title: ChIP-Seq analysis of H3K4me3 in human cultured CD34 cells; 30E62AAXX090709-7-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12900
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2239
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2238
****************
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: GSM537629_BI.CD34_Cultured_Cells.H3K4me3.cultured_CD34_2_20_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30E62AAXX090709-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD34 Cultured Cells, Donor cultured CD34_2/20/09 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.4696
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.5108
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4645
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9885
IROC_PERCENTILE: 5
POISSON_SCORE: 0.5793
POISSON_PERCENTILE: 73

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

ANALYSIS FILE NAME: GSM537629_BI.CD34_Cultured_Cells.H3K4me3.cultured_CD34_2_20_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30E62AAXX090709-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD34 Cultured Cells, Donor cultured CD34_2/20/09 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.4970
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD34 H3K4me3 20
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells Histone H3K4me3 Donor cultured CD34_2/20/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.5108
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4645
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9885
IROC_PERCENTILE: 5
POISSON_SCORE: 0.5793
POISSON_PERCENTILE: 73

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

source_name: flow sorted CD34+ cells from cord blood expanded in short term culture; 30E62AAXX090709-7-S

value: FHCRC

value: Primary Cell

value: CD34 Cultured Cells

value: cultured CD34_2/20/09

value: short term

value: Histone H3K4me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Millipore


title: Chromatin accessibility assay of Fetal Kidney Primary Tissue; DS12635

status: Public on Apr 28 2010

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS12635
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2462
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2461
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM530655_UW.FetalKidney.ChromatinAccessibility.fKidney-DS12635.wig
ANALYSIS ALIAS: UW.FetalKidney.ChromatinAccessibility.DS12635
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Kidney 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2646
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM530655_UW.Fetal_Kidney.ChromatinAccessibility.H-22676.DS12635.bed
ANALYSIS ALIAS: DS12635.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-22676, Library DS12635 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.4111
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5644
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.4251
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9916
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4979
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM530655_UW.Fetal_Kidney.ChromatinAccessibility.H-22676.DS12635.wig
ANALYSIS ALIAS: DS12635.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Kidney, Donor H-22676, Library DS12635 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.4071
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 2
BROWSER_TRACK_NAME: FK DNase 76 35
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-22676 Library DS12635 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5644
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.4251
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9916
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4979
POISSON_PERCENTILE: 40

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal Kidney primary tissue, day 122; DS12635

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

value: genomic DNA

tag: disease

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

value: Primary Tissue

value: fetal kidney

value: UW

value: fetal

value: 122 days

value: Unknown

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol


title: mouse_ES_input

status: Public on Apr 27 2010

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description: input DNA

data_processing:
Sequenced tags of 51 bp in length were mapped to the mouse genome (build mm9) using Bowtie aligner. Only uniquely mapped tags with no more than two mismatches in the first 28 base pairs of the read were retained. Positions in genome with the numbers of mapped tags above the significance threshold defined by a Z-score of 7 were identified as anomalous, potentially resulting from amplification bias, and the tags mapped to those positions were discarded. The tag frequency at each genome position was calculated separately for DNA positive and negative strands.

The tab files (processed data) provide information about binding of lysine demethylase enzyme KDM2A in mouse embryonic stem cells.
The tab files (input.tab and kdm2a.tab) list Solexa read coordinates for the input and IP samples used in ChIP-Seq experiment.
The format of these files is as follows:
<chromosome> <strand> <coordinate> <read count in the library>

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: Murine V6.5 ES cells (C57BL/6(F) x 129/sv(M)) were cultured on inactivated MEFs in DMEM supplemented with 15% FCS, leukemia-inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino-acids.  Prior to use in ChIP experiments, V6.5 cells were cultured for two passages under feeder-free conditions on 0.2% gelatin

extract_protocol: Chromatin Immunoprecipitation was performed with a KDM2A-specific antibody.  ChIP DNA was prepared for Illumina Genome Analyzer II sequencing using by blunting the DNA with a mixture of T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK (NEB) according to manufacturer's instruction. dA overhangs were then added and Illumina adapters ligated. Adapter-ligated DNA was subject to 18 cycles of PCR before size selection by agarose gel electrophoresis. Amplified DNA was purified using the Qiaquick gel extraction kit (Qiagen). The purified DNA was quantified both with an Agilent Bioanalyzer and Invitrogen Qubit and diluted to a working concentration of 10 nM prior sequencing. Sequencing on a Illumina Genome Analyzer II instrument was carried out according to the manufacturer’s instructions.

tag: strain

tag: cell type

value: V6.5 embryonic stem cells

tag: chip antibody


title: mouse_ES_KDM2A

description: Chromatin IP against KDM2A


title: Chromatin accessibility assay of Fetal Heart Primary Tissue; DS12531

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS12531
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2453
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2452
****************
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: GSM530654_UW.FetalHeart.ChromatinAccessibility.fHeart-DS12531.wig
ANALYSIS ALIAS: UW.FetalHeart.ChromatinAccessibility.DS12531
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Heart 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2636
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM530654_UW.Fetal_Heart.ChromatinAccessibility.H-22662.DS12531.bed
ANALYSIS ALIAS: DS12531.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-22662, Library DS12531 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.4118
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6641
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.5319
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9959
IROC_PERCENTILE: 30
POISSON_SCORE: 0.5904
POISSON_PERCENTILE: 85

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

ANALYSIS FILE NAME: GSM530654_UW.Fetal_Heart.ChromatinAccessibility.H-22662.DS12531.wig
ANALYSIS ALIAS: DS12531.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Heart, Donor H-22662, Library DS12531 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.4078
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 2
BROWSER_TRACK_NAME: FH DNase 62 31
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-22662 Library DS12531 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6641
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.5319
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9959
IROC_PERCENTILE: 30
POISSON_SCORE: 0.5904
POISSON_PERCENTILE: 85

source_name: Fetal Heart primary tissue, day 96; DS12531

value: fetal heart

value: 96 days


title: short RNA from Mucor circinelloides DCL2 mutant

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

country: United Kingdom

institute: University of East Anglia

description: Total endogenous short RNA from Mucor circinelloides DCL2 knockout

library_source: transcriptomic

data_processing: Removed adaptors. Sequences without adapters were discarded. Mapped sequences to genome sequence (http://genome.jgi-psf.org/Mucci1/download/assembly/Mucci1_genomic_scaffolds.fasta.gz).

molecule: total RNA

organism: Mucor circinelloides

source_name: dcl2- fungus grown on plate (YPG media, pH:4.5; 48hours)

growth_protocol: Mucor circinelloides was grown on plate (YPG media, pH:4.5; 48hours)

extract_protocol: Total RNA was extracted using the miRVana kit by Ambion

tag: original entry

value: 48 hours culture on plate containing mycelium and spores

tag: genotype

value: dcl2 mutant


title: Chromatin accessibility assay of human CD34 Primary Cells; DS12339

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: DS12339
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2398
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2397
****************
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: GSM530652_UW.CD34.ChromatinAccessibility.CD34+-DS12339.wig
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.DS12339
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cell Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from CD34 Primary Cells 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2638
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM530652_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01536.DS12339.bed
ANALYSIS ALIAS: DS12339.hg19.level.1
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 01536, Library DS12339 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.4131
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.4797
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.3943
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9966
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4442
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM530652_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01536.DS12339.wig
ANALYSIS ALIAS: DS12339.hg19.level.2
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 01536, Library DS12339 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.4091
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 2
BROWSER_TRACK_NAME: MCD34 DNase 36 39
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01536 Library DS12339 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.4797
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.3943
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9966
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4442
POISSON_PERCENTILE: 25

source_name: flow sorted CD34+ cells from cord blood; DS12339

value: FHCRC HEIMFELD

value: Primary Cell

value: CD34 Primary Cells

tag: markers

value: 27 years

value: Female

value: Hispanic


title: Chromatin accessibility assay of Fetal Heart Primary Tissue; DS12810

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS12810
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2457
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2456
****************
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: GSM530661_UW.FetalHeart.ChromatinAccessibility.fHeart-DS12810.wig
ANALYSIS ALIAS: UW.FetalHeart.ChromatinAccessibility.DS12810
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Heart 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2637
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM530661_UW.Fetal_Heart.ChromatinAccessibility.H-22727.DS12810.bed
ANALYSIS ALIAS: DS12810.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Heart, Donor H-22727, Library DS12810 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.4135
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5488
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.3944
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9944
IROC_PERCENTILE: 22
POISSON_SCORE: 0.5928
POISSON_PERCENTILE: 87

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

ANALYSIS FILE NAME: GSM530661_UW.Fetal_Heart.ChromatinAccessibility.H-22727.DS12810.wig
ANALYSIS ALIAS: DS12810.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Heart, Donor H-22727, Library DS12810 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.4095
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 2
BROWSER_TRACK_NAME: FH DNase 27 10
BROWSER_TRACK_DESCRIPTION: UW Fetal Heart DNase Hypersensitivity Donor H-22727 Library DS12810 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5488
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.3944
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9944
IROC_PERCENTILE: 22
POISSON_SCORE: 0.5928
POISSON_PERCENTILE: 87

source_name: Fetal Heart primary tissue, day 101; DS12810

value: genomic DNA

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

value: Primary Tissue

value: UW

value: fetal

value: 101 days


title: Input DNA Hs68-FBS

city: Barcelona

first: Klaus

last: Fortschegger

address: C/ Dr. Aiguader 88

department: Gene Regulation

country: Spain

institute: Center for Genomic Regulation

data_processing:
Sequences were mapped to human genome (NCBI36/hg18) using GEM-mapper (open source software from Paolo Ribeca) allowing less than 3 mismatches.
Wiggle files were created from reads unambiguously mapped to NCBI36/hg18 using ChIP-center tool (http://ccg.vital-it.ch/chipseq/chip_center.html; tag shift 60bp; count cut-off 10; resolution 20bp).
Peaks were called using Genomatix RegionMiner (unambiguously mapped reads; window 100bp; Poisson threshold). Clusters overlapping with regions also called in respective negative control were filtered out later.

