title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in BMP4 Mesendoderm Cells; renlab.H3K27ac.BMP4M.04.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK313
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11187
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11184
****************
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: GSM864799_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K27ac.AK313.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.BMP4M.04.01.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK313, 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.12855
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,825,040
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4073
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4843
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9916
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5012
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM864799_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K27ac.AK313.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.BMP4M.04.01.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK313, 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.12864
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDM H3K27ac 13
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK313 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,825,040
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4073
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4843
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9916
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5012
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K27ac.BMP4M.04.01

value: Histone H3K27ac

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in BMP4 Trophoblast Cells; renlab.H3K27ac.BMP4T.03.01

status: Public on Jan 24 2012

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK316
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11194
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
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: GSM864800_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K27ac.AK316.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.BMP4T.03.01.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AK316, 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.12856
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,490,469
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4429
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4992
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9975
IROC_PERCENTILE: 100
POISSON_SCORE: 0.517
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM864800_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K27ac.AK316.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.BMP4T.03.01.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AK316, 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.12865
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDT H3K27ac 16
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27ac Library AK316 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,490,469
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4429
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4992
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9975
IROC_PERCENTILE: 100
POISSON_SCORE: 0.517
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K27ac.BMP4T.03.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

tag: passage

tag: medium

tag: Sex

value: Male

tag: batch

value: Biorupter

value: 500 micrograms


title: UNC_FaireSeq_NHEK

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

source_name: NHEK

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

tag: datatype

value: FaireSeq

tag: datatype description

value: FAIRE-seq Open Chromatin

tag: controlid

tag: labversion

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

tag: replicate

tag: cell organism

value: human

tag: cell description

value: epidermal keratinocytes

tag: cell karyotype

value: normal

tag: cell lineage

value: ectoderm

tag: cell sex

value: U

value: align_on_cluster_bwa.pl v 1

tag: replicate description

value: tier 1


title: UNC_FaireSeq_HUVEC

source_name: HUVEC

value: HUVEC/Input

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

value: umbilical vein endothelial cells

value: mesoderm


title: UNC_FaireSeq_MCF-7_Hypoxia_LacAcid

tag: treatment description

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

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.1

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

value: cancer

value: F

tag: treatment


title: CD4_H3K4me2_ChIAPET_Exp1_Seq1

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

data_processing: The raw sequences were trimmed to the first 36-bp and the linker sequences from the 36-bp reads were removed.  The sequences of the two ends of PETs were separately mapped to the hg18 human genome using the bowtie algorithm (Langmead et al., 2009. Genome Biol 10, R25) ensuring  that only uniquely mapped reads with zero mismatches to the reference genome were retained and taking into account the base-quality values. To identify long-range chromatin interactions, we represented paired-end tags by points in the 2-dimensional space Genome × Genome and identified regions with significantly enriched points

source_name: CD4+ T cells

extract_protocol: 100 million CD4+ T cells were isolated from human blood as previous described (Barski et al., 2007). Cells were then cross-linked with 1% formaldehyde for 10 minutes at room temperature, followed by sonication of the cells to obtain chromatin fragments ranging in size from 150 to 300 bp. The ChIP assay was carried out using the antibody against H3K4me2 (Millipore, 07-030) and the immunoprecipitated chromatin was stored in TE buffer. ChIA-PET libraries were prepared as described (Fullwood et al., 2009. Nature 462, 58-64.) and pair-end sequencing was carried out using Illumina Hi-seq sequencer.

tag: cell type

value: CD4+ T cells

tag: antibody

tag: vendor

value: Millipore, 07-030


title: CD4_H3K4me2_ChIAPET_Exp1_Seq2


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in hESC H9 Cells; renlab.H2BK15ac.hESC.H9.03.01

status: Public on Jan 21 2012

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2B1K5ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY28
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11175
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM864034_UCSD.H9.H2BK15ac.AY28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.hESC.H9.03.01.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK15ac ChIP-Seq on H9 Cell Line, Library AY28, 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.12857
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,321,882
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0088
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1516
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6722
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3623
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM864034_UCSD.H9.H2BK15ac.AY28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.hESC.H9.03.01.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK15ac ChIP-Seq read mappings from the H9 Cell Line, Library AY28, 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.12866
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: H9 H2BK15ac 28
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H2BK15ac Library AY28 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,321,882
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0088
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1516
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6722
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3623
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H2BK15ac.hESC.H9.03.01

tag: sample alias

tag: sample common name

value: H9 Cell Line

tag: molecule

value: genomic DNA

tag: disease

value: James Thompson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

tag: passage

value: Between 30 and 50

tag: medium

value: mTeSER

tag: Sex

value: Female

tag: batch

value: Histone H2BK15ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Input from BMP4 Mesendoderm Cells; renlab.Input.BMP4M.03.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK318
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11182
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11177
****************
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: GSM864037_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Input.AK318.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.BMP4M.03.01.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK318, 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.12850
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,676,287
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0111
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.1395
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.7919
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3699
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM864037_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Input.AK318.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.BMP4M.03.01.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK318, 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.12859
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDM Input 18
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK318 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,676,287
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0111
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.1395
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.7919
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3699
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.Input.BMP4M.03.01

value: James Thomson Laboratory

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Between 25 and 35

value: Male

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in BMP4 Mesendoderm Cells; renlab.H3K27ac.BMP4M.03.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK310
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11178
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11177
****************
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: GSM864035_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K27ac.AK310.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.BMP4M.03.01.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK310, 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.12854
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,328,715
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2955
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3771
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9832
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4484
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM864035_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K27ac.AK310.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.BMP4M.03.01.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK310, 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.12863
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDM H3K27ac 10
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK310 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,328,715
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2955
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3771
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9832
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4484
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K27ac.BMP4M.03.01

value: genomic DNA

value: Cell Line

value: Embryonic Stem Cell

value: Histone H3K27ac

value: Active Motif


title: Whole genome shotgun bisulf. sequencing: mesenchymal cells derived from H1 embryonic stem cells; methylC-seq_h1-msc_r1a

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of mesenchymal cells derived from H1 embryonic stem cells
Library name: methylC-seq_h1-msc_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11129
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11127
****************
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: GSM864032_UCSD.H1_Derived_Mesenchymal_Stem_Cells.Bisulfite-Seq.methylC-seq_h1-msc_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-msc_r1a.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library methylC-seq_h1-msc_r1a were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12974
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HDMSC BS 1a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r1a EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 953,202,149
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.02
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM864032_UCSD.H1_Derived_Mesenchymal_Stem_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-msc_r1a-methylC-seq_h1-msc_r2a.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 Derived Mesenchymal Stem Cells combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12977
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HDMSC BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Combined Libraries EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,592,748,764
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.01

