title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in Neural Progenitor Cells; renlab.H2BK15ac.NPC.02.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK15ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY9
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13356
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM956004_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK15ac.CY9.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.NPC.02.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK15ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library CY9, 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.16373
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,727,078
FINDPEAKS_SCORE: 0.0909
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2502
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8867
IROC_PERCENTILE: 100
POISSON_SCORE: 0.466
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956004_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK15ac.CY9.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.NPC.02.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK15ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library CY9, 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.16527
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 9
BROWSER_TRACK_NAME: HDNP H2BK15ac Y9
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK15ac Library CY9 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,727,078
FINDPEAKS_SCORE: 0.0909
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2502
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8867
IROC_PERCENTILE: 100
POISSON_SCORE: 0.466
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H2BK15ac.NPC.02.01

value: Male


title: Reference Epigenome: ChIP-Seq Analysis of H2BK120ac in BMP4 Mesendoderm Cells; renlab.H2BK120ac.BMP4M.02.01

status: Public on Jul 07 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: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK120ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK410
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13089
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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM955999_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK120ac.AK410.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.BMP4M.02.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK120ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK410, 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.16450
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,914,486
FINDPEAKS_SCORE: 0.0322
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1756
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.7444
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3211
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM955999_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK120ac.AK410.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.BMP4M.02.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK120ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK410, 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.16604
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 9
BROWSER_TRACK_NAME: HBDM H2BK120ac 10
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK120ac Library AK410 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,914,486
FINDPEAKS_SCORE: 0.0322
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1756
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.7444
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3211
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

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 mesendoderm by treatment with BMP4.; renlab.H2BK120ac.BMP4M.02.01

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 mesendoderm by treatment with BMP4

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

tag: passage

value: Between 25 and 35

tag: medium

tag: Sex

tag: batch

value: Histone H2BK120ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in BMP4 Mesendoderm Cells; renlab.H2BK15ac.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK15ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK419
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13099
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: GSM956002_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK15ac.AK419.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.BMP4M.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK15ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK419, 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.16431
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,946,315
FINDPEAKS_SCORE: 0.0424
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.1883
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.7815
IROC_PERCENTILE: 75
POISSON_SCORE: 0.3329
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956002_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK15ac.AK419.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.BMP4M.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK15ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK419, 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.16585
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 9
BROWSER_TRACK_NAME: HBDM H2BK15ac 19
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK15ac Library AK419 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,946,315
FINDPEAKS_SCORE: 0.0424
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.1883
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.7815
IROC_PERCENTILE: 75
POISSON_SCORE: 0.3329
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

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.H2BK15ac.BMP4M.01.01

value: Histone H2BK15ac

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H2BK120ac in Neural Progenitor Cells; renlab.H2BK120ac.NPC.02.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK120ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY8
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13354
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM956001_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK120ac.CY8.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.NPC.02.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK120ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library CY8, 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.16348
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,509,197
FINDPEAKS_SCORE: 0.0189
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.193
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.7867
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3971
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956001_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK120ac.CY8.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.NPC.02.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK120ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library CY8, 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.16502
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 9
BROWSER_TRACK_NAME: HDNP H2BK120ac Y8
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK120ac Library CY8 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,509,197
FINDPEAKS_SCORE: 0.0189
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.193
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.7867
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3971
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H2BK120ac.NPC.02.01

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress


title: TAX577580N

status: Public on Jul 06 2012

city: Lund

first: Helena

last: Persson

address: Scheelevagen 2

department: Dept of Clinical Sciences, Oncology

country: Sweden

institute: Lund University

library_source: transcriptomic

data_processing:
Reads were filtered using Illumina Pipeline 1.0 default purity filter (chastity >= 0.6).
The 3' adaptor, TCGTATGCCGTCTTCTGCTTG, was removed from the raw reads using ungapped alignment taking base quality into account.
The number of reads was then counted for each unique sequence.
Sequences were aligned to the human genome (UCSC hg18 assembly) and identified by comparison against the positions of mature miRNAs and miRNA precursors from miRBase release 14.
Genome_build: UCSC hg18 assembly, miRBase release 14
Supplementary_files_format_and_content: adaptor-trimmed sequences and counts

molecule: total RNA

source_name: Breast

extract_protocol: Total RNA was extracted using TRIzol and fractionated on a 15% acrylamide, 8M urea gel. Small RNAs 18-35 nt were isolated and ligated sequentially to 5' and 3' adapters as supplied in the Illumina Small RNA v 1 sample preparation kit. Reverse transcription and PCR amplification were performed according to the manufacturer's instructions.

tag: breast cancer patient

tag: tissue type

value: Normal


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in Neural Progenitor Cells; renlab.H2AK5ac.NPC.02.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2AK5ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY7
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM955998_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2AK5ac.CY7.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.NPC.02.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2AK5ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library CY7, 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.16467
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,323,012
FINDPEAKS_SCORE: 0.0156
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1511
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8044
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4164
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM955998_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2AK5ac.CY7.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.NPC.02.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2AK5ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library CY7, 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.16621
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 9
BROWSER_TRACK_NAME: HDNP H2AK5ac Y7
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2AK5ac Library CY7 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,323,012
FINDPEAKS_SCORE: 0.0156
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1511
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8044
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4164
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H2AK5ac.NPC.02.01

value: genomic DNA

value: James Thomson Laboratory

value: Male

value: Histone H2AK5ac


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in Neural Progenitor Cells; renlab.H2AK5ac.NPC.01.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2AK5ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK420
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13101
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10100
****************
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: GSM955997_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2AK5ac.AK420.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.NPC.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2AK5ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK420, 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.16413
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,186,677
FINDPEAKS_SCORE: 0.0042
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0882
HOTSPOT_PERCENTILE: 50
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2138
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM955997_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2AK5ac.AK420.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.NPC.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2AK5ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK420, 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.16567
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 9
BROWSER_TRACK_NAME: HDNP H2AK5ac 20
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2AK5ac Library AK420 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,186,677
FINDPEAKS_SCORE: 0.0042
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0882
HOTSPOT_PERCENTILE: 50
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2138
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H2AK5ac.NPC.01.01