growth_protocol: Cells were grown in DMEM with antibiotics and with or without 10 % FCS as indicated.

extract_protocol: Cells were fixed in 1% formaldehyde for 10 min at RT. Lysed material was sonicated (Diagenode Bioruptor) and ChIP was performed with 2 µg of antibody and chromatin containing approx. 10 µg of genomic DNA. On average 10 ng of DNA were IPed and used for end repair, adapter ligation and pre-amplification. Fragments of 135 +/- 25 bp (adapters excluded) were selected, used for cluster generation and sequenced by Solexa/Illumina (36 - 50 nucleotide read length).

treatment_protocol: Hs68 cells were grown in medium without FCS for 4 days and either processed directly (serum-starved) or after 4 hours of restimulation (serum-stimulated).

tag: cell line

tag: culture condition

value: 4 days without serum

value: none (Input DNA )


title: Input DNA Hs68+FBS

value: 4 days without, 4 hours with serum


title: H3K4me3 ChIP-seq Hs68+FBS

value: rabbit Abcam ab8580 (H3K4me3)


title: H3K4me3 ChIP-seq Hs68-FBS


title: Normal IgG ChIP-seq HeLa

source_name: HeLa S3

value: HeLa S3

value: with serum

value: rabbit Santa Cruz sc-2027 (normal IgG)


title: short RNA from Mucor circinelloides DCL1 mutant

description: Total endogenous short RNA from Mucor circinelloides DCL1 knockout

source_name: dcl1- fungus grown on plate (YPG media, pH:4.5; 48hours)

value: 48 hours culture on plate containing mycelium and spores

value: dcl1 mutant


title: PHF8 ChIP-seq Hs68+FBS

value: rabbit Abcam ab35471 (PHF8)


title: Chromatin accessibility assay of IMR90 Cell Line; DS13229

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS13229
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2437
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632
****************
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: GSM530666_IMR90-DS13229.uniques.36.hg18.bed
ANALYSIS ALIAS: DS13229-align
ANALYSIS TITLE: Alignments DS13229
ANALYSIS DESCRIPTION: Eland alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome NCBI Build 36 (hg18)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Eland
SOFTWARE_VERSION: 1.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

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

ANALYSIS FILE NAME: GSM530666_UW.IMR90.ChromatinAccessibility.IMR90-DS13229.wig
ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.DS13229
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the IMR90 Cell Line 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2650
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM530666_UW.IMR90.ChromatinAccessibility.DS13229.bed
ANALYSIS ALIAS: DS13229.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the IMR90 Cell Line, Library DS13229 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.4103
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 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.4505
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.3425
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9962
IROC_PERCENTILE: 35
POISSON_SCORE: 0.4422
POISSON_PERCENTILE: 22

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

ANALYSIS FILE NAME: GSM530666_UW.IMR90.ChromatinAccessibility.DS13229.wig
ANALYSIS ALIAS: DS13229.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the IMR90 Cell Line, Library DS13229 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.4063
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 2
BROWSER_TRACK_NAME: IMR90 DNase 29 29
BROWSER_TRACK_DESCRIPTION: UW IMR90 Cell Line DNase Hypersensitivity Library DS13229 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.4505
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.3425
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9962
IROC_PERCENTILE: 35
POISSON_SCORE: 0.4422
POISSON_PERCENTILE: 22

source_name: IMR90 Cell Line; DS13229

value: IMR90 cells

value: ATCC

value: Cell Line

tag: line

tag: lineage

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Eagle's Minimum Essential Medium, Catalog No. 30-2003.

tag: Sex

value: Female

tag: batch

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol


title: PHF8 ChIP-seq Hs68-FBS

value: 4 days without serum


title: short RNA from Mucor circinelloides DCL double mutant

description: Total endogenous short RNA from Mucor circinelloides DCL1/DCL2 knockout

source_name: fungus grown on plate (YPG media, pH:4.5; 48hours)

value: dcl1-/dcl2- 48 hours culture on plate containing mycelium and spores

value: dcl1 dcl2 double mutant


description: Total endogenous short RNA from Mucor circinelloides wildtype

source_name: wildtype fungus grown on plate (YPG media, pH:4.5; 48hours)

value: wild type


title: PHF8 ChIP-seq 293T

value: with serum


title: PHF8 ChIP-seq HeLa

value: HeLa S3


title: short RNA from Mucor circinelloides RDR2 mutant

description: Total endogenous short RNA from Mucor circinelloides RDR2 knockout

source_name: rdr2- fungus grown on plate (YPG media, pH:4.5; 48hours)

value: 48 hours culture on plate containing mycelium and spores

value: rdr2 mutant


title: Vitis vinifera leaf parallel analysis of RNA ends

status: Public on Apr 29 2010

description: Total RNA degradome from Vitis vinifera cv. Pinot noir, clone ENTAV115

data_processing: Removed adaptors. Sequences without adapters were discarded.

organism: Vitis vinifera

source_name: Vitis vinifera cv. Pinot noir, clone ENTAV115, leaves and stem

growth_protocol: Samples were collected from plants grown in growth chambers at 25 degrees celcius, photoperiod 14h-10h d/n.

extract_protocol: Isolated polyadenilated RNA from total RNA extracts of  Vitis vinifera leaves, were ligated to 5'-adapter that include san MmeI recognition site. The ligated products were purified again, reverse transcribed and cleaved with MmeI. The 5' fragments were purified from gel and to a 3'- dsDNA adapter and PCR amplified. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

tag: tissue

value: RNA extracted from stem and leaves


title: ChIP-Seq analysis of H3K36me3 in human cultured CD34 cells; 42LP1AAXX090808-7-S

city: Cambridge

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12291
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2218
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2217
****************
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: GSM537655_BI.CD34_Cultured_Cells.H3K36me3.cultured_CD34_2_20_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LP1AAXX090808-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD34 Cultured Cells, Donor cultured CD34_2/20/09 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.4639
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.472
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.3809
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9815
IROC_PERCENTILE: 72
POISSON_SCORE: 0.6233
POISSON_PERCENTILE: 76

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

ANALYSIS FILE NAME: GSM537655_BI.CD34_Cultured_Cells.H3K36me3.cultured_CD34_2_20_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LP1AAXX090808-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD34 Cultured Cells, Donor cultured CD34_2/20/09 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.4913
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD34 H3K36me3 20
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells Histone H3K36me3 Donor cultured CD34_2/20/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.472
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.3809
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9815
IROC_PERCENTILE: 72
POISSON_SCORE: 0.6233
POISSON_PERCENTILE: 76

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

source_name: flow sorted CD34+ cells from cord blood expanded in short term culture; 42LP1AAXX090808-7-S

tag: molecule

value: genomic DNA

value: FHCRC

value: Primary Cell

value: CD34 Cultured Cells

value: cultured CD34_2/20/09

value: Unknown

value: short term

value: Histone H3K36me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Abcam


title: short RNA from Mucor circinelloides RDR1 mutant

description: Total endogenous short RNA from Mucor circinelloides RDR1 knockout

source_name: rdr1- fungus grown on plate (YPG media, pH:4.5; 48hours)

value: 48 hours culture on plate containing mycelium and spores

value: rdr1 mutant


title: Normal IgG ChIP-seq 293T

value: with serum

value: rabbit Santa Cruz sc-2027 (normal IgG)


title: e9p5_rep4

status: Public on Apr 26 2010

first: H. Rosaria

last: Chiang

address: 9 Cambridge Center

department: Biology

institute: MIT/Whitehad Institute

description: sample name: FC4004.7

data_processing: Small RNA sequences 16-27 nt long are provided with the number of reads for each unique sequence. Small RNA 5p ends were observed as the 5p end of the Illumina read. Small RNA 3p ends were determined using matches to ligated linker sequences.

source_name: day 9.5 embryo

extract_protocol: The small RNA cDNA libraries were made as described (Grimson et al. 2008), except for the 3' adaptor ligation, which was 5' adenylated pTCGTATGCCGTCTTCTGCTTGidT. For a detailed protocol, see http://web.wi.mit.edu/bartel/pub/protocols.html.

