description:
design description: H3K4me3 ChIP-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A03502) using Illumina HiSeq 2000
library name: A03502
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 15 ug
SIZE_FRACTION: 74-314 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 2,4
****************
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: GSM806940_UCSF-UBC.Brain_Germinal_Matrix.H3K4me3.HuFGM02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03502-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Germinal Matrix Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Germinal Matrix, Donor HuFGM02 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.10418
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,260,048
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5816
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.5831
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5857
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM806940_UCSF-UBC.Brain_Germinal_Matrix.H3K4me3.HuFGM02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03502-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 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.10433
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 5
BROWSER_TRACK_NAME: BGM H3K4me3 02 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix Histone H3K4me3 Donor HuFGM02 Library A03502 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,260,048
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5816
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.5831
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5857
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.99

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


status: Public on Nov 21 2011

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: H3K4me3 ChIP-Seq analysis of fetal brain tissue from HuFNSC02 (A03494) using Illumina HiSeq 2000
library name: A03494
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 15 ug
SIZE_FRACTION: 102-413 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 2
****************
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: GSM806935_UCSF-UBC.Fetal_Brain.H3K4me3.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03494-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Fetal Brain, Donor HuFNSC02 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.10412
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,328,168
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3766
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.3834
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3928
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM806935_UCSF-UBC.Fetal_Brain.H3K4me3.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03494-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC02 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.10427
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 5
BROWSER_TRACK_NAME: FB H3K4me3 02 94
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K4me3 Donor HuFNSC02 Library A03494 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,328,168
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3766
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.3834
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3928
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: female

tag: body site

value: Brain

tag: histological type

value: Brain tissue

tag: is tumor

value: No

value: primary tissue

value: fetal brain tissue


description:
design description: H3K4me1 ChIP-Seq analysis of fetal brain tissue from HuFNSC02 (A03493) using Illumina HiSeq 2000
library name: A03493
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 105-409 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 15 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
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: GSM806934_UCSF-UBC.Fetal_Brain.H3K4me1.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03493-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Fetal Brain, Donor HuFNSC02 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.10417
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,294,713
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0038
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.1088
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.723
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2403
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM806934_UCSF-UBC.Fetal_Brain.H3K4me1.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03493-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC02 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.10432
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 5
BROWSER_TRACK_NAME: FB H3K4me1 02 93
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K4me1 Donor HuFNSC02 Library A03493 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,294,713
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0038
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.1088
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.723
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2403
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.9

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


title: Return_to_Control_P-H2AX_ChIPSeq_1

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

description: Chromatin IP against P-H2AX

data_processing: Sequence tags were mapped to the mouse genome using the Solexa Analysis Pipeline as described previously (Barski et al, Cell, 129(4):823, 2007). The unique reads were retained and converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. The read number and genomic coordinates were summarized in 300 bp windows.

organism: Mus musculus

growth_protocol: mIMCD3 cells  were grown in medium containing 45% DME Low Glucose, 45% F12 Coon’s Modification  and 10% fetal bovine serum.

extract_protocol: ChIP was performed using Enzymatic Chromatin IP kit (No.9003, Cell Signaling Technology, Danvers, MA). mIMCD3 cells were crosslinked with 1% formaldehyde for 10min. Chromatin was digested with MNase to generate mainly mononucleosomes with a minor fraction of dinucleosomes. For each sample chromatin from 1 × 107 cells was immunoprecipitated with anti-γH2AX antibody (No.05-636, Millipore, Billerica, MA). The proteins and RNA in the samples were enzymatically digested and the DNA was further purified by phenol-chloroform extraction in, followed by ethanol precipitation. Conversion of the ChIP-enriched DNA into libraries suitable for sequencing using the Illumina Genome Analyzer was performed using the previously published protocol (Schmidt D et al, Methods 48: 240, 2009).  The ChIP DNA ends were repaired using T4 PNK (New England BioLabs (NEB, Ipswich, MA), and Klenow DNA polymerase (NEB), followed by treatment with Klenov 3’-5’ exo minus polymerase (NEB) to generate the protruding 3′ A base used for adaptor ligation. Ligation of a pair of Solexa adaptors to the repaired ends was performed using forty-fold diluted Genomic Adapter Oligo Mix (Illumina, San Diego, CA) and Quick T4 DNA Ligase (NEB). Adapter-modified ChIP DNA was amplified using Adapter primers (Illumina) and Phusion DNA polymerase (NEB) with 17 cycles and the fragments between 250bp  and 300bp (mononucleosome + adaptors) were isolated from 2% agarose TAE gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Solexa 1G Genome Analyzer following manufacturer protocols.  Sequence tags were obtained and mapped to the mouse genome using the Solexa Analysis Pipeline as described previously (Barski et al, Cell, 129(4):823, 2007). The unique reads were retained and converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. The read number and genomic coordinates were summarized in 300 bp windows.