value: Cell Line

value: Embryonic Stem Cell


title: TAX577580TN

value: Tumor-adjacent


title: TAX577453T

value: Tumor


title: TAX577580T


title: TAX577453TN


title: TAX577453N


title: Reference Epigenome: ChIP-Seq Input from Neural Progenitor Cells; renlab.Input.NPC.04.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK407
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13085
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM956029_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Input.AK407.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.NPC.04.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK407, 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.16388
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,184,641
FINDPEAKS_SCORE: 0.0055
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0089
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.0
IROC_PERCENTILE: 21
POISSON_SCORE: 0.0855
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956029_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Input.AK407.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.NPC.04.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK407, 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.16542
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 9
BROWSER_TRACK_NAME: HDNP Input 07
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Library AK407 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,184,641
FINDPEAKS_SCORE: 0.0055
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0089
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.0
IROC_PERCENTILE: 21
POISSON_SCORE: 0.0855
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.Input.NPC.04.01

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms


title: TAX577579TN


title: TAX577579T


title: TAX577745TN


title: TAX577745N


title: TAX577745T


title: TAX577579N


title: hst4_cdc25_0min_IP

city: Beijing

first: Zhi-Xiong

last: Zhou

address: No.7, ZGC Life Science Park

country: China

institute: National Institute of Biological Sciences, Beijing

data_processing:
Basecalling by Illumina Casava software
Sequencing reads were trimmed for index sequence, and mapped to S. pombe reference genome using SOAP2 software, allowing only perfectly and uniquely-matched reads
Genome_build: S. pombe 972 strain
Supplementary_files_format_and_content: bed file. The values indicate the number of sequencing reads mapped to certain location.

organism: Schizosaccharomyces pombe

source_name: Haploid cells

growth_protocol: Cells used for ChIP assay were cultured in EMM (Edinburgh Minimal Medium) with necessary supplements at 30°C unless otherwise noted.

extract_protocol: ChIP DNA or input DNA was pre-denatured at 95°C and quenched on ice. The DNA was mixed with two pre-annealed adaptors added at final concentrations of 1.5 uM each. Adaptor 1 was composed of oligo A (5'-GCTCTTCCGATCXXXXCNNNNNN-3') and oligo B (5'-p-GXXXXGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-NH2-3'). XXXX in the oligo sequence denotes 4-nucleotide multiplex indexes. Adaptor 2 was composed of oligo C (5'-NNNNNNGTTCAGAGTTCTGCGACAGGAGAG-NH2-3') and oligo D (5'-CAAGCAGAAGACGGCATACGACCTCTCCTGTCGCAGAACTCTGAAC-3'). The ligation reaction was conducted using the Quick Ligation Kit (New England Biolabs) at 16°C overnight. The ligation product was then separated on a Low Range Ultra agarose gel (Bio-Rad). DNA in the 250-500-bp range was retrieved with the GFX PCR DNA and Gel Band Purification Kit (GE Healthcare). The gel-purified DNA was amplified by PCR using primers P1 (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA-3') and P2 (5'-CAAGCAGAAGACGGCATACGA-3') for 25 cycles. The PCR product was processed by gel-based size selection, again retaining DNA in the 250-500-bp range. Equal amounts of DNA tagged with different multiplex indexes were mixed together and sequenced on an Illumina GA-II instrument using the sequence primer 5'-ACACTCTTTCCCTACACGACGCTCTTCCGATC-3'.

tag: genotype

value: h- leu1-32 hst4D::kanMX cdc25-22 rad22-CFP-TAP-natMX

tag: chip antibody

value: IgG Sepharose 6 Fast Flow

tag: antibody vendor/catalog#

value: GE Healthcare, 17-0969-02


title: TAX577740T


title: TAX577740N


title: Reference Epigenome: ChIP-Seq Analysis of H2BK120ac in Neural Progenitor Cells; renlab.H2BK120ac.NPC.01.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK120ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK421
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13103
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10100
****************
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: GSM956000_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK120ac.AK421.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.NPC.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK120ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK421, 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.16365
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,820,910
FINDPEAKS_SCORE: 0.009
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1173
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.537
IROC_PERCENTILE: 33
POISSON_SCORE: 0.19
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956000_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK120ac.AK421.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.NPC.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK120ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK421, 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.16519
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 9
BROWSER_TRACK_NAME: HDNP H2BK120ac 21
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK120ac Library AK421 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,820,910
FINDPEAKS_SCORE: 0.009
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1173
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.537
IROC_PERCENTILE: 33
POISSON_SCORE: 0.19
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H2BK120ac.NPC.01.01

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Histone H2BK120ac

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: MG3_hiPSM2_H3K4me3_rep2_ChipSeq

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
05282010_6226EAAXX_B2
Chromatin IP against MG3_hiPSM2_H3K4me3_rep2.