SPECIAL NOTE: generated from combined data in GSM864032, GSM864033 (thus .wig files on these records are identical)

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

source_name: H1-Mesenchymal Stem Cell Line, biological replicate 1 (r1); methylC-seq_h1-msc_r1a

extract_protocol: Library construction protocol: Five µg of genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 300-500 bp, followed by concentration and size selection with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA) at 0.9 X volume, then end repair with dCTP-free dNTPs and addition of a 3'A base. Paired-end cytosine methylated adapters (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16degC for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads at 0.9 X volume. Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 31 µM dNTPs, 1 µl P7 primer (10 µM), 1 µl Primer5+3 (10 µM), for a final reaction volume of 50 µl. The thermocycling parameters were: 95degC 2 min, 98degC 30 sec, then 6 cycles of 98degC 15 sec, 60degC 30 sec and 72degC 4 min, ending with one 72degC 10 min step. The reaction products were purified using AMPure XP beads at 0.9X volume (two rounds).  Two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding two independent libraries from the same biological sample.

value: H1 Derived Mesenchymal Stem Cells

value: Thomson Laboratory

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: Replicate 1

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: [E-MTAB-607] Smed_SOLiD_1hr

status: Public on Jan 20 2012

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

description: Performer: DKFZ-SFG

library_source: transcriptomic

data_processing: processed data not provided

molecule: total RNA

organism: Schmidtea mediterranea

growth_protocol: grow | Animals were kept at 20C in Montjuic solution (1 mM CaCl2, 0.1 mM KCl, 1.6 mM NaCl, 1.2 mM NaHCO3, 0.1 mM MgCl2, 1mM MgSO in water) and fed with veal liver once per week.

extract_protocol:
nucleic_acid_extraction | Total RNA was extracted using TRIzol (Invitrogen). Strand-specific sequencing libraries were prepared from polyA RNA selected material using Applied Biosystems Whole Transcriptome Library Preparation protocol (Part number 4409491 Rev. C). In brief, 1 mg of polyA RNA was isolated using the MicroPoly(A)Purist kit (Ambion), fragmented using RNAse III (Applied Biosystems) and column purified. SOLiD sequencing adapters were ligated to the RNA RNA using components from the SOLiD Small RNA Expression Kit (Applied Biosystems). Afterwards, the RNA was reverse transcribed using ArrayScript Reverse Transcriptase and cDNA purified using the MinElute PCR purification kit (Qiagen). cDNA fragments were separated using by electropheresis on Novex 6% TBE-Urea gels, stained with SYBR Gold nucleic acid gel stain and sequences between 100-200 nt were selected. Afterwards, fragments were PCR amplified using AmpliTaq for 15 cycles to obtain templates for emulsion PCR and sequencing.
sequencing |  Emulsion PCR and sequencing was performed according to the manufacturers instructions and each sample was sequenced in one quadrant of a flow cell using SOLiD Version 3 chemistry.

treatment_protocol: specified_biomaterial_action | For each sample, 5 planarian trunks were dissected from heads and tails. For control samples, samples were frozen immediately after dissection. The 1 and 6 hr samples were generated the following way:  At timepoint 0, the head and the tail was amputated, so there were now 3 pieces: one animal => head + trunk + tail. These 3 pieces were kept in the same culture vessel together and all allowed to regenerate. Each piece started to regenerate at each wound.  After 1 hr or 6 hrs, all three pieces (including whatever regenerated in this short period of time) were extracted together (head + trunk + tail).

tag: material type

tag: organismpart

value: head, trunk and tail fragments

value: asexual

tag: strainorline

tag: genotype


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in BMP4 Mesendoderm Cells; renlab.H3K27me3.BMP4M.03.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK311
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11180
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11177
****************
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: GSM864036_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K27me3.AK311.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.BMP4M.03.01.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK311, 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.12852
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,486,599
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.1888
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.329
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8875
IROC_PERCENTILE: 57
POISSON_SCORE: 0.4081
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM864036_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K27me3.AK311.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.BMP4M.03.01.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK311, 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.12861
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDM H3K27me3 11
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK311 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,486,599
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.1888
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.329
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8875
IROC_PERCENTILE: 57
POISSON_SCORE: 0.4081
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K27me3.BMP4M.03.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Between 25 and 35

value: Male

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Whole genome shotgun bisulf. sequencing: mesenchymal cells derived from H1 embryonic stem cells; methylC-seq_h1-msc_r2a

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing of mesenchymal cells derived from H1 embryonic stem cells
Library name: methylC-seq_h1-msc_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11130
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11128
****************
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: GSM864033_UCSD.H1_Derived_Mesenchymal_Stem_Cells.Bisulfite-Seq.methylC-seq_h1-msc_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-msc_r2a.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library methylC-seq_h1-msc_r2a were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12971
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HDMSC BS 2a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r2a EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 639,546,615
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 83

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

ANALYSIS FILE NAME: GSM864033_UCSD.H1_Derived_Mesenchymal_Stem_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-msc_r1a-methylC-seq_h1-msc_r2a.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 Derived Mesenchymal Stem Cells combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12977
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HDMSC BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Combined Libraries EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,592,748,764
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.01

SPECIAL NOTE: generated from combined data in GSM864032, GSM864033 (thus .wig files on these records are identical)

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

source_name: H1-Mesenchymal Stem Cell Line, biological replicate 2 (r2); methylC-seq_h1-msc_r2a

value: H1 Derived Mesenchymal Stem Cells

value: Thomson Laboratory

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: Replicate 2

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 16degC for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: WT

city: Utrecht

last: Wösten

address: Padualaan 8

country: Netherlands

institute: Utrecht University

data_processing: The sequenced reads were mapped to the genome sequence using the program Tophat 1.0.13 and Bowtie 0.12.5, using default settings with the exception of the minimum and maximum intron length (10 and 400 bp, respectively).

molecule: polyA RNA

organism: Schizophyllum commune

source_name: Whole colony

growth_protocol: Colonies were grown from plug inoculum. Plugs of the compatible monokaryons were placed next to each other. Cultures were incubated for 5 days at 25 degrees C in continuous light.

extract_protocol: Three biological replicates were pooled. Colonies were frozen in liquid nitrogen and powdered. Total RNA was isolated using the Trizol reagent. The quality of the RNA was analysed on a RNA 6000 Lab-on-a-Chip using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). The Illumina mRNA-Seq Sample Prep Kit was used to process the samples. The sample preparation was performed according the Illumina protocol "Preparing Samples for Sequencing of mRNA" (1004898 Rev. D).