value: day 9.5 embryo

value: small RNA


title: e7p5_rep4

description: sample name: FC4004.8

source_name: day 7.5 embryo

value: day 7.5 embryo


title: e12p5_rep4

description: sample name: FC4004.6

source_name: day 12.5 embryo

value: day 12.5 embryo


title: newborn_rep4

description: sample name: FC4004.5

source_name: newborn

value: whole newborn


title: e7p5_rep1

description: sample name: FC3241.3


title: newborn_rep1

description: sample name: FC3241.2


title: e7p5_rep3

description: sample name: FC3983.8


title: e9p5_rep1

description: sample name: FC3241.6


title: newborn_rep3

description: sample name: FC3983.5


title: e9p5_rep3

description: sample name: FC3983.7


title: e7p5_rep2

description: sample name: FC3500.8


title: e9p5_rep2

description: sample name: FC3500.7


title: brain_rep3

description: sample name: FC3983.4

source_name: brain

value: brain


title: e12p5_rep2

description: sample name: FC3500.6


title: brain_rep4

description: sample name: FC4004.4


title: newborn_rep7

description: sample name: FC5282.3


title: e12p5_rep3

description: sample name: FC3983.6


title: newborn_rep2

description: sample name: FC3500.5


title: e12p5_rep1

description: sample name: FC3241.8


title: ovary_rep4

description: sample name: FC4004.2

source_name: ovary

value: ovary


title: CD4_S2_phos_Pol2_ChIPSeq

status: Public on Apr 25 2010

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

description: Chromatin IP against serine 2 phospho Pol II

data_processing: Illumina Genome Analyzer Pipeline produced short sequence reads that were matched to the hg18 human genome using ELAND alignment algorithm.

source_name: CD4+ T cells, ChIP_Seq

extract_protocol: CD4+ T cells were purified from human blood using human CD4+ T cell isolation kit II kits (Miltenyi). For chromatin immunoprecipitation (ChIP) using  antibodies for S2P-PolII, the formaldehyde cross-linked cells were sonicated to obtain DNA fragments ranging in size from ~200 bp. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) .

value: CD4+ T cells


title: brain_rep1

description: sample name: FC3241.7


title: ovary_rep1

description: sample name: FC3241.4


title: CD4_Pol3_ChIPSeq

description: Chromatin IP against Pol III (RPC155)

extract_protocol: CD4+ T cells were purified from human blood using human CD4+ T cell isolation kit II kits (Miltenyi). For chromatin immunoprecipitation (ChIP) using  antibodies for PolIII, the formaldehyde cross-linked cells were sonicated to obtain DNA fragments ranging in size from ~200 bp. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) .

value: anti-PolIII


title: brain_rep2

description: sample name: FC3500.4


title: ovary_rep2

description: sample name: FC3500.2


title: HeLa_H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

source_name: HeLa, ChIP_Seq

growth_protocol: HeLa cells were maintained in Dulbeccos modified Eagles medium (DMEM) supplemented with 10% fetal bovine serum and 1 mM glutamine.

extract_protocol:
MNase digested, mononucleosome sized DNA fragments were used for chromatin immunoprecipitation (ChIP) using  antibodies for H3K4me3.
Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) .

value: HeLa


title: newborn_rep5

description: sample name: FC5282.1


title: 293cand4_rep1

description: sample name: 293cand

source_name: transfected with candidate hairpins

value: HEK293T cell line


title: 293cand5_rep2

description: sample name: 293RC3-2


title: ovary_rep3

description: sample name: FC3983.2


title: 293DroshaTN_cand5

description: sample name: 293DroshaTN_RC3

source_name: transfected with TNDrosha and hairpin plasmids


title: 293cand4_rep2

description: sample name: 293cand-2


title: CD4_totalRNA_RNAseq

description: RNA-seq experiment for total RNA in CD4+ cells

source_name: CD4+ T cells, RNA_Seq

extract_protocol:
CD4+ T cells were purified from human blood using human CD4+ T cell isolation kit II kits (Miltenyi).
Total RNAs were prepared using miRNeasy kit from Qiagen. rRNA was depleted from total RNA by hybridization to biotinylated oligonucleotides using Invitrogen Ribominus kit. The resulting RNAs were reverse-transcribed using random primers, converted to double-stranded cDNAs, sonicated and ligated to Solexa adaptors for sequencing.

value: CD4+ T cell


title: HeLa_TFIIIC_ChIPSeq

description: Chromatin IP against TFIIIC 220

extract_protocol: For chromatin immunoprecipitation (ChIP) using  antibodies for TFIIIC, the formaldehyde cross-linked cells were sonicated to obtain DNA fragments ranging in size from ~200 bp. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) .

value: anti-TFIIIC


title: HeLa_TFIIIB_ChIPSeq

description: Chromatin IP against Brf1

extract_protocol: For chromatin immunoprecipitation (ChIP) using  antibodies for TFIIIB (Brf1), the formaldehyde cross-linked cells were sonicated to obtain DNA fragments ranging in size from ~200 bp. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) .


title: testes_rep1

description: sample name: FC3241.5

source_name: testes

value: testes


title: testes_rep4

description: sample name: FC4004.3


title: 293GFP

description: sample name: 293GFP

source_name: transfected with GFP plasmid


title: 293Red

description: sample name: 293Red_TN

source_name: transfected with dsRed plasmid


title: Thymocytes_wt_H3K4me3

status: Public on Apr 20 2010

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description: WT thymocytes; H3K4me3 IP

data_processing:
Image analysis, base calling, quality filtering: Standard settings of GAPipeline 1.3+ using PhiX control; Fastq files contain full length reads (36nts) that passed the chastity filter. Qualities are phred64.
Alignment and peak finder: Nucleotides 1-35 of reads were aligned with Bowtie 0.9.9.3 against mm9, allowing 1 mismatch. Reads that aligned uniquely were then filtered to remove redundancy and SICER 1.0.3 was used to identify regions with higher read density than expected from a random background model. A bedGraph-formated file of the peaks was created by normalizing density to 1M aligned reads.

source_name: Total thymocytes

extract_protocol:
Flow cytometry: Developing lymphocytes were analyzed or purified by flow cytometry using a Becton-Dickinson FACS Caliber or FACS Aria. Cells were stained with the following antibodies from BD Biosciences: anti-mouse CD4-PE (#553653), anti-mouse CD8-PE-Cy5 (#553034).  Thymocytes were almost entirely CD4+CD8+ pre-T cells.
Chromatin immunoprecipitation - A) Crosslinking and sonication of chromatin: Thirty million cells were resuspended in 9 ml RPMI/2% fetal bovine serum in a 15 ml conical tube and 0.25 ml of 37% formaldehyde (J. B. Baker #2106-10) were added and the tube rocked for 15 min at room temperature (RT). Glycine (American Bioanalytical #56-40-6) was added to a final concentration of 0.125 M using a 1.25 M stock solution (pH 7.4) to terminate crosslinking.  Cells were pelleted (3K, 3 min, 4°C) and washed twice with 10 ml cold PBS. Wash solutions contained 1 mM PMSF and 1 ug/ul pepstatin A, which were included in all subsequent steps.  After the second wash, cells were resuspended in 1 ml PBS and transferred to a 1.5 ml microfuge tube, pelleted (3K, 3 min, 4°C), and the supernatant removed.  Unless used immediately, cell pellets were frozen on dry ice and stored at -80°C. A cell pellet was resuspended in 600 ul RIPA buffer (10 mM Tris pH 7.4, 1 mM EDTA, 1% TritonX100, 0.1% sodium deoxycholate, 0.1% SDS) containing 0.8 M NaCl and incubated for 10 min on ice.  Chromatin was sheared using a water bath sonicator (Diagenode) (4 x 5 min, high power) resulting in DNA of 300 to 500 bp.  Samples were centrifuged (14K, 10 min, 4°C) and the supernatant transferred to a new microfuge tube. If not used immediately, 0.1 vol 50% glycerol was added and the sheared chromatin was stored at -80°C.  Chromatin derived from 3-5 million cells was used for one ChIP experiment (one IP with a single antibody).
B) Pre-clearing of chromatin with Protein G beads: To create sufficient Protein G beads loaded with rabbit Ig to pre-clear the chromatin from 20 million cells, the following were mixed:  25 ul (bed volume) of magnetic Protein G agarose beads (Invitrogen #100-03D), 40 ul normal rabbit serum (Invitrogen, #16120-099), and 40 ul PBS.  The mixture was rocked for 15 min at RT, spun (3K, 1 min), the pellet washed twice with 1 ml RIPA (0.8 M NaCl), and the buffer removed. A 10X volume of RIPA (0.8 M NaCl) was added to sheared chromatin, and the chromatin was then added to the rabbit Ig-loaded beads and rocked 1 hr at 4°C.  Beads sedimented and the supernatant transferred to a new tube which contained a second batch of rabbit Ig-loaded beads, and rocked 1 hr at 4°C.  Beads were sedimented again and the supernatant transferred to new tube.  The precleared chromatin was stored at -80°C in aliquots if not used immediately.
C) Immunoprecipitation: Precleared chromatin was mixed with 2% fish skin gelatin (Sigma G7756) and 0.5 mg/ml heparin (Sigma H6279), BSA (final concentration 0.5 ug/ul), and 5 ug anti-RAG1, anti-RAG2 or anti-H3K4me3 and rocked at 4°C overnight.  The binding reaction was centrifuged to remove any particulate matter (14K, 10 min, 4°C) and the supernatant transferred to a new tube containing 5 ul (bed volume) protein G beads (preblocked with 2% BSA for 1 hr at RT). This mixture was rocked for 3 hr at 4°C, beads were sedimented magnetically, and washed three times (10 min, 4°C) with 1 ml RIPA (0.8 M NaCl) containing 1 mM DDT, 100 mM PMSF, then once (10 min, 4°C) with 1 ml RIPA (0.3 M NaCl) containing 1 mM DDT, 100 mM PMSF, then once (10 min, 4°C) with 1 ml RIPA containing 1 mM DDT, 100 mM PMSF, and finally once (10 min, 4°C) with 1 ml TE (10 mM Tris-HCl (pH 7.4), 1 mM EDTA).  Beads were resuspended in 100 ul TE containing 50 ug Proteinase K and 0.25% SDS, and incubated at 60°C overnight.  Proteinase K digests were extracted with 100 ul phenol/chloroform and after transferring the aqueous phase to a new tube, the organic phase was back extracted with 100 ul of water, and the aqueous phases were pooled.  The aqueous material was extracted with 200 ul chloroform and after transferring the aqueous phase to a new tube, the organic phase was back extracted with 200 ul of water, and the aqueous phases were pooled. NaCl was added to a final concentration of 0.2 M and DNA precipitated with 20 ug glycogen and 1 ml ethanol.  The DNA pellet was washed with 70% ethanol and resuspended in 50 ul water.
D) Library preparation: For the RAG2 antibody, three immunoprecipitations (each using chromatin from 30 x 106 cells) were pooled to obtain sufficient DNA for sequencing. The ChIP DNA ends were repaired using PNK and Klenow enzymes, followed by treatment with Taq polymerase to generate a protruding 3? A base used for Illumina adaptor ligation. ChIP DNA was then amplified using adaptor primers for 17 cycles and fragments of approximately 200 bp (mononucleosome + adaptors) were isolated using an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis.