data_processing:
Images analysis and base calling were done using the Solexa pipeline.
Reads were aligned to human genome build hg18 using Bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: Aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: hiPSC_M23F, H3K4me3 ChIP

growth_protocol: hiPS cells M23F (Soldner et al. 2009 [PMID 19269371]) (Whitehead Institute Center for Human Stem Cell Research) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: cell type

value: human induced pluripotent stem cells (hiPSCs)

tag: cell line/clone

tag: antibody vendor

value: Abcam

tag: antibody catalog number


title: BEAF-32_Wingchip3

city: Atlanta

first: Gurudatta

last: Baraka Vishwanathan

state: GA

address: 1510 clifton road ne

department: Biology Department

institute: Emory University

data_processing:
Bowtie 0.12.5
Sequence reads ( all 4 runs were pooled ) were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Data were filtered using the following specifications:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples and a p-value cutoff of 1e-10.
Genome_build: DM3

organism: Drosophila melanogaster

source_name: ChIP against BEAF-32 Wing

growth_protocol: The third instar cells  Wondering cells - strain of Drosophila melanogaster -Oragon R

extract_protocol: 200 imaginal disc were disected in sterile PBS. Cells were crosslinked with 1% formaldehyde in culture media for 10 min at room temperature.  Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200-500 bp DNA fragments.  Chromatin was pre-cleared overnight at 4C with protein A sepharose beads and then incubated overnight with antibody at 4C.  Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4C.  After washing and eluting from beads the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair ('End-It DNA End Repair Kit'  - Epicentre Cat# ER0720) and addition of 'A' base to 3' ends (Klenow 3'-5' exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat#1501300) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.

treatment_protocol: Orgon R  - Wing imaginal tissue

tag: strain

value: Orgon R

tag: tissue

value: L3 Wing imaginal disc-3rd instar

value: BEAF-32B (Bushey et. al 2009)


title: BEAF-32_Input1

source_name: Chromatin Input

tag: sample type

value: input DNA


title: BEAF-32_Wingchip4


title: BEAF-32_Wingchip1


title: BEAF-32_Wingchip2


title: WT-Seedling-RNAseq-3

city: Madison

first: Yufeng

last: Wu

state: WI

address: 1575 Linden Drive

institute: UW-Madison

description: RNAseq of wild type seedling leaf replicate 3

data_processing:
ath_leaf_rep3.bam; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Homozygous seeds of Arabidopsis thaliana mutants in the background of Columbia ecotypes for ddm1-2 were kindly provided by Dr. Olivier Mathieu from Clermont Université in France. After five-day germination in half of MS medium, the seedlings of wild type (Col-0) and ddm1-2 either continued to grow under 16-hour light/8-hour dark cycles at 23 degree for collecting young leave tissues or were transferred into potting soil to grow under the same light-dark condition until flowering. Two-week old leave tissues and closed flower buds from both wild type and ddm1-2 were collected and immediately frozen in liquid nitrogen, respectively. All collected samples were ground into powder for the following DNased-seq and RNA-seq experiments.

extract_protocol: Protocols for nuclei isolation, DNaseI digestion and DNased-seq library preparation were performed exactly as described ( Zhang et al., 2012 in press, GSE26734).  Two biological DNased-seq replicates from leave and flower tissues of both wild type and ddm1-2 were sequenced by using Illumina Genome Analyzer II. The experimental procedures for the total RNA extraction, cDNA synthesis and preparation of barcoded RNA-seq libraries were the same as the published protocol (Zhang et al., 2012 in press). Three biological RNA-seq replicates from both leave and flower tissues of the wild type Col-0 were prepared for Illumina sequencing.  We generated 58 M RNA-seq reads of flower and 43M of leaf. We found that 90.3% ind leaf and 89.6% in flower can be mapped on TAIR10 reference genome using TopHat. Then we use Cufflink to measure the expression level (FPKM) of arabidopsis annotated genes.

value: seedling

tag: genotype/variation

value: wild type


title: WT-Flower-RNAseq-3

description: RNAseq of wild type flower replicate 3

data_processing:
ath_buds_rep3.bam; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)

source_name: flower

value: flower


title: WT-Seedling-RNAseq-1

description: RNAseq of wild type seedling leaf replicate 1

data_processing:
ath_leaf_rep1.bam; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: WT-Seedling-RNAseq-2

description: RNAseq of wild type seedling leaf replicate 2

data_processing:
ath_leaf_rep2.bam; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: WT-Flower-RNAseq-1

description: RNAseq of wild type flower replicate 1

data_processing:
ath_buds_rep1.bam; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: ddm1-flower-replicate1-lane1

description: ddm1 flower replicate 1

data_processing:
ddm1buds_lan1_bowtie.txt; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: WT-flower-replicate2-lane1

description: wild type flower replicate 2

data_processing:
wdbuds_lan2_bowtie.txt; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: ddm1-seedling-replicate1-lane2

description: leaf of ddm1 seedling replicate 2

data_processing:
ddm1leaf_lan2_bowtie.txt; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: WT-flower-replicate1-lane1

description: wild type flower replicate 1

data_processing:
wdbuds_lan1_bowtie.txt; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: TAX577740TN

data_processing:
Reads were filtered using Illumina Pipeline 1.0 default purity filter (chastity >= 0.6).
The 3' adaptor, TCGTATGCCGTCTTCTGCTTG, was removed from the raw reads using ungapped alignment taking base quality into account.
The number of reads was then counted for each unique sequence.
Sequences were aligned to the human genome (UCSC hg18 assembly) and identified by comparison against the positions of mature miRNAs and miRNA precursors from miRBase release 14.
Genome_build: UCSC hg18 assembly, miRBase release 14
Supplementary_files_format_and_content: adaptor-trimmed sequences and counts

value: Tumor-adjacent


title: ddm1-seedling-replicate1-lane1

description: leaf of ddm1 seedling replicate 1

data_processing:
ddm1leaf_lan1_bowtie.txt; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: MG4_hiPSM2_H3K27me3_rep2_ChipSeq

description:
05282010_6226EAAXX_B3
Chromatin IP against H3K27me3 in hIPSC (clone M23F).