tag: parental strain

value: Cross of H4-8 and H4-8b

value: wild-type


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in BMP4 Mesendoderm Cells; renlab.H3K27me3.BMP4M.04.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK314
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11189
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11184
****************
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: GSM864801_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K27me3.AK314.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.BMP4M.04.01.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK314, 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.12853
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,815,995
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.1592
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.2976
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.8836
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3899
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM864801_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K27me3.AK314.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.BMP4M.04.01.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK314, 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.12862
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDM H3K27me3 14
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK314 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,815,995
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.1592
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.2976
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.8836
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3899
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K27me3.BMP4M.04.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Male

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: [E-MTAB-607] Smed_Illumina_7

description: Performer: DKFZ-GPCF

extract_protocol:
nucleic_acid_extraction |Total RNA was extracted from planarian fragments using Trizol. 0.5 microgram of polyA RNA was isolated from total RNA using the MicroPoly(A)Purist kit (Ambion), fragmented and precipitated. First strand cDNA was synthesized using SuperScript II (Invitrogen) and the second strand was added using RNAseH and DNA Polymerase I. cDNA was purified with the QIAquick PCR purification kit (QIAGEN) and ends were repaired with Klenow DNA polymerase. The 3 prime ends were adynlated with Klenow exo (3 prime to 5 prime exo minus) enzyme and ligated to the sequencing adapters. cDNA templates were separated by Agarose gel electrophoresis and ca. 200 bp sequences were selected. Templates for sequencing were PCR amplified using Phusion DNA polymerase (Finnzymes Oy) and purified with the QIAquick PCR purification kit (QIAGEN).
sequencing | 2x36 bp paired-end sequencing was performed on a Genome Analyzer II instrument according to the manufacturer's instructions.

treatment_protocol: specified_biomaterial_action | Asexual planarians of the species Schmidtea mediterranea were starved for one week prior to decapitation with a razor blade. Regeneration was allowed to occur for 16 different periods of time (30 min, 1, 2, 3, 4, 5, 6, 8, 10, 12, 16, 18, 24, 36, 48, 72h). A second cut anterior to the pharynx (pre-pharyngeal cut) was performed to separate the anterior regenerating part from the rest of the body. 8 planarian pre-pharyngeal pieces from similar time points were pooled (Library 1: 30 min and 1h, four animals each; Library 2: 2h and 3h, four animals each; Library 3: 4, 5, 6, and 8h, two animals each; Library 4: 10, 12, 16, and 18h, 2 animals each; Library 5: 24, 36, 48, and 72h, 2 animals each), and immediately deep-frozen. 16 non-regenerating pieces served as two independent biological replicates (8 animals each; Library 6 and 7). Samples were processed in two batches: material from control Library 6 was processed together with Libraries 1-3, while contrl Library 7 was processed together with Libraries 4 and 5.

value: pre-pharyngeal fragment, regenerating the head

value: asexual


title: [E-MTAB-607] Smed_Illumina_6

description: Performer: DKFZ-GPCF


title: [E-MTAB-607] Smed_SOLiD_ctrl2

description: Performer: DKFZ-SFG


title: Reference Epigenome: ChIP-Seq Input from BMP4 Trophoblast Cells; renlab.Input.BMP4T.03.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK315
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11192
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
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: GSM864803_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.Input.AK315.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.BMP4T.03.01.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on H1 BMP4 Derived Trophoblast Cultured Cells, Library AK315, 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.12851
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,078,623
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0134
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.1571
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.6949
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3439
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM864803_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.Input.AK315.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.BMP4T.03.01.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AK315, 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.12860
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDT Input 15
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Library AK315 EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,078,623
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0134
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.1571
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.6949
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3439
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.Input.BMP4T.03.01

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

value: ChIP-Seq Input

value: Input


title: UNC_FaireSeq_NHBE

source_name: NHBE

tag: datatype

value: FaireSeq

tag: datatype description

value: FAIRE-seq Open Chromatin

tag: controlid

tag: labversion

value: input was generic_male (should have been female),baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_female,p-value cutoff:0.1

tag: replicate

tag: cell organism

value: human

tag: cell description

value: bronchial epithelial cells

tag: cell karyotype

value: normal

tag: cell lineage

value: endoderm

tag: cell sex

value: F

value: align_on_cluster_bwa.pl v 1

tag: replicate description

value: tier 1


title: [E-MTAB-607] Smed_Illumina_5

description: Performer: DKFZ-GPCF

tag: batch

tag: Sex


title: Hom2

value: Cross of H4-8 and H4-8b

value: Hom2 deletion


title: Fst4

value: Fst4 deletion


title: [E-MTAB-607] Smed_SOLiD_ctrl1

description: Performer: DKFZ-SFG

tag: material type

tag: organismpart

value: asexual


title: CD4_H3K4me2_ChIAPET_Exp2

tag: cell type

value: CD4+ T cells

tag: antibody

tag: vendor

value: Millipore, 07-030


title: [E-MTAB-607] Smed_Illumina_3

description: Performer: DKFZ-GPCF

value: pre-pharyngeal fragment, regenerating the head

tag: strainorline

tag: genotype


title: [E-MTAB-607] Smed_Illumina_4

description: Performer: DKFZ-GPCF


title: Deep-sequenced simplified Hi-C

city: Montpellier

first: Tom

last: Sexton

address: 141, rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS UPR 1142

data_processing:
deep10k_normalized.txt; genome build: dm3
deep20k_normalized.txt; genome build: dm3
deep40k_normalized.txt; genome build: dm3
deep80k_normalized.txt; genome build: dm3
deep160k_normalized.txt; genome build: dm3
Paired-end reads were mapped to the Drosophila melanogaster genome (assembly dm3) using the maq program with standard parameters (quality>30). Unmapped or non-unique mapped reads were discarded. We then divided read pairs into four groups: SS (reads mapping to the same restriction fragment, or to two adjacent restriction fragments); S2 (reads in which both ends mapped precisely on the DpnII site); S1 (reads in which one of the ends mapped precisely on the DpnII site); S0 (reads in which both ends did not map precisely to a DpnII site). SS, S2 and S1 pairs were discarded from subsequent analysis. Mapped reads were then associated with the first restriction fragment end encountered when moving from the mapped position in the appropriate strand. All subsequent analysis was done in the space of fragment end pairs. The Drosophila genome contains 464,246 restriction fragments. After discarding low mappability fragments 301,687 fragments are left (and each defines two fragment ends). A model accounting for systematic biases in contact probability was constructed as previously (Yaffe and Tanay; Nature Genetics, 43, p.1059-65). Briefly, we used the local G+C content of up to 200 bp from the restriction site (agc, bgc), and the DpnII restriction fragment lengths (alen, blen), to correct for systematic biases in Hi-C coverage by modeling: P(Xa,b) = Pprior . Flen(alen,blen) . Fgc(agc,bgc). We estimated maximum likelihood model parameters (the matrices Flen and Fgc) through application of an iterative algorithm as described, using 20 bins for G+C content and 20 bins for fragment length.