treatment_protocol: Osmolality of control medium was 300-320 mosmol/kg. High NaCl medium was prepared by adding NaCl to the total osmolality of 500 mosmol/kg. To elevate NaCl, control medium was replaced by the high NaCl media. For “High NaCl” sample cells were exposed to high NaCl medium for 22h. For “Return to Control” samples cells were exposed to high NaCl medium for 22h and then high NaCl medium was replaced by control medium for 15 min. Cells were exposed to 15 J/m2 of UV light in a Stratalinker UV Crosslinker. Bleomycin was used at concentration of 5 µg/ml for 30 min.

tag: cell type

tag: antibody

tag: vendor

value: No.05-636, Millipore

tag: treatment

value: osmolality at 500 mosmol/kg for 22 hr and then 300-320 mosmol/kg 15 min


description:
design description: H3K36me3 ChIP-Seq analysis of fetal brain tissue from HuFNSC01 (A03489) using Illumina HiSeq 2000
library name: A03489
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 94-304 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
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: GSM806946_UCSF-UBC.Fetal_Brain.H3K36me3.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03489-1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Fetal Brain, Donor HuFNSC01 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.10424
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,746,101
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1629
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.2154
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9375
IROC_PERCENTILE: 53
POISSON_SCORE: 0.4295
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM806946_UCSF-UBC.Fetal_Brain.H3K36me3.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03489-1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Fetal Brain, Donor HuFNSC01 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.10439
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 5
BROWSER_TRACK_NAME: FB H3K36me3 01 89
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain Histone H3K36me3 Donor HuFNSC01 Library A03489 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,746,101
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1629
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.2154
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9375
IROC_PERCENTILE: 53
POISSON_SCORE: 0.4295
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.98

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


title: Control_P-H2AX_ChIPSeq

description: Chromatin IP against P-H2AX

value: osmolality at 300-320 mosmol/kg


title: Bleomycin_P-H2AX_ChIPSeq

description: Chromatin IP against P-H2AX

value: bleomycin was used at concentration of 5 µg/ml for 30 min


title: whole heart input 3

city: Chicago

first: Noboru

middle: Jo

last: Sakabe

state: IL

address: 920 E 58th st

department: Human Genetics

institute: University of Chicago

description: input DNA

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Peak calling: peaks were called with QuEST 2.3 with the TF setting and ChIP-to-background = 30, against whole heart input reads.

source_name: whole heart

extract_protocol: Libraries were generated according to Illumina single-end ChIP-seq library preparation

tag: strain

tag: tissue

value: whole heart

tag: age

tag: chip antibody


title: whole heart input 2

description: input DNA


title: whole heart input 1

description: input DNA


title: Return_to_Control_P-H2AX_ChIPSeq_2

description: Chromatin IP against P-H2AX


title: DamK9A-hERalpha DamIPseq

status: Public on Nov 19 2011

city: Houston

first: Rui

last: Xiao

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

description: library strategy : DamIP-seq

data_processing: Short sequence tags generated from Illumina pipeline were mapped to human genome h18 (NCBI36) with Bowtie. First 6 nucleotides were removed before Bowtie mapping. Bowtie aligned sequences tags were subjected to peak-calling by MACS

growth_protocol: Human breast cancer cell line MCF-7 was maintained in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS) and 1x nonessential amino acids (NEAA, Invitrogen). For experiments with ligand treatment, MCF-7 cells were plated in phenol red-free DMEM supplemented with 10% charcoal-stripped FBS and 1x NEAA for at least 3 days before treatment.