source_name: hiPSC_M23F, H3K27me3 ChIP


title: BEAF-32_Input2


title: WT-seedling-replicate2-lane1

description: leaf of wild type seedling replicate 2

data_processing:
wdleaf_lan2_bowtie.txt; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: WT-Flower-RNAseq-2

description: RNAseq of wild type flower replicate 2

data_processing:
ath_buds_rep2.bam; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: UNG+/+ 3

status: Public on Jul 05 2012

city: Madrid

first: Pablo

last: Perez-Duran

address: Melchor Fernandez Almagro, 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description: PCR amplified Smu fragment

data_processing:
Base calling was done with Illumina's Casava 1.7
Reads were aligned with Novoalign v2.07.04
SAM alignments were processed with samtools 0.1.11 into pileup format
A custom perl script was used to filter the positions with Q<20 and compile statistics for each sequence position
Supplementary_files_format_and_content: Complete mutation data in Excel format, description of the columns in the Legend tab

organism: Mus musculus

source_name: Activated primary B cells

growth_protocol: Spleen B cells from the different genotypes were stained with 5uM CFSE (Invitrogen) and were cultured in 50 µM 2-β-Mercaptoethanol (Invitrogen), 10 mM Hepes (Invitrogen), 10 ng/ml IL4 (PeproTech), 25 µg/ml LPS (Sigma-Aldrich), 20 ng/ml BAFF (R&D Systems), and 10% FCS RPMI medium for 4 days. B cells that had undergone five or more cell divisions were isolated by sorting. A fragment of Smu sequence cwas PCR-ed with Pfu Ultra for 25 cycles.

extract_protocol: PCR products were fragmented to a range of 100-300 pb (Covaris S2). DNA was processed through successive enzymatic treatments of end repair, dA tailing, and ligation to adapters according to the manufacturer’s instructions (Illumina). Adapter-ligated libraries were further amplified by PCR with Phusion High-Fidelity DNA Polymerase (Finnzymes) using Illumina PE primers for 10 cycles.

value: UNG+/+

tag: stimulus

tag: sorting

value: Low CFSE (5 divisions or more)


title: UNG+/+ 4

description: PCR amplified Smu fragment


title: UNG-/- 2

description: PCR amplified Smu fragment

value: UNG-/-


title: UNG-/- 3

description: PCR amplified Smu fragment


title: UNG-/- 4

description: PCR amplified Smu fragment


title: UNG+/+ 1

description: PCR amplified Smu fragment


title: AID-/- 1

description: PCR amplified Smu fragment

value: AID-/-


title: UNG+/+ 2

description: PCR amplified Smu fragment


title: Exp3 UNG AID

description: PCR amplified mOrangeSTOP

source_name: Co-transduced NIH-3T3 cells

growth_protocol: Retroviral supernatants were produced in 293T cells by transient calcium phosphate cotransfection with pCL-ECO (Imgenex) and a combination of AID-ER, AIDE58Q-ER, pMX-PIE-OrangeSTOP,adn pBABE-Ugi, pBABE-UNG or pBabe-Empty retroviral vectors. NIH-3T3 cells were transduced with retroviral supernatants for 16 h in the presence of 8 µg/ml polybrene (Sigma-Aldrich) and selected with 0.4 µg/ml puromycin or 100 µg/ml hygromycin. Transduced NIH-3T3 cells were cultured in the presence of 1 µM OHT for 11 days. Orange sequence was PCR-ed with Pfu Ultra for 25 cycles.

tag: vector 1

value: mOrangeSTOP

tag: vector 2

value: AID-ER

tag: vector 3

value: UNG


title: Exp3 Ugi AID-E58Q

description: PCR amplified mOrangeSTOP

value: Ugi


title: Exp3 UNG AID-E58Q

description: PCR amplified mOrangeSTOP


title: Exp3 Ugi AID

description: PCR amplified mOrangeSTOP


title: WT-seedling-replicate1-lane2

data_processing:
wdleaf_lan3_bowtie.txt; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: Exp2 UNG AID-E58Q

description: PCR amplified mOrangeSTOP


title: Exp3 Control AID

description: PCR amplified mOrangeSTOP

value: Empty


title: Exp2 Ugi AID-E58Q

description: PCR amplified mOrangeSTOP


title: Exp2 UNG AID

description: PCR amplified mOrangeSTOP


title: WT-seedling-replicate1-lane1

data_processing:
wdleaf_lan1_bowtie.txt; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01.   To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)


title: Exp2 Ugi AID

description: PCR amplified mOrangeSTOP


title: Exp2 Control AID

description: PCR amplified mOrangeSTOP


title: Exp2 Control AID-E58Q

description: PCR amplified mOrangeSTOP


title: Chip Seq H3K4me3 in ER:Ras-induced senescent IMR90 with Lenti-sh-Rb SLX3617

status: Public on Jul 09 2012

first: Rafik

last: Salama

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg18 genome assembly using bwa 0.6.1 with the default parameters
BAM files were filtered and all reads with quality score below 15 are skipped, then the resulting BAM is filtered using the UCSC Duke excluded regions for hg18
Rseg differential was used to identify significant domains in the data using mode 2 versus input
Genome_build: NCBI Build 36.1 (HG18)
Supplementary_files_format_and_content: UCSC bed format of significant regions identified by Rseg

source_name: IMR90 Human Diploid Fibroblasts

growth_protocol: DMEM supplemented with 10% FBS and antibiotics in 5% oxygen for IMR90 cells