value: WT

value: primary cells

value: total thymocytes

value: H3K4me3 (#07-473, Millipore)


title: 293DcrTN_cand5

description: sample name: 293DcrTN_RC3

source_name: transfected with TNDicer and hairpin plasmids

value: small RNA


title: 293DcrTN

description: sample name: 293DcrTN

source_name: transfected with TNDicer plasmid


title: 293cand1

description: sample name: 293vert2


title: 293cand4_rep3

description: sample name: 293cand-3


title: HeLa_Pol3_ChIPSeq

description: Chromatin IP against Pol III (RPC155)

extract_protocol: For chromatin immunoprecipitation (ChIP) using  antibodies for PolIII, the formaldehyde cross-linked cells were sonicated to obtain DNA fragments ranging in size from ~200 bp. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) .


title: Thymocytes_wt_RAG2

description: WT thymocytes; RAG2 IP

value: RAG2 (rabbit polyclonal antibody raised to RAG2 aa 70-516 (Leu and Schatz, PMID:7565717))


title: Thymocytes_D708A-R1-/-beta_H3K4me3

description: D708A transgene-positive Rag1-/- 2B4 Tcrb transgenic thymocytes; H3K4me3 IP


title: lyrata_inflorescenece_rep1

status: Public on Apr 22 2010

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

institute: Pennsylvania State University

description: 5' ends of uncapped polyA mRNA.

data_processing:
alignment (.shrimp, SHRiMP-rmapper-cs format) files were created as follows:  Raw 35color .csfasta reads were mapped to the appropriate transcriptome using rmapper-cs (from the SHRiMP package), using non-default settings -o 10000 -M 35bp,fast.  The initial, "raw" shrimp results were then filtered as follows:  a) for each read, only the alignments with the minimum alignment score were retained (i.e., only the best mapping position(s) of each read were kept, b) The maximum overall edit distance allowed for an aligned read was 6 (1 point for insertions, deletions, substitutions, or colorspace cross-overs), c) nucleotides 1-6 of the read had to exactly match the transcript in question., d) the alignment had to extend to at least position 29 of the read, and e) the alignment must be to the sense strand of the transcript in question.

degradome density files were generated from the filtered shrimp files by tallying the abundances of the 1st position of aligned reads (thus, the 5' ends of the underlying uncapped RNAs) at each position on each transcript.  For each transcript, the data are presented in 5 tab-delimited fields.  1) the position along the transcript, 2) the number of raw reads with 5' ends at that position, 3) the repeat-normalized number of reads with 5' ends at that positon (accounts for reads which mapped to more than one transcript), 4) the number of uniquely mapped reads with 5' ends at that position, and 5) the 'degradome category' of that position.  Cat 0:  Category 0: >1 raw read at the position, abundance at position is equal to the maximum on the transcript, and there is only one maximum on the transcript  Category 1: >1 raw read at the position, abundance at position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript  Category 2: >1 raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript  Category 3: >1 raw read at the position, abundance at position is equal to or less than the median for the transcript  Category 4: Only 1 raw read at the position.

organism: Arabidopsis lyrata

source_name: inflorescences

growth_protocol: A. thaliana plants were grown at ~22C under 16hr. days for about 8 weeks prior to harvest of inflorescences and RNA extraction.  A. lyrata plants were grown at ~22C under 16hr. days for about 12 weeks, then vernalized at ~6C for 6 weeks under 8 hr. days, followed by return to ~22C, 16hr. days to induce flowering

extract_protocol: Total RNA was extracted with Tri-reagent and polyA+ RNA purified. The untreated polyA+ RNA was used in conjunction with the ABI SOLiD RNAseq kit, except the fragmentation with RNAseIII was omitted.  This results in adapter ligation only to the 5' ends of RNAs with a 5'-monophosphate.  Further steps in library construction were per the manufacturer's suggestion, except that size selection of the final amplicons prior to emulsion PCR was very broad (~80nt to ~3kb).  The library was sequenced only from the 5' adapter, resulting in 35color tags representing the 5' ends of uncapped, polyA+ messages.

tag: ecotype/subspecies

value: ssp. lyrata


title: 293DroshaTN

description: sample name: 293DroshaTN

source_name: transfected with TNDrosha plasmid


title: NFI ChIP-Seq in NFI-C knock-out MEF

status: Public on Apr 24 2010

city: Lausanne

first: Milos

last: Pjanic

state: VD

address: EPFL CH B1 426 Station 6

department: Institute of Biotechnology

country: Switzerland

institute: Faculty of Biology and Medicine, University of Lausanne

description: Chromatin IP against CTF/NFI (wild-type MEF)

data_processing:
Obtained sequence tags were aligned to the reference mouse genome (mm9) using Illumina ELAND software. Clustering and correlation analyses of mapped reads were performed using ChIP-peak and ChIP-cor tools available on the ChIP-Seq Analysis Server (http://www.isrec.isb-sib.ch/chipseq/). In vivo NFI sites were defined using the ChIP-peak tool and applying the following parameters: window width - 1000bp, vicinity range - 1bp, peak threshold - 5 tags, count cut-off - 1 tag, centering - 75bp (for visualization in UCSC Genome browser: upload corresponding peaks.wig files).

File formats described at http://www.isrec.isb-sib.ch/chipseq/sga_specs.html

source_name: mouse embryonic fibroblasts (MEF)

growth_protocol: Mouse embryonic fibroblasts were extracted from mouse embryos of 14.5 days. Cells from WT (wild-type) and NFI-C knock-out embryos were cultured under the following conditions: 37°C, 5% CO2, DMEM (GIBCO, 41966), Supplementary 10% FBS (GIBCO, Fetal Bovine Serum, qualified origin US, 26140-079), 1% v/v nonessential amino-acids (GIBCO, 11140-035), 1% v/v L-glutamine (GIBCO, 25030-024).

extract_protocol: Chromatin was extracted from approximately 20,000,000 cultured MEFs and cross-linked using 11% formaldehyde. Extracted chromatin was fragmented to the average fragment size of 1000bp using high-frequency sound sonication on VibraCell-75455 (Bioblock Scientific). ChIP was performed using the commercial antibody against NFI group of proteins (NFI (H300): sc-5567, SantaCruz Biotechnology). Antibody complexes were precipitated using rProtein A Sepharose Fast Flow (Amersham Biosciences). ChIP DNA was processed using the contents of the ChIP-Seq Sample Prep Kit (Illumina). Size range of templates was selected by loading the entire processed sample on a 2% agarose gel and excising the gel region of 50-400bp. PCR amplification of the gel-extracted DNA was performed for 18 cycles using adapter-specific primers. Each sample was loaded into 3 separate flow cell channels of the Illumina Cluster Station and then subjected to sequencing-by-synthesis on the Illumina Genome Analyzer sequencing system.

tag: strain

tag: passages

value: NFI (H300):sc-5567, SantaCruz Biotechnology


title: testes_rep2

description: sample name: FC3500.3


title: Thymocytes_D708A-R1-/-beta_RAG2

description: D708A transgene-positive Rag1-/- 2B4 Tcrb transgenic thymocytes; RAG2 IP

tag: cell type

tag: chip antibody


title: thaliana_inflorescence_rep1

description: 5' ends of uncapped polyA mRNA.

organism: Arabidopsis thaliana


title: 4.71 yr old H3K4me3_NeuN-_rep1 #6n

first: Hennady

last: Shulha

address: 44 Cummington st

department: BME

institute: Boston University

description: Chromatin IP against H3K4me3

data_processing: mapped to hg18

source_name: prefrontal cortex

growth_protocol: Samples used in the study were postmortem tissues from prefrontal cortex BA10.