extract_protocol: DamIP DNA were first converted to dsDNA by Klenow exo- and random hexamers. Then libraries were constructed with general ChIP-seq protocol.

treatment_protocol: Cells were treated with beta-estradiol (100nM) for 24hours before harvesting.

tag: cell line

tag: transfected with

tag: damip antibody

tag: damip antibody vendor

value: Megabase Research Products

tag: damip antibody cat#

tag: damip antibody lot


title: DamK9A DamIPseq

description: library strategy : DamIP-seq


title: High_NaCl_P-H2AX_ChIPSeq

description: Chromatin IP against P-H2AX

value: osmolality at 500 mosmol/kg


title: trm44del tan1del tRNASer(CGA) U6:A67 (JMW561) 6 hr Replicate 1

status: Public on Nov 17 2011

city: Cambridge

first: Jeremy

middle: E

last: Wilusz

state: MA

address: 77 Massachusetts Ave, Bldg 76-461

department: Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

library_source: transcriptomic

data_processing: The resulting sequencing files were processed by collapsing identical reads and reverse complementing the sequences (as this sequencing strategy actually sequences the reverse complement of a given transcript).

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: trm44 tan1 deletion strain containing tRNASer(CGA) U6:A67 mutant

growth_protocol: Strains were grown in YPD medium at 28 degrees until OD600 ~1.5 and then shifted to 37 degrees for the indicated amounts of time.

extract_protocol: At the indicated time points, 2 mL of culture was harvested, pelleted, rinsed with 1 mL of cold sterile water, pelleted, and frozen on dry ice. RNA was purified from cells using hot phenol. A pre-adenylated oligo (miRNA Linker 3, IDT; 5’-rAppTTTAACCGCGAATTCCAG/3ddC/) was ligated to the 3’ ends of 1.5 micrograms of total RNA using the truncated form of T4 RNA Ligase 2 (New England Biolabs). Ligation reactions were incubated at room temperature for 2 hr followed by a phenol/chloroform extraction and ethanol precipitation. Reverse transcription was then performed using Superscript III (Invitrogen) as per the manufacturer’s instructions and 5 pmol of primer complementary to the 3’ linker sequence (5’-GACTAGCTGGAATTCGCGGTTAAA). cDNAs were amplified by PCR using AmpliTaq DNA Polymerase (Applied Biosystems). To sequence the 3’ ends of the endogenous tRNASer(CGA) and tRNASer(UGA)  transcripts (due to their high similarity, this sequencing approach can not distinguish between them), the following forward (5’- CAAGCAGAAGACGGCATACGAGGxxxxxxxGGCTCTGCCCGCGCTGG, where xxxxxxx is a unique 7-nucleotide barcode for each RNA prep so that multiple samples can be run together in a single lane of an Illumina flow cell) and reverse (5’-AATGATACGGCGACCACCGAGGACTAGCTGGAATTCGCGGTTAAA) primers were used. These forward and reverse primers were also used to amplify the U6:A67 tRNASer(CGA) variant from strain JMW561 – however, only reads that contained the A67 mutation were included in the downstream analysis. To sequence the 3’ ends of the G51:C63, C6:G67, G2:C71 tRNASer(CGA) variant (strain JMW1251) or the G51:C63 tRNASer(CGA) variant (strain JMW316), the following forward (5’- CAAGCAGAAGACGGCATACGAGGxxxxxxxGCGGGTTCAAATCCCGC, where xxxxxxx is a unique 7-nucleotide barcode) and reverse (5’-AATGATACGGCGACCACCGAGGACTAGCTGGAATTCGCGGTTAAA) primers were used to avoid amplification of the endogenous tRNASer(UGA) loci. PCR reactions were incubated at 94º for 2 min, followed by 21 cycles of 94º for 15 sec, 58º for 30 sec, and 72º for 30 sec. All PCR reactions were then combined in one tube and extracted with phenol/chloroform and ethanol precipitated. Using a 2% low melting point agarose gel, the PCR products (~110 to 120 bp) were purified and then cleaned up using a phenol extraction, followed by a phenol/chloroform extraction, followed by a chloroform extraction. The purified DNA was resuspended in water and subjected to deep sequencing using the Illumina HiSeq 2000 Sequencing System and the following sequencing primer (5’-CCGAGGACTAGCTGGAATTCGCGGTTAAA). 58 nucleotide reads from the 3’ ends of each transcript were obtained.