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. After end-repair and addition of an ‘A’ base to the 3’ ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of fourtyfold diluted ‘Adapter oligo mix’ in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with MinElute PCR Purification Kit, and eluted with 32 µl of 10 mM tris buffer at pH8.5. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. 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: 100 nM 4OHT for 6 days in ER:Ras-expressing IMR90 cells to induced ER:Ras

tag: chip antibody catalog #

tag: chip antibody manufacturer

value: Wako

tag: treatment

value: Lenti-sh-Rb

tag: transgene

tag: gender

value: female

tag: cell line

value: H3K4me3 CMA304


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in BMP4 Mesendoderm Cells; renlab.H3K18ac.BMP4M.02.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K18ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK411
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13093
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: GSM956006_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K18ac.AK411.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.BMP4M.02.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K18ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK411, 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.16359
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,874,494
FINDPEAKS_SCORE: 0.1651
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2642
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9326
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4177
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956006_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K18ac.AK411.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.BMP4M.02.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K18ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK411, 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.16513
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 9
BROWSER_TRACK_NAME: HBDM H3K18ac 11
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K18ac Library AK411 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,874,494
FINDPEAKS_SCORE: 0.1651
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2642
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9326
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4177
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

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.H3K18ac.BMP4M.02.01

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 mesendoderm by treatment with BMP4

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

tag: passage

value: Between 25 and 35

tag: medium

tag: Sex

value: Male

tag: batch

value: Histone H3K18ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: AID-/- 2

description: PCR amplified Smu fragment

tag: genotype

value: AID-/-

tag: stimulus

tag: sorting

value: Low CFSE (5 divisions or more)


title: Exp1 UNG AID-E58Q

description: PCR amplified mOrangeSTOP

tag: vector 1

value: mOrangeSTOP

tag: vector 2

tag: vector 3

value: UNG


title: Exp1 Ugi AID-E58Q

description: PCR amplified mOrangeSTOP

value: Ugi


title: UNG-/- 1

description: PCR amplified Smu fragment

value: UNG-/-


title: Exp3 Control AID-E58Q

description: PCR amplified mOrangeSTOP

value: Empty


title: Exp1 UNG AID

description: PCR amplified mOrangeSTOP

value: AID-ER


title: Exp1 Control AID

description: PCR amplified mOrangeSTOP


title: Exp1 Ugi AID

description: PCR amplified mOrangeSTOP


title: SC0017.4_EV_GM

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
GERALD within CASAVA version 1.6.0 (GA184.8_E47_2d,GA184.7_Hdac2_GM,SC0017.2_Snai1_GM,SC0017.4_EV_GM)
GERALD within CASAVA version 1.7.0 (HI022.3_Hdac1_GM)
Genome_build: mm9
Supplementary_files_format_and_content: Illumina ELAND format

source_name: Empty Vector control, Myoblast (for Snai1)

growth_protocol: Muscle satellite cells were isolated from adult C57BL/6 mice and cultured on collagen-coated plates (Roche-Boehringer) in Ham’s complete medium (Ham’s F-10, 20% fetal calf serum, 1% penicillin/streptomycin, and 2.5ng/ml human recombinant bFGF.

extract_protocol: For each transcription factor cTAP were engineered with the in-frame addition of a C-terminal TAP tag, composed of 6 histidine residues and a 3x FLAG tag separated by a Tobacco Etch Virus (TEV) cleavage sequence. Retrovirus was produced in 293FT cells by transient transfection of expression constructs using Calcium Phosphate or linear polyethylenimine (PEI). Virus-containing supernatant was used to infect low-passage primary myoblasts supplemented with Ham’s complete medium and 8µg/ml polybrene. Transgenic cells were obtained by antibiotic selection and maintained in Ham’s complete medium containing 1.0 µg/ml puromycin.     Satellite cell-derived myoblasts stably expressing a C-terminus TAP tagged fusion protein were cross-linked using 1% formaldehyde in 1x PBS for 10 minutes. A solution containing 0.125 M glycine in 1x PBS was used for quenching the cross-linked reaction for 5 minutes at room temperature by gentle horizontal shaking. Cells were harvested by scraping and the cell pellet was dissolved in ChIP lysis buffer (40 mM Tris-HCl, pH 8.0; 1% Triton-X100; 4 mM EDTA; 300 mM NaCl) containing protease inhibitors (Aprotinin, 1 µg/ml; Leupeptin, 5µg/ml, Pepstatin A 1 µg/ml; PMSF, 1mM). Chromatin was fragmented by sonication in a water bath Bioruptor at 4ºC to an average length of 200 base pairs. The lysate was spun at 14K RPM for 15 minutes in a refrigerated centrifuge and the supernatant was diluted 1:1 in ChIP dilution buffer (40 mM Tris-HCl, pH 8.0; 4 mM EDTA, pH 8.0) plus protease inhibitors to reduce the concentration of salt and detergents. The first immunoprecipitation was done using anti 3xFLAG antibody conjugated to agarose beads (Sigma Aldrich) using 20 milligram of cell lysate (protein) as input for 2 hours at 4ºC. Beads containing antigen/antibody complex were washed 3 times with 10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 0.1% Triton-X100 containing protease inhibitors. Protein complex was eluted from M2-conjugated agarose beads using proteolytic cleavage with Tobacco Etch Virus (TEV) protease (Invitrogen) together with competition with 3xFLAG peptide (Sigma Aldrich) at 4ºC overnight. Two additional rounds of elution with 3xFLAG peptides were done using 200 µg/ml of 3xFLAG peptide in TBS (50 mM Tris-HCl, pH 7.4; 150 mM NaCl). The eluted product was used as input for the second affinity pull-down using His-Select nickel beads (Sigma-Aldrich) for three hours at 4ºC following manufacture’s recommendations. Beads were washed three times with wash buffer (20 mM Tris-HCl, pH 7.4; 150 mM NaCl; 5 mM Imidazole). Final DNA/protein complex was eluted by 400 mM imidazole at room temperature. DNA/protein complexes were reverse cross-linked and ChIP DNA was purified by phenol/chloroform extraction followed by ethanol precipitation.