organism: Drosophila melanogaster

source_name: 16-18 hr embryos

growth_protocol: Oregon-R w1118 flies were raised in standard cornmeal yeast extract media at 25°C. Egg laying was performed on plates with standard vinegar medium and yeast. Embryos were collected in 0.03% Triton-X100, 0.4% NaCl 16-18 hr after egg laying.

extract_protocol: ~3000-4000 embryos were dechorionated for 5 min in fresh bleach, before douncing in 5 ml fix buffer (2% formaldehyde, 15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 0.1% Triton-X100, 0.5 mM DTT, protease inhibitor cocktail (Roche)) and fixed for a total of 10 min at 25°C, 750 rpm on a shaker. After quenching with 5 ml 2 M glycine, nuclei were collected by centrifugation for 5 min at 4500 g, 4°C, then washed once with 5 ml fix buffer (without formaldehyde) and once with 1.25 x NEB3 buffer (New England Biolabs), with centrifugation for 5 min at 4500 g, 4°C each time. Nuclei were resuspended in 300 µl 1.25 x Dpn II buffer (New England Biolabs) plus 0.3% SDS and incubated for 1 hr at 37°C, 1000 rpm on a shaker. Triton-X100 was added to a final concentration of 2% and the nuclei were incubated for a further 1 hr at 37°C, 1000 rpm, before overnight digestion with 1500 U Dpn II (New England Biolabs) at 37°C, 1000 rpm. The restriction enzyme was inactivated by incubation for 20 min at 65°C, 1000 rpm with SDS at a final concentration of 1.3%, before dilution of the chromatin in 10 ml 1x T4 DNA ligase buffer (New England Biolabs) plus 1% Triton-X100 and incubation for 1 hr at 37°C, 750 rpm. The chromatin was ligated for 4 hr at 25°C, 750 rpm with 40,000 U T4 DNA ligase (New England Biolabs) then crosslinks were reversed overnight at 65°C, 750 rpm in the presence of 150 µg/ml proteinase K. The 3C DNA was then purified by 1 hr treatment with 40 µg/ml RNase A at 37°C, 750 rpm, phenol extraction, phenol/chloroform extraction and ethanol precipitation. The DNA was quantified with the Qubit dsDNA assay (Invitrogen). Aliquots of 5 µg 3C DNA were sonicated in a Bioruptor (Diagenode) in 50 µl volumes in sonication buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS) to obtain a smear between 500-1500 bp. The sonicated 3C DNA was then purified by phenol/chloroform extraction and ethanol precipitation and quantified with the Qubit dsDNA assay (Invitrogen). Libraries for paired-end sequencing were made from 500 ng aliquots of sonicated 3C DNA using Illumina reagents and protocols, with size selection for products of ~800 bp for the deep-sequenced sample, or 300-800 bp for the pilot sample.

tag: developmental stage

value: Embryo

tag: age

value: Oregon-R w1118


title: [E-MTAB-607] Smed_Illumina_1

description: Performer: DKFZ-GPCF


title: [E-MTAB-607] Smed_Illumina_2

description: Performer: DKFZ-GPCF


title: [E-MTAB-607] Smed_SOLiD_6hr

description: Performer: DKFZ-SFG

value: head, trunk and tail fragments


title: [E-MTAB-652] PH-ChIP d5

description: Performer: MAX-PLANCK-INSTITUTE

source_name: PH-ChIP d5

growth_protocol: grow | S2 cells were grown in Schneiders Drosophila medium (Serva) supplemented with 10% fetal calf serum and antibiotics (0.3 mg/ml penicillin, 0.3 mg/ml streptomycin and 0.75 ug/ml amphotericin B).

extract_protocol:
nucleic_acid_extraction | 4x107 S2 cells in 40 ml Schneider's medium were fixed for 10 minutes at room temperature by addition of 1% formaldehyde. After 2 ice-cold washes in PBS, cells were lysed in 2.6ml of L2 buffer (L2: 1% SDS, 5mM EDTA, 50mM Tris pH8). The lysate was sonicated to fragment genomic DNA to an average length of around 500 bp, and then diluted 10-fold in DB (DB: 0.5 % NP40, 5 mM EDTA, 200 mM NaCl, 50 mM Tris pH8). Anti-mouse IgG M280 magnetic beads were coated with mouse monoclonal anti-GFP antibody (clone 496) by rotating together for 6 hours at 4C (80mg antibody for 160 ml M280 slurry), followed by washing in DB. For each immunoprecipitation, 160 ml slurry of anti-GFP-coated beads were added to the sonicated lysate from 107 cells and rotated overnight at 4C. Beads were washed once quickly and then 3x for 5 minutes on ice in WB (WB: 0.1% SDS, 1% NP40, 2mM EDTA, 500mM NaCl, 20mM Tris pH8), followed by 3x for 5 minutes on ice in TE (TE: 1mM EDTA, 10mM Tris pH8). Precipitated chromatin was eluted from the beads, and fixation reversed, by incubation overnight at 65C in 60ml EB (EB: 2% SDS, 1mM EDTA, 10mM Tris pH8). DNA was purified using a Qiagen MinElute clean-up kit, and eluted in 30ml (elution buffer: 10mM Tris pH8.5).
sequencing | paired-end strategy (2x36bp)
data_generation | Base calls were done by Solexa/Illumina software pipeline. SRF files were created from the Illumina qseq files with illumina2srf from the sequenceread package version 2.1.4 (options: -P -N '<run id>:%l:%t:' -n '%x:%y').
alignment | The bowtie software was used to align reads against the Dm5.30 reference genome. Up to two mismatches in each read were allowed. The options for bowtie were: -S -p 20 -v 2 -X 600 --tryhard -m 1 --best --strata

treatment_protocol: specified_biomaterial_action | Cells were transfected with FuGENE 6 Transfection Reagent (Roche) and stable lines were selected with 100 mg/ml Hygromycin-B as previously described 25 or in case of co-transfection with pCoPuro with 100mg/ml puromycin. Cells containing stably integrated arrays of Lac Operators on chromosome 3R were obtained by co-transfection with pAFS51 56 and pCoPuro, followed by subsequent cloning of the cell line. Pulse-overexpression of CID and pulse-co-overexpression of CID and HP1 were induced using the metallothionein promoter (pMT/V5 vectors) with 500 mM CuSO4 for 48 h (start day -2). At day 0 Fluorescent Activated Cell Sorting (FACS) was used to select the cells with the highest levels of GFP expression (>75% of max.) on a MoFlo sorter using 70 mm 11 diameter nozzle at 60 psi. Cells were immediately plated in fresh medium lacking inducing reagents for the chase. For HDAC inhibition cells were incubated with 75nM Trichostatin A (Cell Signaling Technology, Inc) from the beginning of CIDGFP pulse (day -2).