tag: hours at 37 degrees

tag: replicate number


title: trm44del tan1del tRNASer(CGA) U6:A67 (JMW561) 6 hr Replicate 2


title: Tbx20 (fused to GFP) ChIP-seq

description: Chromatin IP against GFP

source_name: adult whole heart

value: 2 months

value: Goat anti-GFP (kindly provided by Kevin P White, University of Chicago)


title: trm44del tan1del tRNASer(CGA) U6:A67 (JMW561) 0 hr Replicate 3


title: CTCF/activated B cells/wt

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing: Image analysis, base calling, quality filtering: Standard settings of GAPipeline using PhiX control; ***Raw data***: Fastq files contain full length reads (36 nts) that passed the chastity filter. Qualities are in phred64 format for all files.  ***Wig file***: Reads were aligned to the mouse genome (build mm9) with bowtie accepting only reads that had a unique match in the genome in their top quality stratum.  Redundant reads were removed, DNA fragment size was estimated (96 nts), and shifted reads were counted in 100 nt bins across the genome.  Counts were normalized to the non redundant library size and bin size such that the final units are reads per kb per million (RPKM).

source_name: Mouse Mature B cells, Spleen, in vitro LPS/IL-4 activated

growth_protocol: CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech).  Following isolation, resting B cells were stimulated with LPS (50 mcg/ml) and IL-4 (2.5 ng/ml) for 72 hrs.

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-CTCF antibody following standard protocols.  Immunoprecipitates were processed according to Illumina's standard protocol and sequenced on a Genome Analyzer II.

value: in vitro activated mouse B cells

tag: source

value: spleen

tag: isolation

value: CD43 negative magnetic beads selection

value: anti-CTCF

value: 07-729 Millipore rabbit polyclonal ab

tag: chip target

value: CTCF


title: trm44del tan1del tRNASer(CGA) U6:A67 (JMW561) 0 hr Replicate 2


title: trm44del tan1del tRNASer(CGA) G51:C63 (JMW316) 0 hr Replicate 3

source_name: trm44 tan1 deletion strain containing tRNASer(CGA) G51:C63 mutant


title: trm44del tan1del tRNASer(CGA) U6:A67 (JMW561) 0 hr Replicate 1


title: trm44del tan1del tRNASer(CGA) G51:C63 (JMW316) 6 hr Replicate 2


title: trm44del tan1del tRNASer(CGA) G51:C63 (JMW316) 0 hr Replicate 1


title: trm44del tan1del tRNASer(CGA) G51:C63 (JMW316) 0 hr Replicate 2


title: trm44del tan1del tRNASer(CGA) G51:C63 (JMW316) 6 hr Replicate 3


title: trm44del tan1del tRNASer(CGA) G51:C63 C6:G67 G2:C71 (JMW1251) 6 hr Replicate 3

source_name: trm44 tan1 deletion strain containing tRNASer(CGA) G51:C63 C6:G67 G2:C71 mutant


title: trm44del tan1del tRNASer(CGA) G51:C63 C6:G67 G2:C71 (JMW1251) 6 hr Replicate 1