tag: cell type

value: Myoblasts

tag: strain

tag: transcription factor

value: empty vector

tag: tissue

value: skeletal muscle

tag: sample type

value: control


title: GA184.8_E47_2d

source_name: TAP-tagged E47 in 2d differentiating Myoblasts

treatment_protocol: For each transcription factor cTAP were engineered with the in-frame addition of a C-terminal TAP tag, composed of 6 histidine residues and a 3x FLAG tag separated by a Tobacco Etch Virus (TEV) cleavage sequence. Retrovirus was produced in 293FT cells by transient transfection of expression constructs using Calcium Phosphate or linear polyethylenimine (PEI). Virus-containing supernatant was used to infect low-passage primary myoblasts supplemented with Ham’s complete medium and 8µg/ml polybrene. Transgenic cells were obtained by antibiotic selection and maintained in Ham’s complete medium containing 1.0 µg/ml puromycin.     Satellite cell-derived myoblasts stably expressing a C-terminus TAP tagged fusion protein were cross-linked using 1% formaldehyde in 1x PBS for 10 minutes. A solution containing 0.125 M glycine in 1x PBS was used for quenching the cross-linked reaction for 5 minutes at room temperature by gentle horizontal shaking. Cells were harvested by scraping and the cell pellet was dissolved in ChIP lysis buffer (40 mM Tris-HCl, pH 8.0; 1% Triton-X100; 4 mM EDTA; 300 mM NaCl) containing protease inhibitors (Aprotinin, 1 µg/ml; Leupeptin, 5µg/ml, Pepstatin A 1 µg/ml; PMSF, 1mM). Chromatin was fragmented by sonication in a water bath Bioruptor at 4ºC to an average length of 200 base pairs. The lysate was spun at 14K RPM for 15 minutes in a refrigerated centrifuge and the supernatant was diluted 1:1 in ChIP dilution buffer (40 mM Tris-HCl, pH 8.0; 4 mM EDTA, pH 8.0) plus protease inhibitors to reduce the concentration of salt and detergents. The first immunoprecipitation was done using anti 3xFLAG antibody conjugated to agarose beads (Sigma Aldrich) using 20 milligram of cell lysate (protein) as input for 2 hours at 4ºC. Beads containing antigen/antibody complex were washed 3 times with 10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 0.1% Triton-X100 containing protease inhibitors. Protein complex was eluted from M2-conjugated agarose beads using proteolytic cleavage with Tobacco Etch Virus (TEV) protease (Invitrogen) together with competition with 3xFLAG peptide (Sigma Aldrich) at 4ºC overnight. Two additional rounds of elution with 3xFLAG peptides were done using 200 µg/ml of 3xFLAG peptide in TBS (50 mM Tris-HCl, pH 7.4; 150 mM NaCl). The eluted product was used as input for the second affinity pull-down using His-Select nickel beads (Sigma-Aldrich) for three hours at 4ºC following manufacture’s recommendations. Beads were washed three times with wash buffer (20 mM Tris-HCl, pH 7.4; 150 mM NaCl; 5 mM Imidazole). Final DNA/protein complex was eluted by 400 mM imidazole at room temperature. DNA/protein complexes were reverse cross-linked and ChIP DNA was purified by phenol/chloroform extraction followed by ethanol precipitation.

tag: flag immunoprecipitation

value: anti-FLAG M2 agarose resin

tag: 6xhis immunoprecipitation

value: His-Select nickel beads

value: ChIP


title: GA184.7_Hdac2_GM

source_name: TAP-tagged HDAC2 in Myoblasts


title: HI022.3_Hdac1_GM

source_name: TAP-tagged HDAC1 in Myoblasts


title: SC0017.2_Snai1_GM

source_name: TAP-tagged Snai1 in Myoblasts


title: siCtl_KLA_RNA_Seq

first: Joshua

middle: D

last: Stender

address: 9500 Gillman

institute: University of California at San Diego

description: Control siRNA Treated cells

data_processing:
Alignment: Reads were truncated to 36 bp and aligned to the mouse mm9 genome (NCBI Build 37) using eland.  Only reads that mapped to a single, unique position were used for downstream analysis.
Data analysis was performed using HOMER, a software suite for high throughput sequencing analysis (http://biowhat.ucsd.edu/homer/).  Each RNA-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped. Mapped tags only corresponding to the CDS were included in the analysis.
Genome_build: mm9
Supplementary_files_format_and_content: annotatedRNACDS.txt: Matrix showing the values for all ref-seq annotated RNAs for each RNA-seq experiment.  Linked as supplementary file on the Series record.

molecule: polyA RNA

growth_protocol: Cells were grown in DMEM, 10% heat-inactivated FBS, supplemented with penicillin-streptomycin, 5% CO2.

extract_protocol:
RNA was purified using RNeasy Mini Kit (Qiagen) and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit (Ambion, Austin, TX, USA). For quantification, cDNA was generated using the Superscript kit (Invitrogen) and quantitative real-time PCR was performed using gene specific primers.  For sequencing, RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by a P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with Antarctic phosphatase (New England Biolabs, Ipswich, MA, USA) followed by heat-inactivation and overnight precipitation. Poly(A)-tailing and cDNA synthesis was performed as previously described (Ingolia et al., 2009).  However, for reverse transcription, oligos with custom barcodes (see below in []) were used: 5'-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3'.
Custom barcode: siCtl_KLA [AC]
After cDNA synthesis, exonuclease was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of 50-150 nucleotides were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen, Carlsbad, CA, USA). The recovered cDNA was circularized, linearized, amplified for 15 cycles and gel purified as previously described (Ingolia et al., 2009).  The library was sequenced on the Illumina Genome Analyzer 2 according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with siRNA for 48 hours, followed by 4 hours 100 ng/ml KLA.