extract_protocol:
ChIPed DNA was first blunt-ended by End-it DNA Repair Kit (Epicentre) at RT for 1hr. Reaction was cleaned by column (Qiagen), and DNA was A-tailed by exo- Klenow DNA Polymerase (Epicentre) at RT for 1hr. Reaction was again cleaned by column, and DNA was ligated to Genomic Adpater Oligo Mix (Illumina) by Fast-link DNA Ligation Kit (Epicentre) at RT for 2 hours followed by 16°C O/N. Reaction was cleaned by column, and ligated DNA was amplified using  PfuUltra II Fusion HS DNA Polymerase (Stratagene) with 250µM dNTPs and 1µL of each of the Genomic PCR Primers (Illimina) in 100µL volume with the following cycling conditions: 95°C 1min; 15 cycles of 95°C 50sec, 65°C 1min, 72°C 30sec; 72°C 5min. PCR product was cleaned and volume reduced by column before loading onto a 1.8% agarose gel. Typically a strong smear of 160-230bp (including 92bp from the Illumina primers) was observed.
30sec; 72°C 5min. PCR product was cleaned and volume reduced by column before loading onto a 1.8% agarose gel. Typically a strong smear of 160-230bp (including 92bp from the Illumina primers) was observed.

tag: population

value: NeuN-

tag: age

value: neurons from prefrontal cortex


title: 69 yr old H3K4me3_NeuN-_rep1 #11n

description: Chromatin IP against H3K4me3


title: lyrata_inflorescenece_rep2

description: 5' ends of uncapped polyA mRNA.


title: testes_rep3

description: sample name: FC3983.3


title: 293cand5_rep1

description: sample name: 293RC3


title: NFI ChIP-Seq in wild-type MEF

data_processing:
Obtained sequence tags were aligned to the reference mouse genome (mm9) using Illumina ELAND software. Clustering and correlation analyses of mapped reads were performed using ChIP-peak and ChIP-cor tools available on the ChIP-Seq Analysis Server (http://www.isrec.isb-sib.ch/chipseq/). In vivo NFI sites were defined using the ChIP-peak tool and applying the following parameters: window width - 1000bp, vicinity range - 1bp, peak threshold - 5 tags, count cut-off - 1 tag, centering - 75bp (for visualization in UCSC Genome browser: upload corresponding peaks.wig files).

File formats described at http://www.isrec.isb-sib.ch/chipseq/sga_specs.html

Please see 'readme.txt' for details about the additional processed data files: boundaries_closest_external_NFI_in_vivo_site.txt and boundaries_closest_internal_NFI_in_vivo_site.txt (8 txt files); NFI_peaks_wtMEF_300bpwindow_300bpvicinity_range.bed and sga (1 file each); miRNA_with_NFI_site (3 txt files).


title: thaliana_inflorescence_rep2

description: 5' ends of uncapped polyA mRNA.


title: 293cand3

description: sample name: 293cand2


title: Thymocytes_R2-/-beta_RAG2

description: Rag2-/- 2B4 Tcrb transgenic thymocytes; RAG2 IP

tag: genotype


title: smallRNA_Flowers 1

description: smallRNA_Flowers 1

data_processing: Barcoded samples were first parsed to separate different samples mixed in the same run.  Small RNA inserts were separated from adapter sequences by identifying the common adapter sequence at the 3' end of each read.  An edit distance (substitution, insertion, or deletion) of 2 was the maximum allowable match to the adapter sequence, and only inserts >= 20 and <=25nts in length were retained.  The processed file is the .csfasta colorspace reads after adapter trimming.

source_name: flowering tissues

growth_protocol: Arabidopsis lyrata plants were grown until the rosette stage at 22C, with 16 hr. days.  Plants were then vernalized by growth at 15C under 8hr. days for 6 weeks, followed by transfer back into 22C, 16hr days.

extract_protocol: Total RNA was extracted using Tri-Reagent.  Small RNAs were fractionated by the use of the Ambion Flash Page system.  Barcoded small RNA libraries were prepared using the Ambion / ABI SOLiD Small RNA sequencing kit, per the manufacturer's instructions

tag: organ

value: Flowering tissues


title: 69 yr old H3K4me3_NeuN+_rep2 #11.2

description: Chromatin IP against H3K4me3

value: NeuN+


title: smallRNA_Flowers 2

description: smallRNA_Flowers 2


title: 69 yr old H3K4me3_NeuN+_rep1 #11.1

description: Chromatin IP against H3K4me3


title: 68 yr old H3K4me3_NeuN+_rep1 #9

description: Chromatin IP against H3K4me3


title: 8.78 yr old H3K4me3_NeuN+_rep1 #7

description: Chromatin IP against H3K4me3


title: 69 yr old H3K4me3_NeuN+_rep1 #10

description: Chromatin IP against H3K4me3


title: 13.99 yr old H3K4me3_NeuN+_rep1 #8

description: Chromatin IP against H3K4me3


title: 4.71 yr old H3K4me3_NeuN+_rep1 #6

description: Chromatin IP against H3K4me3


title: 2.8 yr old H3K4me3_NeuN+_rep1 #5

description: Chromatin IP against H3K4me3


title: 0.01ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA

status: Public on Apr 19 2010

city: Bethesda

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
S2 mRNA is the same sample as GSM410196. Sequences and abundance information of ERCC phase V pool 15 used in this study were provided separately with the supplementary files:
GSE20555_ERCC_phaseV_pool15_sequence.txt
GSE20555_ERCC_phaseV_pool15_abundance.txt
PCR amplification was done before size selection during library construction.
Run32-091022_s_8

data_processing: We retained reads that passed default quality filtering parameters in the Illumina pipeline (v1.4.0).  We aligned reads passing quality filtering using Bowtie (v0.10.0; parameter -m 1 -v 2).  Sequences of the ERCC RNAs (*ERCC_map.txt) were used as the alignment reference.  Additionally, Drosophila genome sequence (BDGP release 5, dm3) and ERCC RNA sequences were combined into a reference  (*ERCC_dm3_map.txt).  We used unique mapped reads with less than 2 mismatches for analysis.

organism:
Drosophila melanogaster
synthetic construct

source_name: Drosophila S2 cell and ERCC RNA controls, 0.01ng

growth_protocol: Drosophila S2 cells were grown at 25°C in Schneider's Drosophila Medium (Invitrogen, Carlsbad, CA) supplemented with 10% Fetal Bovine serum (SAFC Biosciences, Lenexa, KS) and Penicillin-Streptomycin. S2 cell mRNA aliquots are from GSM410196.

extract_protocol:
Total RNA from S2 cells was extracted using Trizol (Invitrogen, Carlsbad, CA), followed by mRNA isolation using the Oligotex poly(A) extraction kit (Qiagen, Valencia CA).

A master mRNA mixture was made from 300ng S2 mRNA and 7.5ng ERCC phase V pool15 RNA controls and serially diluted. Libraries were prepared according to GSM410196 with two variations. In method-A, size selection preceeded PCR amplification. In method-B, PCR amplification preceeded size selection. The library concentration of sample 100ng_library_methA_S2_2.5%ERCC_phaseV_pool15mRNA was measured by Nanodrop spectrophotometer and the concentration of all other libraries were measured by RT-PCR using the concentration of sample 100ng_library_methA_S2_2.5%ERCC_phaseV_pool15mRNA as a reference. The primers used in the real-time PCR are identical to PCR amplification primers in the library construction. 10nm DNA from each library was used for clustering on the flow cell.

tag: cell line

tag: external rna control

value: ERCC phase V pool 15

tag: rna quantity

tag: library preparation method

value: B


title: 100ng_S2_2.5ng_ERCC_phaseV_pool15_mRNA-seq

description:
Sequences and abundance information of ERCC phase V pool 15 used in this study were provided separately with the supplementary files:
ERCC_phaseV_pool15_sequence.txt
ERCC_phaseV_pool15_abundance.txt

source_name: Drosophila S2 cell and 2.5ng ERCC RNA controls

growth_protocol: Drosophila S2 cells ("SL2" originally obtained from the Drosophila RNAi Screening Center, Boston MA) were grown at 25°C in Schneider's Drosophila Medium (Invitrogen, Carlsbad, CA) supplemented with 10% Fetal Bovine serum (SAFC Biosciences, Lenexa, KS) and Penicillin-Streptomycin.

extract_protocol: Libraries were made with 100ng S2 mRNA or 100ng mRNA from S2 RNAi-treated cells with 5ng, 2.5ng or 1ng ERCC mRNAs and with 50ng ERCC mRNAs only following the standard procedure. See Zhang et al. PLoS Biology 2010 for details.

treatment_protocol: S2 cells were mock or RNAi treated with 10ng dsRNA using standard procedure. See Zhang et al., PLoS Biology 2010 for details.

tag: s2 treatment

value: msl2 RNAi

tag: rna quantity (s2)

tag: rna quantity (ercc)


title: 100ng_S2_1ng_ERCC_phaseV_pool15_mRNA

source_name: Drosophila S2 cell and 1ng ERCC RNA controls

value: mof RNAi


title: Rice_Seedling

city: Madison

first: Yufeng

last: Wu

state: WI

address: 1575 Linden Drive

institute: UW-Madison

description: mCIP DNA

data_processing: We first blasted mCIP-seq reads against all CentO satellite repeats in the genome and classified these with .20 bp alignments as CentO-related reads. We then used ELAND from the Solexa pipeline and SOAP (Li et al., 2008a) to map the remaining reads to the rice nuclear genome reference sequences (http://rice.plantbiology.msu.edu/), as well as to the mitochondrial (BA000029) and chloroplast (NC_001320) sequences. Based on a cut-off of at least a 25 bp alignment and no more than 2 mismatches, only reads that had a single best match in the three reference sequences were retained. In cases where multiple reads (>3) were co-mapped to the same genomic location, some likely representing artifacts caused by the amplification step, we retained only three for the subsequent analysis. We chose this number based on our published results from 454 sequencing of unamplified ChIP products using CENH3 antibody (Yan et al., 2008), where 20% of the mapped reads each has 2-3 identical copies that were assigned to the same genomic locations. To identify regions showing significant local enrichment of read count, we generated a null distribution for each chromosome by randomly assigning mapped reads to unique locations and then identified peaks (p value .e-3) using 200 bp sliding windows, spaced every 20 bp. The resulting peaks were refined for their boundaries, where peaks separated by <40 bp were merged and small peaks of <50 bp were filtered out.