value: cell

tag: cellline

value: Schneider S2

value: male

tag: immunoprecipitate

value: CID island


title: [E-MTAB-652] PH-Input d5

description: Performer: MAX-PLANCK-INSTITUTE

source_name: PH-Input d5

extract_protocol:
nucleic_acid_extraction | 4x107 S2 cells in 40 ml Schneider's medium were fixed for 10 minutes at room temperature by addition of 1% formaldehyde. After 2 ice-cold washes in PBS, cells were lysed in 2.6ml of L2 buffer (L2: 1% SDS, 5mM EDTA, 50mM Tris pH8). The lysate was sonicated to fragment genomic DNA to an average length of around 500 bp, and then diluted 10-fold in DB (DB: 0.5 % NP40, 5 mM EDTA, 200 mM NaCl, 50 mM Tris pH8).
sequencing | paired-end strategy (2x36bp)
data_generation | Base calls were done by Solexa/Illumina software pipeline. SRF files were created from the Illumina qseq files with illumina2srf from the sequenceread package version 2.1.4 (options: -P -N '<run id>:%l:%t:' -n '%x:%y').
alignment | The bowtie software was used to align reads against the Dm5.30 reference genome. Up to two mismatches in each read were allowed. The options for bowtie were: -S -p 20 -v 2 -X 600 --tryhard -m 1 --best --strata


title: Rpb3-chIP-seq Asynchronous fkh1Δfkh1Δ2C 2

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description: IP-DNA (Rpb3) from Asynchronous S. cerevisiae cells

data_processing: Reads were mapped allowing 2 mismatches to the S. cerevisiae genome (release r.64). Reads were then binned into 50 bp bins and quantile normalized across experiments.

organism: Saccharomyces cerevisiae

source_name: Rpb3-chIP-seq Asynchronous fkh1Δfkh1Δ2C

growth_protocol: Cells grown in YEPD at room temp.

extract_protocol: Samples were prepared for sequencing using Illumina chIP-seq protocol.

treatment_protocol: chIP was performed as described in Viggiani, C.J., Aparicio, J.G., and Aparicio, O.M. (2009). ChIP-chip to analyze the binding of replication proteins to chromatin using oligonucleotide DNA microarrays. Methods Mol Biol 521, 255-278.

tag: strain

tag: cell stage

value: Asynchronous


title: Rpb3-chIP-seq G1 Arrested fkh1Δfkh1Δ2C 2

description: IP-DNA (Rpb3) from G1-arrested S. cerevisiae cells

source_name: Rpb3-chIP-seq G1 Arrested fkh1Δfkh1Δ2C

growth_protocol: Cells grown in YEPD at room temp with α-factor for 4 hours.


title: Rpb3-chIP-seq G1 Arrested fkh1Δfkh1Δ2C 1


title: Pilot simplified Hi-C

data_processing:
10k_bins.txt; genome build: dm3
20k_bins.txt; genome build: dm3
40k_bins.txt; genome build: dm3
80k_bins.txt; genome build: dm3
160k_bins.txt; genome build: dm3
pilot10k_normalized.txt; genome build: dm3
pilot20k_normalized.txt; genome build: dm3
pilot40k_normalized.txt; genome build: dm3
pilot80k_normalized.txt; genome build: dm3
pilot160k_normalized.txt; genome build: dm3
Paired-end reads were mapped to the Drosophila melanogaster genome (assembly dm3) using the maq program with standard parameters (quality>30). Unmapped or non-unique mapped reads were discarded. We then divided read pairs into four groups: SS (reads mapping to the same restriction fragment, or to two adjacent restriction fragments); S2 (reads in which both ends mapped precisely on the DpnII site); S1 (reads in which one of the ends mapped precisely on the DpnII site); S0 (reads in which both ends did not map precisely to a DpnII site). SS, S2 and S1 pairs were discarded from subsequent analysis. Mapped reads were then associated with the first restriction fragment end encountered when moving from the mapped position in the appropriate strand. All subsequent analysis was done in the space of fragment end pairs. The Drosophila genome contains 464,246 restriction fragments. After discarding low mappability fragments 301,687 fragments are left (and each defines two fragment ends). A model accounting for systematic biases in contact probability was constructed as previously (Yaffe and Tanay; Nature Genetics, 43, p.1059-65). Briefly, we used the local G+C content of up to 200 bp from the restriction site (agc, bgc), and the DpnII restriction fragment lengths (alen, blen), to correct for systematic biases in Hi-C coverage by modeling: P(Xa,b) = Pprior . Flen(alen,blen) . Fgc(agc,bgc). We estimated maximum likelihood model parameters (the matrices Flen and Fgc) through application of an iterative algorithm as described, using 20 bins for G+C content and 20 bins for fragment length.

source_name: 4-12 hr embryos


title: Rpb3-chIP-seq Asynchronous WT 1

source_name: Rpb3-chIP-seq Asynchronous WT

value: WT


title: Rpb3-chIP-seq Asynchronous WT 2


title: Rpb3-chIP-seq Asynchronous fkh1Δfkh1Δ2C 1


title: RNA-seq G1 Arrested WT 2

description: rDNA Filtered RNA from G1-arrested S. cerevisiae cells

source_name: RNA-seq G1 Arrested WT

extract_protocol: ssRNA-seq was performed as described in Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H., and Soldatov, A. (2009). Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37, e123. Instead of polyA purification, rRNA was removed using Ribominus (Invitrogen).

treatment_protocol: RNA was isolated from 20 ml OD 1.0 cells using RiboPure Yeast Kit (Ambion)


title: RNA-seq Asynchronous WT 2

description: rDNA Filtered RNA from Asynchronous S. cerevisiae cells

source_name: RNA-seq Asynchronous WT


title: RNA-seq G1 Arrested fkh1Δfkh1Δ2C 2

source_name: RNA-seq G1 Arrested fkh1Δfkh1Δ2C


title: Rpb3-chIP-seq G1 Arrested WT 2

source_name: Rpb3-chIP-seq G1 Arrested WT


title: Rpb3-chIP-seq G1 Arrested WT 1


title: RNA-seq Asynchronous fkh1Δfkh1Δ2C 1

source_name: RNA-seq Asynchronous fkh1Δfkh1Δ2C


title: RNA-seq Asynchronous fkh1Δfkh1Δ2C 2


title: Nodular tumor 8, lane 2

status: Public on Feb 01 2012

city: New Haven

first: Christopher

last: Heffelfinger

state: Ct

address: 333 Cedar Street

institute: Yale University

description: Tumor was extracted via mohs surgery. Total RNA was extracted via mirVana total RNA extraction kit

data_processing: miRExpress was used to collapse raw fastq files into unique tags and number of appearances, and trim adapter sequences from each unique tag (see *merge.trim.txt files). Data table for raw expression was created by aligning sequences to annotated miRNA precursor sequences in miRBase ver 15.0 then the number of hits on each annotated miRNA was calculated.