value: Macrophage

tag: gender

value: Female

tag: genotype/variation

tag: agent

value: LPS (Kdo2-LipidA)


title: siPhF2_KLA_RNA_Seq

description: siPhf2 Treated Cells

extract_protocol:
RNA was purified using RNeasy Mini Kit (Qiagen) and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit (Ambion, Austin, TX, USA). For quantification, cDNA was generated using the Superscript kit (Invitrogen) and quantitative real-time PCR was performed using gene specific primers.  For sequencing, RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by a P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with Antarctic phosphatase (New England Biolabs, Ipswich, MA, USA) followed by heat-inactivation and overnight precipitation. Poly(A)-tailing and cDNA synthesis was performed as previously described (Ingolia et al., 2009).  However, for reverse transcription, oligos with custom barcodes (see below in []) were used: 5'-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3'.
Custom barcode: siPhf2_KLA [CA]
After cDNA synthesis, exonuclease was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of 50-150 nucleotides were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen, Carlsbad, CA, USA). The recovered cDNA was circularized, linearized, amplified for 15 cycles and gel purified as previously described (Ingolia et al., 2009).  The library was sequenced on the Illumina Genome Analyzer 2 according to the manufacturer’s instructions.

value: Phf2 knockdown


title: siCtl_Veh_RNA_Seq

description: Control siRNA Treated cells

extract_protocol:
RNA was purified using RNeasy Mini Kit (Qiagen) and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit (Ambion, Austin, TX, USA). For quantification, cDNA was generated using the Superscript kit (Invitrogen) and quantitative real-time PCR was performed using gene specific primers.  For sequencing, RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by a P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with Antarctic phosphatase (New England Biolabs, Ipswich, MA, USA) followed by heat-inactivation and overnight precipitation. Poly(A)-tailing and cDNA synthesis was performed as previously described (Ingolia et al., 2009).  However, for reverse transcription, oligos with custom barcodes (see below in []) were used: 5'-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3'.
Custom barcode: siCtl_Veh  [GT]
After cDNA synthesis, exonuclease was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of 50-150 nucleotides were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen, Carlsbad, CA, USA). The recovered cDNA was circularized, linearized, amplified for 15 cycles and gel purified as previously described (Ingolia et al., 2009).  The library was sequenced on the Illumina Genome Analyzer 2 according to the manufacturer’s instructions.

value: vehicle


title: siSmyd5_KLA_RNA_Seq

description: siSmyd5 Treated Cells

extract_protocol:
RNA was purified using RNeasy Mini Kit (Qiagen) and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit (Ambion, Austin, TX, USA). For quantification, cDNA was generated using the Superscript kit (Invitrogen) and quantitative real-time PCR was performed using gene specific primers.  For sequencing, RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by a P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with Antarctic phosphatase (New England Biolabs, Ipswich, MA, USA) followed by heat-inactivation and overnight precipitation. Poly(A)-tailing and cDNA synthesis was performed as previously described (Ingolia et al., 2009).  However, for reverse transcription, oligos with custom barcodes (see below in []) were used: 5'-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3'.
Custom barcode: siSmyd5-KLA [AC]
After cDNA synthesis, exonuclease was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of 50-150 nucleotides were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen, Carlsbad, CA, USA). The recovered cDNA was circularized, linearized, amplified for 15 cycles and gel purified as previously described (Ingolia et al., 2009).  The library was sequenced on the Illumina Genome Analyzer 2 according to the manufacturer’s instructions.

value: Smyd5 knockdown


title: siSmyd5_Veh_RNA_Seq

description: siSmyd5 Treated Cells

extract_protocol:
RNA was purified using RNeasy Mini Kit (Qiagen) and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit (Ambion, Austin, TX, USA). For quantification, cDNA was generated using the Superscript kit (Invitrogen) and quantitative real-time PCR was performed using gene specific primers.  For sequencing, RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by a P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with Antarctic phosphatase (New England Biolabs, Ipswich, MA, USA) followed by heat-inactivation and overnight precipitation. Poly(A)-tailing and cDNA synthesis was performed as previously described (Ingolia et al., 2009).  However, for reverse transcription, oligos with custom barcodes (see below in []) were used: 5'-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3'.
Custom barcode: siSmyd5_Veh [GT]
After cDNA synthesis, exonuclease was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of 50-150 nucleotides were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen, Carlsbad, CA, USA). The recovered cDNA was circularized, linearized, amplified for 15 cycles and gel purified as previously described (Ingolia et al., 2009).  The library was sequenced on the Illumina Genome Analyzer 2 according to the manufacturer’s instructions.


title: SC0017_siSna1-2_GM

data_processing:
GERALD within CASAVA version 1.7.0
edgeR 2.2.5 count and fold change analysis
Genome_build: mm9
Supplementary_files_format_and_content: count and fold change

source_name: Myoblast siRNA knockdown of Snai1 & Snai2

extract_protocol: mRNA was purified from 2 µg of total RNA and fragmented according to  the manufacturer’s (Illumina) recommendations. The first and the  second strand cDNA were synthesized followed by end repairing and 3’  end adenylation and adaptor ligation. Ligation products were purified  followed by PCR amplification and the resulting library was analyzed  by Bioanalyzer (Agilent Technologies). Cluster generation was carried  out following Illumina TruSeq SR Cluster Kit v5 and Illumina Cluster  Station was used for cluster generation.

treatment_protocol: Muscle satellite cells were isolated from the hind limb of wild type,  4-6 weeks old mice by Fluorescent Activated Cell Sorting (FACS). Cells  were propagated in growth media (Ham F10 supplemented with 20% FBS, 1%  penicillin/streptomycin, 2.5 ng/ml bFGF).    siRNAs directed against Snai1, Snai2 or both were applied by transient  transfection using Lipofectamin. Total RNA was isolated with RNeasy  Kit 48 hours post transfection.