title: trm44del tan1del tRNASer(CGA) G51:C63 C6:G67 G2:C71 (JMW1251) 6 hr Replicate 2


title: trm44del tan1del tRNASer(CGA) G51:C63 C6:G67 G2:C71 (JMW1251) 0 hr Replicate 1


title: UV_P-H2AX_ChIPSeq

description: Chromatin IP against P-H2AX

tag: cell type

tag: antibody

tag: vendor

value: 15 J/m2 of UV light in a Stratalinker UV Crosslinker


title: trm44del tan1del tRNASer(CGA) G51:C63 C6:G67 G2:C71 (JMW1251) 0 hr Replicate 2

tag: strain


title: xrn1del (ISC725) 6 hr Replicate 2

source_name: xrn1 deletion strain


title: xrn1del (ISC725) 6 hr Replicate 3


title: trm44del tan1del tRNASer(CGA) G51:C63 C6:G67 G2:C71 (JMW1251) 0 hr Replicate 3


title: xrn1del (ISC725) 3 hr Replicate 3


title: xrn1del (ISC725) 3 hr Replicate 2


title: xrn1del (ISC725) 6 hr Replicate 1


title: xrn1del (ISC725) 0 hr Replicate 3


title: xrn1del (ISC725) 0 hr Replicate 2


title: met22del (JMW510) 6 hr Replicate 3

source_name: met22 deletion strain


title: xrn1del (ISC725) 0 hr Replicate 1


title: trm44del tan1del tRNASer(CGA) G51:C63 (JMW316) 6 hr Replicate 1


title: met22del (JMW510) 6 hr Replicate 1


title: met22del (JMW510) 6 hr Replicate 2


title: met22del (JMW510) 3 hr Replicate 2


title: met22del (JMW510) 3 hr Replicate 3


title: met22del (JMW510) 3 hr Replicate 1


title: met22del (JMW510) 0 hr Replicate 1


title: met22del (JMW510) 0 hr Replicate 2


title: trm8del trm4del (JMW009) 0.5 hr Replicate 3

source_name: trm8 trm4 deletion strain


title: trm8del trm4del (JMW009) 0.5 hr Replicate 2


title: trm8del trm4del (JMW009) 0.5 hr Replicate 1


title: trm8del trm4del (JMW009) 0.1 hr Replicate 2


title: trm8del trm4del (JMW009) 0.1 hr Replicate 3


title: trm8del trm4del (JMW009) 0.1 hr Replicate 1


title: trm8del trm4del (JMW009) 0 hr Replicate 2


title: trm8del trm4del (JMW009) 0 hr Replicate 1


title: trm44del tan1del xrn1del (ISC850) 3 hr Replicate 3

source_name: trm44 tan1 xrn1 deletion strain


title: xrn1del (ISC725) 3 hr Replicate 1


title: trm44del tan1del xrn1del (ISC850) 6 hr Replicate 3


title: trm44del tan1del xrn1del (ISC850) 6 hr Replicate 1


title: trm44del tan1del xrn1del (ISC850) 0 hr Replicate 2


title: trm44del tan1del xrn1del (ISC850) 3 hr Replicate 1


title: trm8del trm4del (JMW009) 0 hr Replicate 4


title: trm44del tan1del xrn1del (ISC850) 3 hr Replicate 2


title: met22del (JMW510) 0 hr Replicate 3


title: trm8del trm4del (JMW009) 0 hr Replicate 3


title: trm8del trm4del (JMW009) 0.5 hr Replicate 4


title: trm44del tan1del xrn1del (ISC850) 0 hr Replicate 3


title: trm44del tan1del met22del (LY1729) 6 hr Replicate 6

source_name: trm44 tan1 met22 deletion strain


title: trm44del tan1del xrn1del (ISC850) 0 hr Replicate 1


title: trm8del trm4del (JMW009) 0.1 hr Replicate 4


title: trm44del tan1del met22del (LY1729) 6 hr Replicate 4


title: trm44del tan1del met22del (LY1729) 6 hr Replicate 1


title: trm44del tan1del met22del (LY1729) 6 hr Replicate 3


title: trm44del tan1del xrn1del (ISC850) 6 hr Replicate 2


title: trm44del tan1del met22del (LY1729) 6 hr Replicate 5