source_name: Nodular basal cell carcinoma

extract_protocol: Illumina Small RNA version 1.5 protocol

value: Basal Cell Carcinoma, nodular


title: RNA-seq G1 Arrested fkh1Δfkh1Δ2C 1


title: RNA-seq Asynchronous WT 1


title: BrdU-IP-seq fkh1Δfkh1Δ  2

description: BrdU-IP-DNA from HU arrested S. cerevisiae cells

data_processing: Reads were mapped allowing 2 mismatches to the S. cerevisiae genome (release r.64). Reads were then binned into 50 bp bins, quantile normalized across experiments and median smoothed with a 50 bp window.

source_name: BrdU-IP-seq fkh1Δfkh1Δ

growth_protocol: Cells grown in YEPD at room temp with α-factor for 4 hours. Then cells were spun down and resuspended in YEPD+HU+BrdU and grown for 1hr prior to harvesting.

treatment_protocol: BrdU-Incorperated-DNA was extracted as described in Viggiani et al. 2010, Cold Spring Harbor Protocols.

value: 1hr HU arrest after release from 4hr α-factor arrest


title: BrdU-IP-seq fkh1Δfkh1Δ 1


title: BrdU-IP-seq fkh1Δfkh1Δ2C  2

source_name: BrdU-IP-seq fkh1Δfkh1Δ2C


title: BrdU-IP-seq fkh1Δfkh1Δ2C 1


title: BrdU-IP-seq fkh2Δ 1

source_name: BrdU-IP-seq fkh2Δ


title: Populus yunnanensis, males exposed to salinity stress, leaves

city: chengdu

first: Hao

last: Jiang

address: CIB-CAS

country: China

institute: CIB-CAS,China

description: DGE tag profiling.

data_processing: Counts: 3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences; Empty reads removal (reads with only 3' adaptor sequences but no tags); Low quality Tags removal (Tags with unknown sequences ‘N'); Removal of Tags which are too long or too short, leaving Tags of 21nt long; Removal of Tags with a copy number of 1 (probably be sequencing error); Generate Clean Tags. Clean tags mapped to reference sequences (poplar genome: Populus trichocarpa v1.1) from multiple genes were filtered. Remaining clean tags were designated as the distinct tags for further analysis. The number of distinct tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).

organism: Populus yunnanensis

source_name: leaf, male, salinity stress

growth_protocol: Cuttings were planted in 10-liter plastic pots filled with 8 kg homogenized soil at normal condition for about 4 months.

extract_protocol: Total RNA was extracted from three biological replicates (three plants each) using the E.Z.N.A.TM Plant RNA Kit (Omega, USA) according to the manufacturer’s instructions. Residual genomic DNA was removed with DNase I and its integrity was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). RNA samples from 9 individuals of a treatment were pooled with equal proportion. Double-stranded cDNA was synthesized using oligo (dT) beads. The cDNA was then digested with an anchoring restriction enzyme Nla III, which recognizes and cuts 3’ 'CATG'. The digested cDNA samples were ligated to Illumina specific adapter 'A',  containing a recognition site for enzyme Mme I. Following Mme I digestion, the Illumina specific adapter 'B' containing a 2 bp degenerated 3' overhang was ligated. The adapter-ligated cDNA tag library was then enriched by PCR primers annealing to the adaptor ends. The PCR program was as follows: 30 s at 98 °C, followed by 15 cycles of 98 °C for 10 s, 60 °C for 30 s and 72 °C for 15 s, and then 72 °C for 5 min. After gel-purification, cDNA was used for cluster generation on separated flow cell lane. Sequencing by synthesis was performed using the Illumina Genome Analyzer according to the manufacturer's protocol. Image analysis, base calling, extraction of 17 bp tags and tag counting were performed using the Illumina pipeline.

treatment_protocol: Salt-treated plants were firstly exposed to short-term low concentration salt pre-treatment (25 mM NaCl for 24 h) avoiding large osmotic shock, and then to long-term salinity (50 mM NaCl for 7 days). Control plants were kept in well-watered conditions.

tag: tissue

value: leaf

tag: development stage

value: fourth fully expanded and intact young leaves near the shoot apex of each plant

tag: treatment

value: salinity stress


title: Populus yunnanensis, females without salinity stress, leaves

description: DGE tag profiling.

source_name: leaf, female, no salinity stress

tag: Sex

value: female


title: BrdU-IP-seq fkh1Δ 2

source_name: BrdU-IP-seq fkh1Δ


title: [E-MTAB-698] MaleVNO3_RNA

description: Performer: SC

organism: Mus musculus

growth_protocol: grow | 3 grouped housed male and female mice (C58BL\6J) were euthanized at 8 weeks their vomernasal organs were dissected and the RNA was extracted immediately and stored in RNAlater.

extract_protocol:
nucleic_acid_extraction | RNA was extracted using the RNAeasy kit using a disposable Rance free plastic grinder to homogenize  the sample according to manufactor's instructions.  All RNA was subsequently quantified with a UV-Vis spectrophotometer and visualized for quality using RNA integrity analysis.
specified_biomaterial_action | Total RNA was used to produce RNA-seq libraries as described in Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, 621-628 (2008). Exceptions to the protocol included: i) fragmentation of mRNA was performed by incubating the samples in a 5x fragmentation buffer (Ambion, UK) and at 70ÃâÃÂ° C for 5 minutes followed by removal of fragmentation buffer using sodium acetate/isopropanol precipitation of RNA; ii) after second strand cDNA synthesis, the Illumina Genomic DNA Sample Preparation Kit (Illumina, UK) was used according to manufacturer instructions and with modifications described in Quail, M. A. et al. A large genome center's improvements to the Illumina sequencing system. Nat Methods 5, 1005-1010 (2008).
scanning | Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.
bioassay_data_transformation | SRF file were generated using the standard method for the Illumina platform. Base calling was performed using Illumina pipeline 1.8.70.0 (Bustard 1.8.1a2) with phred quality scores at 64 levels using Illumina pipeline 1.8.70.0 (GERALD). There were 152 cycles of sequencing with 2 reads per cluster, a forward read starting at base 1 and a reverse read starting at base 77.