tag: expression

value: siRNA knockdown of Snai1 & Snai2

value: hind limb

value: wild type


title: SC0017_siSnai2_GM

source_name: Myoblast siRNA knockdown of Snai2

value: siRNA knockdown of Snai2


title: siPhf2_Veh_RNA_Seq

description: siPhf2 Treated Cells

extract_protocol:
RNA was purified using RNeasy Mini Kit (Qiagen) and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit (Ambion, Austin, TX, USA). For quantification, cDNA was generated using the Superscript kit (Invitrogen) and quantitative real-time PCR was performed using gene specific primers.  For sequencing, RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by a P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with Antarctic phosphatase (New England Biolabs, Ipswich, MA, USA) followed by heat-inactivation and overnight precipitation. Poly(A)-tailing and cDNA synthesis was performed as previously described (Ingolia et al., 2009).  However, for reverse transcription, oligos with custom barcodes (see below in []) were used: 5'-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3'.
Custom barcode: siPhf2_Veh [TG]
After cDNA synthesis, exonuclease was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of 50-150 nucleotides were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen, Carlsbad, CA, USA). The recovered cDNA was circularized, linearized, amplified for 15 cycles and gel purified as previously described (Ingolia et al., 2009).  The library was sequenced on the Illumina Genome Analyzer 2 according to the manufacturer’s instructions.


title: SC0017_siSnai1_GM

source_name: Myoblast siRNA knockdown of Snai1

value: Myoblasts

value: siRNA knockdown of Snai1


title: EV-10T1/2

description: Control run with no tagged proteins. Instrument model: Illumina GA-IIx

data_processing: Solexa read alignment and peak calling. Solexa reads (36 bp) were aligned to mouse genome (NCBI37) by Eland (Illumina) with up to two mismatches.

source_name: C3H10T1/2 fibroblasts with empty vector, forced to undergo myogenic differentiation by expression of MyoD

growth_protocol: HAMS's F10 + 20% FBS + bFGF(4ng/ml)

extract_protocol: Cycling cells or differentiated myotubes stably expressing a c-terminus TAP tagged fusion proteins were cross linked with with 1% formaldehyde in 1x PBS for 10 minutes. A solution containing 0.125 M glycine in 1x PBS was used for quenching for 5 minutes at room temperature. Cells were harvested and the pellet dissolved in ChIP lysis buffer (40 mM Tris-HCl, pH8.0; 1% Triton-X100; 4 mM EDTA; 300 mM NaCl) containing protease inhibitors. Chromatin was fragmented by sonication in a water bath sonicator at 4 ºC to an average length of 200 base pairs. The lysate was spun at 14K for 15 minutes and the supernatant was diluted 1:1 in ChIP dilution buffer containing 40 mM Tris-HCl, pH 8.0; 4 mM EDTA plus protease inhibitors. FLAG immunoprecipitation was done on 15 milligram of cell lysate using M2 conjugated agarose beads (Sigma Aldrich) for 2 hours at 4 ºC following manufacture’s recommendation. Beads were washed 3 times with 10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 0.1% Triton-X100 plus protease inhibitors. Protein complex was eluted from M2-conjugated agarose beads using proteolytic cleavage with Tobacco Etch Virus (TEV) protease (Invitrogen) together with 3xFLAG peptide (Sigma Aldrich) competition over night at 4 ºC using 1x TEV buffer (Invitrogen). Two additional rounds of elution with 3xFLAG peptides were done using 200 µg/ml of 3xFLAG peptide in TBS (50 mM Tris-HCl, pH 7.4; 150 mM NaCl). 6xHis immunoprecipitation and purification was done using His-Select nickel beads (Sigma-Aldrich) for three hours at 4 ºC following manufacture’s recommendations. Beads were washed three times with wash buffer (20 mM Tris-HCl, pH 7.4; 150 mM NaCl; 5 mM Imidazole plus protease inhibitors). Final DNA/protein complex was eluted by 400 mM imidazole at room temperature. Reverse cross linking and phenol/chloroform extraction of chromatin were performed. The ChIP DNA library was prepared according to the Illumina protocol (www.illumina.com)

value: Balb/c

tag: tissue of origin

value: skeletal muscle

value: fibroblasts

value: control (empty vector)

tag: growth protocol


title: EV-2DM

source_name: myotubes with empty vector, 48h in differentiating medium

value: myotubes

value: 48h in differentiating medium

value: control


title: EV-10h

source_name: myocytes with empty vector, 10h in differentiating medium

value: myocytes

value: 10h in differentiating medium


title: Exp1 Control AID-E58Q

description: PCR amplified mOrangeSTOP

value: mOrangeSTOP

value: Empty


title: EV-GM

source_name: cycling myoblasts with empty vector

value: myoblasts


title: MyoD-10h

description: Pulldown of FLAG and TAP tagged MyoD. Instrument model: Illumina GA-IIx

source_name: myocytes with TAP tagged MyoD, 10h in differentiating medium

value: MyoD

value: ChIP

value: anti-FLAG M2 agarose resin

value: His-Select nickel beads


title: MyoD-2DM

description: Pulldown of FLAG and TAP tagged MyodD. Instrument model: Illumina GA-IIx

source_name: myotubes with TAP tagged MyoD, 48h in differentiating medium

value: wild type


title: MyoD-10T1/2

source_name: C3H10T1/2 fibroblasts with TAP tagged MyoD, forced to undergo myogenic differentiation by expression of MyoD

value: Balb/c


title: SC0017_siScr_GM

source_name: Myoblast siRNA scramble control for Snai1 & Snai2 knockdowns

value: Myoblasts

value: siRNA scramble control

value: hind limb


title: MyoD-GM

source_name: cycling myoblasts with TAP tagged MyoD

value: skeletal muscle