organism: Oryza sativa

growth_protocol: Rice plants were grown for two weeks at 30-32 centigrade degree and 16 hours lights

extract_protocol: The mCIP DNA was fragmented by nebulization. The condition of nebulization was optimized to generate fragments with dominant sizes ranging from 200 to 250 bp. After the fragments were purified using a QiaQuick PCR purification kit, the ends of fragments were repaired and phosphorylated. A single adenosine triphosphate was added to the 3’ end of the blunt ended and phosphorylated DNA fragments. An Illumina proprietary adapter was then ligated to DNA fragments by T4 DNA ligase. A gel purification procedure was carried out to select the fragments sized from 250 to 300 bp. Twelve cycles of PCR with Illumina proprietary PCR primers were used to generate and amplify the library used for Illumina cluster formation. Cluster formation and sequencing on GAiix platform were performed following the manufacturer’s standard cluster generation and sequencing protocols

tag: antibody


title: 0.5 yr old H3K4me3_NeuN+_rep1 #1

description: Chromatin IP against H3K4me3


title: 1.3 yr old H3K4me3_NeuN+_rep1 #4

description: Chromatin IP against H3K4me3


title: 0.58 yr old H3K4me3_NeuN+_rep1 #2

description: Chromatin IP against H3K4me3


title: 0.75 yr old H3K4me3_NeuN+_rep1 #3

description: Chromatin IP against H3K4me3


title: 1ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA

description:
S2 mRNA is the same sample as GSM410196. Sequences and abundance information of ERCC phase V pool 15 used in this study were provided separately with the supplementary files:
GSE20555_ERCC_phaseV_pool15_sequence.txt
GSE20555_ERCC_phaseV_pool15_abundance.txt
PCR amplification was done before size selection during library construction.
Run32-091022_s_5

source_name: Drosophila S2 cell and ERCC RNA controls, 1ng


title: 0.4ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA

description:
S2 mRNA is the same sample as GSM410196. Sequences and abundance information of ERCC phase V pool 15 used in this study were provided separately with the supplementary files:
GSE20555_ERCC_phaseV_pool15_sequence.txt
GSE20555_ERCC_phaseV_pool15_abundance.txt
PCR amplification was done before size selection during library construction.
Run32-091022_s_6

source_name: Drosophila S2 cell and ERCC RNA controls, 0.4ng


title: 10ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA

description:
S2 mRNA is the same sample as GSM410196. Sequences and abundance information of ERCC phase V pool 15 used in this study were provided separately with the supplementary files:
GSE20555_ERCC_phaseV_pool15_sequence.txt
GSE20555_ERCC_phaseV_pool15_abundance.txt
PCR amplification was done before size selection during library construction.
Run32-091022_s_4

source_name: Drosophila S2 cell and ERCC RNA controls, 10ng


title: 50ng_ERCC_phaseV_pool15_mRNA-seq

molecule: polyA RNA

organism: synthetic construct

source_name: ERCC RNA controls only


title: INPUT DNA in wild-type MEF

description: Non-precipitated genomic DNA (wild-type MEF)

value: no antibody


title: 100ng_library_methA_S2_2.5%ERCC_phaseV_pool15mRNA

description:
S2 mRNA is the same sample as GSM410196. Sequences and abundance information of ERCC phase V pool 15 used in this study were provided separately with the supplementary files:
GSE20555_ERCC_phaseV_pool15_sequence.txt
GSE20555_ERCC_phaseV_pool15_abundance.txt
PCR amplification was done after size selection during library construction.
Run32-091022_s_1

source_name: Drosophila S2 cell and ERCC RNA controls, 100ng

value: A


title: bam H3K27me3 ChIP-seq

status: Public on Apr 16 2010

city: Duarte

first: Dustin

middle: E

last: Schones

state: CA

address: 1500 E Duarte Rd.

institute: City of Hope

description: Chromatin IP against H3K27me3

data_processing: The 25-bp sequencing reads were obtained from the Illumina Genome Analyzer (GA) Pipeline. All reads were aligned to the Drosophila genome (dm3) using the ELAND (Efficient Local Alignment of Nucleotide Data) software, allowing up to two mismatches with the reference sequence. Only uniquely mapped reads were retained. For multiple identical reads, at most three copies were retained to reduce the possibility of biases from PCR amplification. The output of the GA Pipeline was converted to browser extensible data (BED) files. The bedgraph files used for visualization on the UCSC browser were generated from the uniquely mapped reads using a 4-bp window as previously described ( Barski A, et al. Cell 2007).

organism: Drosophila melanogaster

source_name: bam testis

growth_protocol: Flies were raised using standard medium at 25oC unless stated otherwise. The bam1/TM3 and bam114-97 /TM6B stocks were obtained from Bloomington Drosophila Stock Centers.

extract_protocol: For each modified histone and Pol II ChIP experiment, we dissected 200 pairs of bam testes in cold PBS and grouped them in 200ml PBS which contained protease inhibitor (Roche complete mini, # 11836153001) and 0.5mM PMSF (MP Biomedicals, #195381). We then added 5.5ml 37% fresh formaldehyde (Supelco, # 47083-U) and incubated at 37oC for 15 mins. The testes were washed twice with 450ml cold 1x PBS (with inhibitors and PMSF). Then 200ml lysis buffer (50mM Tris-HCl, pH7.6, 1mM CaCl2, 0.2% Triton X-100, 5mM butyrate, 1x proteinase inhibitor cocktail, and 0.5mM fresh PMSF) was added and the tissues were homogenized thoroughly followed by incubation at room temperature (RT) for 10 mins. Chromatin was sheared into approximately 200 bp fragments by sonication using Microtip (Misonix, Inc, Microson XL-2000). Chromatin was prepared and ChIP-seq experiments were performed similarly as described previously ( Barski A, et al. Cell 2007) with the following antibodies: Pol II (Abcam ab5408), H3K4me3 (Abcam ab8580), H3K27me3 (Millipore/Upstate 07-449), H3K36me3 (Abcam ab9050).

value: bam testis

tag: antibody manufacturer

value: Millipore

tag: antibody catalog number


title: bam H3K36me3 ChIP-seq

description: Chromatin IP against H3K36me3

value: Abcam


title: bam PolII ChIP-seq

description: Chromatin IP against Pol II

value: PolII


title: bam H3K4me3 ChIP-seq

description: Chromatin IP against H3K4me3


title: S2 Pol II ChIP-seq

description: Chromatin IP against Pol II

source_name: S2 cells

growth_protocol: The Drosophila S2 cells were cultured following the manufacturer’s protocol. Exponentially growing S2 cells were harvested and resuspended in digestion buffer (50mM Tris-HCl, pH7.6, 1mM CCl2, 0.2% Triton X-100, 5mM butyrate, 1x proteinase inhibitor cocktail and 0.5mM PMSF).

extract_protocol: Chromatin from approximately 2x10^7 cells were used for each ChIP experiment. End repair for ChIP fragments was performed using PNK and Klenow enzyme, followed by treatment with Taq polymerase.  Sequencing adaptors were ligated to the repaired ends and ChIP DNA was amplified using adaptor primers for 17 cycles.  Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols.


title: S2 RNA

description: RNA sequencing

data_processing: The quality-filtered 36 bp short sequence reads were aligned to the reference sequence consisting of dm3 Drosophila melanogaster genome sequences using ELAND (Efficient Local Alignment of Nucleotide Data) software, allowing up to two mismatches with the reference sequence for the first 32bp. To calculate a single number to represent expression level of a gene, all exon regions belonging to a gene are merged and the total number of non-redundant unique reads in the resulting merged exonic region is counted. The resulting number of transcript abundance for the genes was computed as sequencing reads/per kilobase merged exonic region/per million mapped reads (RPKM value provided in GSM480160_GA0840_Drosophila_S2_RNAseq.xls file).

