencing of the endometrium on day 15 of menstral cycle

treatment_protocol: All female rhesus monkeys were evaluated daily by visual examination of the perineum for menses, with the onset of menses defined as day 1 of the menstrual cycle. Female rhesus monkeys showing at least two consecutive menstrual cycles of approximately 28 days were chosen for the study. Estrogen measurement was performed to calculate ovulation and period dates as a double check (26). Endometrial tissues were collected on day 15 (pre-receptive phase, n=3) and day 21 (receptive phase, n=3) of menstrual cycle by hysterectomy. Samples were flash-frozen in liquid nitrogen and stored at -80 Â°C for further analysis.


title: K562-RNA

description: Gene expression analysis on poly(A)+ RNA

extract_protocol: After total RNA extraction, poly(A)+ RNA was purified, chemically fragmented, converted to double-stranded cDNA and sequenced using Illumina Genome Analyzer.


title: CSHL_RnaSeq_HeLa-S3_cytosol_longNonPolyA (superseded by GSE90255)

description:
****************************
GSM767838 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90255
****************************

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell lineage

value: ectoderm

tag: rnaextract

value: longNonPolyA

tag: rnaextract description

value: Poly(A)- RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Paired 76 nt directed reads

tag: spikeinpool

value: Paired 76 n.t. directed reads

tag: replicate

tag: replicate description

value: tier 2


title: DG690_S5_HU

city: Cold Spring Harbor

first: Mikel

last: Zaratiegui

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

description: S5 phosphorylated RNA polII in dcr1 KO arrested cells

data_processing: Analysis was carried out by a custom pipeline using Bowtie to align reads to the S. pombe genome and MACS 1.4 for significance enrichment calls. The Bed files on the Series record were generated by MACS (http://liulab.dfci.harvard.edu/MACS/) and represent the areas of significant difference between two genotypes (WT vs dcr1-). MACS allows for direct comparison of ChIP-seq signal, as long as the strains used do not differ much in sequence. This experiment was done in two different conditions (log phase vs HU treatment).

source_name: cells

growth_protocol: Samples were grown to OD=0.2 in YEA media.

extract_protocol: Chromatin was purified, sonicated and incubated with following anti-RNA Polymerase II antibodies from Abcam: clone pospho-S2 (ab5095), and clone phospho-S5 (ab5131). For ChIP-seq, immunoprecipitated DNA was polished, ligated and amplified with the Illumina ChIP-seq sample preparation kit according to the manufacturerâs instructions. Average insert size 145bp.

treatment_protocol: Samples from log phase dg21 and dg690 S. pombe strains were fixed (dividing cells) or first treated with 15mM hydroxyurea (HU) (Sigma) for 4.5 hr, washed once in HU free media and fixed (HU arrested cells)

tag: genotype

value: Delta-dcr1::kanMX6, otr1R(SphI)::ura4, ura4-DS/E, ade6-210, leu1-32, his7-366

tag: strain

tag: developmental stage

value: arrested

tag: chip antibody

value: Abcam ab5131

tag: average insert size + standard dev


title: sRNA_D21

description: small RNA deep sequencing of endometrium on day 21 of menstral cycle

extract_protocol: Total RNAs were extracted by TRIzol (Invitrogen), followed by a 15% Tris-borate-EDTA (TBE) urea gel electrophoresis. Small RNAs were separated by the size of 18-30 bases from the gel. After purification, small RNAs were ligated to a 5' RNA adapter (5'-GUUCAGAGUUCUACAGUCCGACGAUC-3'). Followed by another TBE gel purification and ligated to a 3' RNA adapter (5'- pUCGUAUGCCGUCUUCUGCUUGidT -3'), the purified small RNAs were reverse transcribed using Illumina's small RNA RT-Primer (5'-CAAGCAGAAGACGGCATACGA-3') and amplified by a 15 cycle PCR using Illumina's small RNA primer set (5'-CAAGCAGAAGACGGCATACGA-3' and 5'-AATGATACGGCGACCACCGA-3'). PCR products were purified and quantified for Illumina sequencing in Shenzhen Huada Gene Sci-Tech Company (Shenzhen, China).

tag: tissue

tag: menstral cycle day


title: DG690_S2_HU

description: S2 phosphorylated RNA polII in dcr1 KO arrested cells

value: Abcam ab5095


title: DG21_S2_HU

description: S2 phosphorylated RNA polII in wt arrested cells


title: DG690_S2_EXP

description: S2 phosphorylated RNA polII in dcr1 KO dividing cells

value: dividing


title: DG690_S5_EXP

description: S5 phosphorylated RNA polII in dcr1 KO dividing cells


title: DG21_S5_EXP

description: S5 phosphorylated RNA polII in wt dividing cells


title: CSHL_RnaSeq_SK-N-SH_RA_cell_longNonPolyA (superseded by GSE90251)

description:
****************************
GSM767845 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90251
****************************

treatment_protocol: retinoic acid

tag: datatype

tag: datatype description

tag: cell description

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

tag: rnaextract

value: tier 1


title: sRNA_D15

description: small RNA deep sequencing of the endometrium on day 21 of menstral cycle

value: endometrium


title: DG21_S2_EXP

description: S2 phosphorylated RNA polII in wt dividing cells


title: DG21_S5_HU

description: S5 phosphorylated RNA polII in wt arrested cells


title: Anthers at 2mm length

status: Public on Jul 28 2011

first: John

middle: F

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description:
Anthers at 2mm length
other (Electrophorese RNA+adaptor ligation samples at 200V for 1 hr.  Stain gels for 2 minutes in 50 ml EtBr/1xTBE solution.  Cut out 40-60 nt gel slices using the Dark Reader.)

data_processing: Tag files were produced via Illumina processing pipeline and simply provide the abundance of each unique sequence in the raw sequence file (includes partial adaptor sequence).

organism: Zea mays

source_name: anthers

growth_protocol: Field-grown under normal conditions.

extract_protocol: RNA was initially extracted using TriReagent from Sigma Chemical exactly as described in the Instruction Manual, dissolved in 0.02 M tris-HCl, pH 7.8,  0.25 M NaCl, 5 mM EDTA and 0.5% SDS, extracted with 2 volumes phenol-chloroform followed by additional extraction with 2 volumes of chloroform.

tag: Stage

value: 2mm anthers

tag: cultivar

value: anther

tag: environment

value: field-grown