tag: material type

value: 8 weeks

tag: developmentalstage

value: adult

tag: biosourcetype

tag: biosourceprovider

value: The Scripps Research Institute, La Jolla, California, USA

tag: celltype

value: Mixed


title: RNA-seq G1 Arrested WT 1


title: [E-MTAB-698] FemaleVNO3_RNA

description: Performer: SC

extract_protocol:
nucleic_acid_extraction | RNA was extracted using the RNAeasy kit using a disposable Rance free plastic grinder to homogenize  the sample according to manufactor's instructions.  All RNA was subsequently quantified with a UV-Vis spectrophotometer and visualized for quality using RNA integrity analysis.
specified_biomaterial_action | Total RNA was used to produce RNA-seq libraries as described in Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, 621-628 (2008). Exceptions to the protocol included: i) fragmentation of mRNA was performed by incubating the samples in a 5x fragmentation buffer (Ambion, UK) and at 70ÃâÃÂ° C for 5 minutes followed by removal of fragmentation buffer using sodium acetate/isopropanol precipitation of RNA; ii) after second strand cDNA synthesis, the Illumina Genomic DNA Sample Preparation Kit (Illumina, UK) was used according to manufacturer instructions and with modifications described in Quail, M. A. et al. A large genome center's improvements to the Illumina sequencing system. Nat Methods 5, 1005-1010 (2008).
scanning | Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.
bioassay_data_transformation | SRF file were generated using the standard method for the Illumina platform. Base calling was performed using Illumina pipeline 1.8.67.0 (Bustard 1.8.1a1) with phred quality scores at 64 levels using Illumina pipeline 1.8.67.0 (GERALD). There were 152 cycles of sequencing with 2 reads per cluster, a forward read starting at base 1 and a reverse read starting at base 77.

tag: organismpart

tag: strainorline


title: BrdU-IP-seq fkh1Δ 1


title: BrdU-IP-seq WT 1

source_name: BrdU-IP-seq WT


title: BrdU-IP-seq WT 2


title: gisChiaPet_K562_RNAPII_saturated_rep2

city: Singapore

first: Guoliang

last: Li

address: 60 Biopolis Street, #02-01, Genome

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description:
Chromatin IP against RNAPII followed by close proximity ligation (ChIA-PET), biological replicate 2
ChIA-PET (Pair end Sequencing)

data_processing:
ChIA-PET data was processed with ChIA-PET Tool software (Li et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 11:R22) with modifications:
a) The linker sequences are GTTGGATAAGATATCGCGG and GTTGGAATGTATATCGCGG. b) Previously, the enriched regions from inter-ligation PETs were called first in the ChIA-PET Tool. Now the overlap of the PETs is examined for PET clustering. C) Interaction clusters with Span < 8Kb are filtered out.
Processed data files based on genome build hg19.
Processed data files linked below as supplementary files.  Bam file linked as supplementary file on Series record.

source_name: K562 cells

growth_protocol: Five cell lines, namely MCF7 (ATCC# HTB-22), K562 (ATCC# CCL-243), HCT116 (ATCC# CCL-247), HeLa (ATCC# CCL-2.2), and NB4 (Roussel and Lanotte, 2001) (provided by Dr. Sherman Weissman, Yale University), were grown under standard culture conditions and harvested at log phase.

extract_protocol:
ChIA-PET: ChIP Chromatin was divided into two aliquots and each aliquot was ligated with two different barcoded biotinylated half-linkers (linker A or linker B) that contain a flanking MmeI site using T4 DNA ligase. These chromatins ligated with different linkers were pooled and molecular circularization/ligation was carried out in extremely dilute condition. After ligation, DNA was purified and digested with MmeI. The biotinylated PETs purified on Streptavidin Dynabeads were ligated with a sequencing adapter by T4 DNA ligase (RT for 16h with rotation). The nick on one strand of the DNA at the ligation site was subsequently repaired by incubation with E. coli DNA polymerase I at RT for 2h, followed by 18-20 rounds of PCR. This PCR product was used as the template for Illumina GAIIx 2x36 bp pair end sequencing.
Average insert size: ~200-300bp

treatment_protocol: no treatment

tag: cell line

value: K562 cells

tag: chip antibody

value: RNA Pol II (8WG16 clone, MMS-126R, Covance)


title: [E-MTAB-698] FemaleVNO1_RNA

description: Performer: SC

tag: age


title: [E-MTAB-698] MaleVNO2_RNA

description: Performer: SC


title: gisChiaPet_HeLa_RNAPII_pilot

description:
Chromatin IP against RNAPII followed by close proximity ligation (ChIA-PET)
ChIA-PET (Pair end Sequencing)

source_name: HeLa cells

value: HeLa cells


title: gisChiaPet_NB4_RNAPII_pilot

source_name: NB4 cells

value: NB4 cells


title: gisChiaPet_K562_RNAPII_saturated_rep1

description:
Chromatin IP against RNAPII followed by close proximity ligation (ChIA-PET), biological replicate 1
ChIA-PET (Pair end Sequencing)


title: gisChiaPet_MCF7_RNAPII_saturated_rep2

description:
Chromatin IP against RNAPII followed by close proximity ligation (ChIA-PET), biological replicate 4
ChIA-PET (Pair end Sequencing)

source_name: MCF-7 breast cancer cells

value: MCF-7 breast cancer cells


title: gisChiaPet_HCT116_RNAPII_pilot

source_name: HCT116 cancer cells

value: HCT116 colorectal cancer cells


title: gisChiaPet_K562_RNAPII_pilot


title: Populus yunnanensis, females exposed to salinity stress, leaves

description: DGE tag profiling.

source_name: leaf, female, salinity stress


title: gisChiaPet_MCF7_RNAPII_saturated_rep1

description:
Chromatin IP against RNAPII followed by close proximity ligation (ChIA-PET), biological replicate 3
ChIA-PET (Pair end Sequencing)


title: [E-MTAB-698] FemaleVNO2_RNA

description: Performer: SC


title: gisChiaPet_MCF7_RNAPII_pilot_rep2


title: H2A.Lap1-2_ChIPSeq

city: Canberra

first: Rohan

last: Williams

state: ACT

address: Garran Rd ACTON

country: Australia

institute: ANU

description: ANU/JCSMR/BRF facility

data_processing: A custom pipeline for processing Illumina sequence data is employed, referred to as ChipPy and implemented in the Python programming language (version 2.7), as an extension of the PyCogent genomic biology library. Critical key components of this pipeline were external alignment algorithms (Bowtie version 0.12.5, 64-bit) and database engines (ENSEMBL release 58). All software is available on request from the authors. (Processed data genome build : NCBI m37)

source_name: Chromatin IP against H2A.Lap1 (technical replicate)

growth_protocol: Testis tubules from wild type Balb/c mice were placed in 1-2 ml of ice-cold PBS-GL buffer (PBS supplemented with 5.6mM D-glucose, 5.4mM DL-lactate, 0.5mM DTT, 0.2mM PMSF, and protease inhibitor cocktail (Roche)) and dissected with scissors followed by homogenisation with 3-4 strokes in a Dounce homogeniser (pestle type A, cell integrity monitored by microscopy). The cellular mixture was filtered through a 70Âµm cell strainer to obtain a single cell suspension.