extract_protocol:
For ~20 µg total RNA from S2 cells, we performed two rounds of mRNA isolation using Dynabeads mRNA purification kit (Invitrogen, #610-06), according to the manufacturer’s instructions. The final mRNAs were eluted in 13.5 µl 10 mM Tris-HCl (pH 7.5) and immediately used to generate the first strand cDNA, using 4 µl random hexamers (ABI, #N8080127) and SuperScript II Reverse Transcription Kit (Invitrogen, #18064-014) in a 30 µl final volume, following the manufacturer’s instructions. The second strand cDNA was generated with the following recipe: 10 µl 5´ second strand buffer (500mM Tris-HCl pH7.8, 50mM MgCl2, 10mM DTT), 30nmol dNTPs (Invitrogen, #18427-013), 2 Units of RNase H (Invitrogen, #18021-014) and 50 Units of DNA Pol I (Invitrogen, #18010-025). The entire reaction mix was incubated at 16°C for 2.5 hours. The double-stranded DNA (dsDNA) was purified with QIAquick PCR purification kit (Qiagen, #28106) and the concentration was quantified by the Qubit fluorometer (Invitrogen).
To generate sequencing libraries, about 300 ng dsDNA of each sample was fragmented by sonication using Bioruptor (Diagenode, UCD-200-TM-EX) under the following conditions: medium power output for 30 min in ice water. The resulting DNA fragments were analyzed by agarose gel to verify they are within ~100-300-bp size range. Sequencing libraries were prepared as the follows: end-repair (DNA end-repair kit from Epicenter, #ER0720); A-tailing (300 ng dsDNA, 5 µl Thermo buffer, 10 nmol dATP, 15 Units of Taq polymerase, at 70oC for 30min); Solexa adaptor ligation (300 ng dsDNA, 4 µl DNA Ligase buffer, 1 ul Solexa adaptor mix, 3 ul DNA Ligase, at 70oC overnight.); PCR (98°C 10 sec, 65°C 30 sec, 72°C 30 sec for 16 cycles; then additional 72°C for 5 min) amplification with adaptor primers and size selection (200-400bp). Then the library dsDNA for S2 cells was used on an Illumina Genome Analyzer (GA) II at a concentration of 10ng per lane


title: S2 H3K36me3 ChIP-seq

description: Chromatin IP against H3K36me3


title: S2 H3K4me3 ChIP-seq

description: Chromatin IP against H3K4me3


title: S2 H3K27me3 ChIP-seq

description: Chromatin IP against H3K27me3


title: Brain_mouse_RE

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

description: RE Library.

data_processing: Sequence reads were mapped to the mouse mm9 genome sequence using the AB SOLiD mate-pair analysis pipeline.  Uniquely mapping DNAs were then filtered based on the existence of restriction sites on at least one end of the fragments.  The ratios of McrBC and RE fragments were normalized and fragments were overlapped with the locations of restriction sites in the genome.

source_name: Brain, RE library

growth_protocol: DNA was extracted from primary tissues. Mouse brain DNA was prepared from the left hemisphere with the cerebellar tissue removed.

extract_protocol: Briefly, DNA was fractionated into methylated (RE) and unmethylated (McrBC) fractions using methylation-sensitive (AciI, BstUI,  HhaI, HpaII, HpyCh4IV) and -dependent (McrBC) enzymes, respectively.  After digestion, fragments were size-selected for everything 800bp and above. Mate-pair sequencing tags were isolated using AB’s mate-pair library protocol with slight modification. Libraries were prepared for sequencing by emulsion PCR and sequenced on an AB SOLiD sequencer per the manufacturer's instructions. For mapping purposes, size cutoffs from 0-15kb were set; 0 since some small fragments will comigrate with larger ones in the gel, and 15kb since very few fragments above that length survived the circularization process.

treatment_protocol: Untreated.

tag: tissue

value: brain

tag: methylation status

value: methylated

tag: strain


title: Brain_human_McrBC

description: McrBC Library.

data_processing: Sequence reads were mapped to the human hg18 (March, 2006) genome sequence using the AB SOLiD mate-pair analysis pipeline.  Uniquely mapping DNAs were then filtered based on the existence of restriction sites on at least one end of the fragments.  The ratios of McrBC and RE fragments were normalized and fragments were overlapped with the locations of restriction sites in the genome.

source_name: Brain, McrBC library

growth_protocol: DNA was extracted from primary human brain (dorsolateral prefrontal cortex) tissues.

value: unmethylated


title: 100ng_S2_5ng_ERCC_phaseV_pool15_mRNA-seq

source_name: Drosophila S2 cell and 5ng ERCC RNA controls

value: untreated


title: Brain_mouse_McrBC

description: McrBC Library.


title: 50ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA

description:
S2 mRNA is the same sample as GSM410196. Sequences and abundance information of ERCC phase V pool 15 used in this study were provided separately with the supplementary files:
GSE20555_ERCC_phaseV_pool15_sequence.txt
GSE20555_ERCC_phaseV_pool15_abundance.txt
PCR amplification was done before size selection during library construction.
Run32-091022_s_3

source_name: Drosophila S2 cell and ERCC RNA controls, 50ng


title: 293cand2

description: sample name: 293vert3

source_name: transfected with candidate hairpins

extract_protocol: The small RNA cDNA libraries were made as described (Grimson et al. 2008), except for the 3' adaptor ligation, which was 5' adenylated pTCGTATGCCGTCTTCTGCTTGidT. For a detailed protocol, see http://web.wi.mit.edu/bartel/pub/protocols.html.

value: HEK293T cell line

tag: molecule

value: small RNA


title: Breast1_human_RE

description: RE Library.

source_name: Breast, RE library

growth_protocol: DNA was extracted from primary human breast tissues.

value: breast


title: Breast2_human_RE

description: RE Library, 2 runs.


title: Breast2_human_McrBC

description: McrBC Library.

source_name: Breast, McrBC library


title: 100ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA

description:
S2 mRNA is the same sample as GSM410196. Sequences and abundance information of ERCC phase V pool 15 used in this study were provided separately with the supplementary files:
GSE20555_ERCC_phaseV_pool15_sequence.txt
GSE20555_ERCC_phaseV_pool15_abundance.txt
PCR amplification was done before size selection during library construction.
Run32-091022_s_2

value: ERCC phase V pool 15


title: Breast1_human_McrBC

description: McrBC Library.


title: KCl_hr6_polyA_b2

status: Public on Apr 15 2010

city: boston

first: jesse

middle: M

last: gray

address: 77 avenue louis pasteur, NRB 356

department: Genetics

description: polyA+

data_processing:
Corona lite read alignment to mm9; discard non-uniquely aligned reads; conversion of uniquely aligned reads (0-3 mismatches) into bigWig (.bw) file
For ChIP-Seq, the .bw file reflects extended 120bp fragments corresponding to each ChIP-Seq read
For RNA-Seq, the .bw files contain information only about the 5' most base of each read; there are separate bigWig files for + and - genomic strands
The .wig files from which the .bw files were derived are also provided.

source_name: 7 DIV E16.5 mouse cortical neurons, before and after membrane depolarization induced by extracellular potassium

growth_protocol: 7 DIV E16.5 mouse cortical neurons grown in B27/NB on PO-coated plastic 15-cm plates

extract_protocol:
Whole Transcriptome sequencing (WT-Seq, RNA-Seq: sequencing of total RNA): WT-Seq was performed according to a protocol/kit now available from Life Technologies, with minor modifications that are included below.  Briefly, 5–10ug of RNA isolated from mouse cortical cultures was depleted of ribosomal RNAs using two rounds of Human/Mouse RiboMinus treatment (Life Technologies) with overnight ethanol precipitations for sample re-concentration.  The removal of ribosomal RNAs was confirmed on a Bioanalyzer Nano Chip (Agilent).  500–1000ng of riboRNA-depleted total RNA was fragmented with 10–18 minutes 37° RNAseIII treatment, and 10 minutes of RNAseIII inactivation at 65°.  Fragmentation was followed by size selection of ~50 to ~150bp fragments using the flashPAGE denaturing PAGE-fractionator (Life Technologies) and ethanol precipitation overnight.  The resulting RNA was directionally ligated, reverse-transcribed, and RNAseH treated. After trial PCR to assess library quality and quantity, 30ul cDNA was run on a native 6% PAGE gel.  The 90–120bp size window (corresponding to 50–80bp RNA insert size) was cut from the gel, shredded, and inserted directly into a 400ul PCR reaction using standard WT-Seq kit components and submitted to 11–15 cycles of PCR.  The PCR product was phenol-chloroform extracted, ethanol precipitated, and resuspended in 20ul WT-Seq gel loading buffer.  The resulting sample was run on a 6% native PAGE gel, and the 150–175bp size range (corresponding to 60–85bp) was cut from the gel, shredded, and extracted overnight in WT-Seq PAGE elution buffer.  The resulting library was filtered through 0.45um spin filters (Life Technologies) to remove gel pieces and ethanol precipitated. We note that WT-Seq can detect neither the 5'-most fragment from transcripts with 5'-modified ends (such as mRNA 5' 7-methyl-guanosine caps) nor the 3'-most fragment from transcripts with 3'-modified ends.  However, for transcripts long enough to produce multiple 50+ bp fragments, WT-Seq should detect the remaining fragments. Mouse cortical neuron WT-Seq data presented in this manuscript are from one specific biological replicate, but each result was confirmed in at least one additional replicate.
Chromatin immunoprecipitation-sequencing (ChIP-Seq): Forty million mouse cortical neurons cultured to in vitro day 7 were used for each ChIP-Seq library construction.  ChIP was performed as described2 using antibodies listed above.  The immuno-precipitated DNA fragments were repaired by the End-It DNA End Repair Kit (Epicentre Biotechnology) according to the manufacturer’s instructions.  The end-repaired ChIP DNA fragments were purified by MinElute Reaction Cleanup Kit (Qiagen) and eluted in 20 ul in EB buffer.  The resulting DNA fragments were ligated with P1 and P2 adaptors for SOLiD genome analyzer (adaptor sequences can be available upon request) for 20 minutes at room temperature using the Quick Ligase Kit (NEB), followed by purification using MinElute Reaction Cleanup Kit (Qiagen).  The purified, adaptor-ligated ChIP DNA fragments were subject to 6% native-PAGE for an in-gel PCR reaction.  A gel slice containing 175–200 bp adaptor-ligated ChIP DNA fragments (corresponding to 125–150bp genomic fragment sizes) was cut and shredded.  PCR Platinum Supermix (100–200 ul, Invitrogen), 50 pmoles of PCR primers (available upon request), 0.5 ul Taq DNA polymerase (NEB), and 0.15 ul Pfu Turbo DNA polymerase (Stratagene) were added into the shredded gel slice.  The adaptor-ligated ChIP DNA fragments were amplified by 15 cycles of in-Gel PCR.  After the PCR reaction, gel pieces were filtered out by 0.45 um filter spin column, and the amplified ChIP-Seq library was purified by MinElute PCR purification kit (Qiagen).  The library was purified by one more round of 6% PAGE.  A gel slice containing 200–250 bp PCR products (110–150bp fragment size) was cut and shredded, and the amplified library was extract out of the gel by passive elution in elution buffer (1.5M ammonium acetate in 1X TE).  Gel pieces were filtered out by filter spin column, and the resulting ChIP-Seq library was purified using the Qiaquick PCR purification kit (Qiagen).