extract_protocol: The nuclear extract was digested for 55-65 minutes at 37Â°C with Micrococcal nuclease (New England Biolabs; 30 units per 220 Î¼l of extract) to obtain â¼ 80% mononucleosomes. Following centrifugation at 10,000g for 5 min, the supernatant (S1) and the resuspended pellet (S2) were dialysed against 10mM Tris, 1mM EDTA, 0.5mM EGTA, pH 7.6, overnight at 4Â°C. The S1 and S2 supernatants were combined and dialysed against 10mM Tris, 1mM EDTA, 0.5mM EGTA, 4% glycerol, pH 7.6, aliquoted and stored at -80Â°C. Histone-DNA complexes were isolated with antibody.

value: Balb/c

value: 30 days old

tag: organ

value: testes

tag: cell type

value: spermatids

tag: chip-antibody


title: H2A.Lap1_ChIPSeq

description: ANU/JCSMR/BRF facility

source_name: Chromatin IP against H2A.Lap1

tag: strain


title: [E-MTAB-698] MaleVNO1_RNA

description: Performer: SC

value: male


title: gisChiaPet_MCF7_RNAPII_pilot_rep1


title: RPB2_Rep1

status: Public on Jan 19 2012

city: Lausanne

first: David

last: Bernasconi

address: Quartier Sorge, Bat. Génopode

department: CIG

country: Switzerland

institute: University of Lausanne

data_processing: Reads mapping at a unique place on the genome (uniquely matching tags) and matching without any mismatch were mapped by Eland. Reads mapping at multiple places on the reference genome (repeated tags) were aligned using “fetchGWI” (www.isrec.isb-sib.ch/tagger/). The number of matches per genome allowed was set to 500 and the reads had to map without any mismatch. ere aligned using “fetchGWI” (www.isrec.isb-sib.ch/tagger/). The number of matches per genome allowed was set to 500 and the reads had to map without any mismatch. Signal from enriched regions were converted into wig format. Genome build: NCBI37/mm9

source_name: Mouse liver cells

growth_protocol: C57/BL6 male, 12-14 week old (at time of sacrifice), mice were housed in a 12h Light/12h dark light regimen for 2 weeks with food and water available ad libitum during night and day.

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

treatment_protocol: They were then entrained with a 12h Light/12h dark light regimen with food access between ZT12 and ZT24 for 7 days (ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off).  At each ZT02 and, as a biological replicate, ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 5 ml of PBS through the spleen and immediately collected. Up to 100 mg of liver was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The rest of the livers was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation.

tag: tissue

value: liver

tag: chip antibody manufacturer

value: Santa Cruz Biotechnology

tag: chip antibody catalog number

tag: chiip antibody lot/batch


title: H3K36_Rep2

value: Abcam


title: Input DNA

description: ANU/JCSMR/BRF facility

source_name: input DNA


title: INPUT_Rep1


title: BrdU-IP-seq fkh2Δ 2

tag: cell stage

value: 1hr HU arrest after release from 4hr α-factor arrest


title: H3K4_Rep2


title: INPUT_Rep2


title: RPC4_Rep2

value: Made in our lab

value: CS681, raised against the C-terminus of RPC4, peptide CSPDFESLLDHKHR (same peptide as CS682, see (Chong, Hu et al. 2001))


title: RPC4_Rep1


title: H3K36_Rep1


title: H3K4_Rep1


title: CGN2

status: Public on Jan 17 2012

city: Columbus

first: Dario

last: Motti

state: Ohio [OH]

address: 700 Childrens Drive

department: Research

institute: Nationwide Children's Hospital

description: Poly-A RNAs from P8 mice CGN neurons in culture

data_processing:
Alignment: Tophat software with default settings except for the following options:  –G option which supplies Tophat with gene model annotation (combined UCSC, Ensembl, and RefSeq annotations) and –i 50 which sets the minimum intron length to 50
Transcript reconstruction and expression estimation: Cufflinks software. At first Cufflinks uses the aligned reads in the dataset to describe a set of transcripts starting from the reads that span splice-junctions. We ran this step using a non-annotated reference genome because without an annotation the software will assemble novel transcripts and isoforms. After transcript assembly, normalized expression levels are estimated and reported as FPKM (Fragments Per Kilobase of exon per Million fragments mapped) together with confidence intervals. A different part of the software, named Cuffcompare (version 0.8.3) classified the reconstructed RNA-species as novel or known according to how they map back to the provided reference annotation. Cuffcompare was run twice, first with a combined reference GTF generated from crossing annotated transcripts found in the UCSC Genome, the Ensembl, and the RefSeq database.  We combined three genome annotations in an effort to minimize falsely identified novel transcripts. UCSC was used as the base since it contained the highest number of annotated RNA species; all non overlapping annotations found in the other databases were added.  We reran Cuffcompare in order to improve the accuracy of read alignment and therefore transcript expression estimation (personal communications with Cole Trapnell).  The nature of the alignment of the reconstructed RNA-specie and the annotated element is reported according to a code letter. For our purposes we isolated from the output only the “=”, “j” and “u” classes (corresponding to a “perfect match” to a known RNA-molecule, new isoforms of known active locus, and to full transcripts never identified before ). We ran Cuffcompare a 2nd time after adding annotation for unknown and novel transcripts assembled by Cufflinks.
Differential expression test: Cuffdiff. Cuffdiff determined statistical significance based on the square root of the Jensen-Shannon divergence between the relative abundance of transcripts. Significance was reported as an uncorrected p-value, and then classified as significant/not –significant after Benjamini-Hochberg correction of the p-value.
Peak data (.bedgraph files) based on mm9 genome build.

source_name: cerebellar granular neurons (CGNs)

growth_protocol: Cells were grown on a Poly-d-lysine (100 ug/mL) and Laminin (5 ug/mL) substrate

extract_protocol: Poly-A selection. RNA was prepared for Next Generation Sequencing following the Illumina mRNA Sample Preparation Guidelines (Illumina, Cat # RS-930-1001)

tag: growth

value: 16 hours in vitro

value: cerebellar granular neurons (CGNs)


title: H2A.Z_ChIPSeq

description: ANU/JCSMR/BRF facility

source_name: Chromatin IP against H2A.Z