treatment_protocol: 0, 1, 2, or 6 hours of 55mM KCl, with overnight quieting with TTX/APV

tag: protein immunoprecipitated

tag: agent

value: KCL

tag: kcl treatment time (hours)

tag: developmental stage

tag: cell type

value: cortical neuron

tag: biological rep

tag: technical rep


title: KCl_hr6_polyA_b1

description: polyA+


title: KCl_hr6_total_RNA_b3

description: total RNA

data_processing:
Corona lite read alignment to mm9; discard non-uniquely aligned reads; conversion of uniquely aligned reads (0-3 mismatches) into bigWig (.bw) file
For ChIP-Seq, the .bw file reflects extended 120bp fragments corresponding to each ChIP-Seq read
For RNA-Seq, the .bw files contain information only about the 5' most base of each read; there are separate bigWig files for + and - genomic strands
The .bedgraph files from which the .bw files were derived are also provided.


title: KCl_hr0_polyA_b1

description: polyA+


title: KCl_hr0_total_RNA_b2

description: total RNA


title: KCl_hr6_total_RNA_b2

description: total RNA


title: KCl_hr0_total_RNA_b1_techreps_t1_t2

description:
total RNA
Processed data file(s) represent data combined from tech. reps #1 and #2

value: 1 and 2


title: ChIP_input_KCl_b1

description: ChIP


title: KCl_hr1_total_RNA_b2

description: total RNA


title: ChIP_input_un_b1

description: ChIP


title: ChIP_input_KCl_b2

description: ChIP


title: KCl_hr6_total_RNA_b1_techreps_t1_t2


title: ChIP_H3K4me1_KCl_b2

description: ChIP

value: Abcam (Ab8895)


title: ChIP_MNase_KCl_b1

description: ChIP


title: ChIP_input_un_b2

description: ChIP


title: ChIP_H3K4me1_un_b1

description: ChIP


title: ChIP_H3K4me1_un_b2

description: ChIP


title: KCl_hr1_polyA_b1

description: polyA+


title: ChIP_H3K27me3_KCl_b2

description: ChIP

value: Millipore (07-449)


title: ChIP_H3K27me3_KCl_b1

description: ChIP


title: ChIP_H3K27me3_un_b2

description: ChIP


title: ChIP_H3K4me3_un_b2

description: ChIP

value: Abcam (Ab1012)


title: ChIP_H3K4me3_KCl_b1

description: ChIP


title: ChIP_H3K4me3_KCl_b2

description: ChIP


title: ChIP_H3K27me3_un_b1

description: ChIP


title: ChIP_SRF_SC_KCl_b2

description: ChIP

value: SRF


title: ChIP_SRF_SC_un_b2

description: ChIP


title: ChIP_H3K4me3_un_b1

description: ChIP


title: ChIP_SRF_SC_KCl_b1

description: ChIP


title: KCl_hr1_total_RNA_b1_techreps_t1_t2


title: ChIP_SRF_SC_un_b1

description: ChIP


title: ChIP_CREB_SC_un_b2

description: ChIP

value: Santa Cruz (Sc-186)


title: ChIP_CREB_SC_KCl_b1

description: ChIP


title: ChIP_CREB_SC_KCl_b2

description: ChIP


title: ChIP_H3K4me1_KCl_b1

description: ChIP


title: ChIP_Npas4_KCl_b1

description: ChIP

value: custom


title: ChIP_CREB_SC_un_b1

description: ChIP


title: ChIP_Npas4_KCl_b2

description: ChIP


title: ChIP_RNAPII_8WG16_un_b1

description: ChIP

value: RNAPII

value: 8WG16, Covance (MMS-126R)


title: ChIP_Npas4_un_b1

description: ChIP


title: ChIP_CBP_ab2832_KCl_b1

description: ChIP

value: CBP

value: Ab2832, Abcam


title: ChIP_CBP_ab2832_un_b1

description: ChIP

value: untreated


title: ChIP_RNAPII_4H8_un_b1

description: ChIP


title: ChIP_CBP_ab2832_KCl_b2

description: ChIP


title: ChIP_CBP_Millipore_KCl_b1

description: ChIP

value: MAB1133 (AC238) Millipore


title: Chlorella_sp.NC64A_RNA-Seq

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

description: RNA sequencing

data_processing: RNA-seq datasets were aligned using Bowtie to both genomic and cDNA scaffolds, allowing up to two mismatches. Roughly five million reads were mapped for each organism . Each cDNA model was assigned a score equal to the number of mapped reads per 1000 bp of sequence. Genomic DNA alignments were used for visual display and to filter repeat datasets.

organism: Chlorella variabilis

source_name: Whole plants

growth_protocol: Cultured in ATCC Medium 5 shaking at 25oC 16/8 light cycle

extract_protocol: RNA-Seq library preparation: Total RNA samples were isolated using RNeasy mini kit (Qiagen #74106) or with TRIzol reagent (Invitrogen #15596-026) followed by a cleanup step using the RNeasy mini kit. DNase treatments were performed on columns for all samples. mRNA was purified from 10-50 µg of total RNA by two cycles of poly-A enrichment using the Oligotex kit (Qiagen #72022), followed by a rRNA removal step using the RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen #A1083702). Precipitated mRNA samples were eluted with 9 µl of RNase free water and fragmented with 1 µl of 10X fragmentation buffer (Ambion, #AM8740) at 70oC. Reactions were stopped after 5 minutes by adding 1 µl Stop buffer and RNA was purified by ethanol precipitation. cDNA was synthesized from 100-300 ng of mRNA using Superscript III reverse transcriptase (Invitrogen #18080-051). Double-stranded DNA was synthesized as described (3). DNA was cleaned with a QIAquick PCR spin column (Qiagen, #28106), sequencing adapters were ligated according to the Illumina protocol and library was amplified by 18 cycles of PCR using Phusion DNA polymerase (NEB, #F-530). Bands around 300 bp were gel-purified and cloned for validation. Traditional sequencing confirmed that the libraries were properly constructed, showing high percentage of mRNA over rRNA. The libraries were sequenced at the UC Berkeley Genomic Sequencing Laboratory, generating single ends (SE) 36 base reads.


title: ChIP_CBP_Millipore_un_b1

description: ChIP


title: Volvox_carteri_RNA-Seq

description: RNA sequencing

organism: Volvox carteri

source_name: Mature colonies

value: UTEX #LB 1885


title: Tribolium_castaneum_BS-Seq

description: Bisulfite sequencing

data_processing:
We used a mixture of paired ends (PE) and single ends (SE) Illumina sequencing datasets for bisulfite sequencing. PE datasets were aligned to genomic scaffolds exactly as described in PMID 19520962 (GEO Series GSE15922). For SE datasets, the 76 base reads were divided into the first 45 and the last 31 bases. Each half of the read was aligned independently using Bowtie (7), allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first. S. moellendorffii is highly polymorphic, so the two haplotypes were assembled by the Joint Genome Institute (ww.jgi.doe.gov) independently, creating a genomic scaffold twice the actual genome size. We discarded scaffolds with a high degree of homology to create a single pseudo-haplotype close to the actual genome size (Table 1) that we used as an alignment scaffold.
Alignment: We used Perl scripts to convert all the Cs in the ‘forward’ reads (and in the scaffold) to Ts, and all the Gs in the ‘reverse’ reads and scaffold to As, and aligned the converted reads to the converted  scaffold, allowing up to two mismatches per read.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).

organism: Tribolium castaneum

source_name: Whole adults

extract_protocol: BS-Seq library preparation: We synthesized custom Illumina adapters in which cytosines were replaced by 5-methylcytosines, so that the adapters would survive bisulfite conversion.   About 1 microgram of genomic DNA was sheared by sonication to fragments of 100-500 bp, and the adapters were ligated following the Illumina protocol. The library was then treated twice with sodium bisulfite (which converts unmethylated Cs to Us) using the Qiagen EpiTect kit, and amplified by 18 cycles of PCR using PfuTurboCx DNA polymerase (Stratagene), a proofreading enzyme that tolerates uracil in the template strand. Bands around 300 bp were gel-purified and cloned for validation.


title: Laccaria_bicolor_BS-Seq

description: Bisulfite sequencing

organism: Laccaria bicolor

source_name: Mycelium

growth_protocol: Grown on YM agar plates at 24oC


title: Laccaria_bicolor_RNA-Seq

description: RNA sequencing


title: Ciona_intestinalis_RNA-Seq

description: RNA sequencing

organism: Ciona intestinalis

source_name: Muscle tissues


title: Volvox_carteri_BS-Seq

description: Bisulfite sequencing


title: Ciona_intestinalis_BS-Seq

description: Bisulfite sequencing