title: trm44del tan1del met22del (LY1729) 3 hr Replicate 7


title: trm44del tan1del met22del (LY1729) 3 hr Replicate 5


title: trm44del tan1del met22del (LY1729) 3 hr Replicate 3


title: trm44del tan1del met22del (LY1729) 3 hr Replicate 4


title: trm44del tan1del met22del (LY1729) 3 hr Replicate 2


title: trm44del tan1del met22del (LY1729) 3 hr Replicate 1


title: trm44del tan1del met22del (LY1729) 1.5 hr Replicate 3


title: trm44del tan1del met22del (LY1729) 1.5 hr Replicate 1


title: trm44del tan1del met22del (LY1729) 0 hr Replicate 7


title: trm44del tan1del met22del (LY1729) 1.5 hr Replicate 2


title: trm44del tan1del met22del (LY1729) 0 hr Replicate 6


title: trm44del tan1del met22del (LY1729) 0 hr Replicate 4


title: trm44del tan1del met22del (LY1729) 0 hr Replicate 3


title: trm44del tan1del met22del (LY1729) 0 hr Replicate 5


title: trm44del tan1del (JMW119) 6 hr Replicate 4

source_name: trm44 tan1 deletion strain


title: trm44del tan1del (JMW119) 6 hr Replicate 5


title: trm44del tan1del (JMW119) 6 hr Replicate 3


title: S2_luciferase_RNAi_unoxidized

city: Boston

first: Jui-Hung

last: Hung

address: 24 cummington st

institute: Boston University

data_processing: The alignment files are included, they are aligned by in-house aligner as described in Ameres et al 2010 Science. [Ameres, S. L., Horwich, M. D., Hung, J.-H., Xu, J., Ghildiyal, M., Weng, Z., & Zamore, P. D. (2010). Target RNA-directed trimming and tailing of small silencing RNAs Science (New York, NY), 328(5985) 1534-1539. doi:10.1126/science.1187058]

organism: Drosophila melanogaster

growth_protocol: S2 cells were cultued in Schneider's Drosophila Medium containing 10%heat-inactivated fetal bovine serum (FBS) at 25 degree

extract_protocol: Described previously (Li, et al. Cell 137, 509â521)

treatment_protocol: 20ug of dsRNA targeting either luciferase or knabber (CG9247) was transfected into S2 cells using Dharmafect4 (Dharmacon)

tag: genotype/variation

value: transfected with dsRNA targeting luciferase

value: Schneider 2 (S2) cells

tag: oxidation

value: unoxidized

tag: fragment length


title: trm44del tan1del met22del (LY1729) 0 hr Replicate 1


title: trm44del tan1del met22del (LY1729) 3 hr Replicate 6


title: trm44del tan1del (JMW119) 6 hr Replicate 2


title: S2_nibbler_RNAi_oxidized

treatment_protocol: 20ug of dsRNA targeting either luciferase or nibbler (CG9247) was transfected into S2 cells using Dharmafect4 (Dharmacon)

value: transfected with dsRNA targeting nibbler

value: oxidized


title: S2_luciferase_RNAi_oxidized


title: trm44del tan1del met22del (LY1729) 6 hr Replicate 2


title: S2_nibbler_RNAi_unoxidized


title: trm44del tan1del (JMW119) 6 hr Replicate 1


title: trm44del tan1del (JMW119) 3 hr Replicate 5


title: trm44del tan1del (JMW119) 3 hr Replicate 6


title: trm44del tan1del (JMW119) 3 hr Replicate 4


title: trm44del tan1del (JMW119) 3 hr Replicate 3


title: trm44del tan1del (JMW119) 3 hr Replicate 2


title: trm44del tan1del met22del (LY1729) 0 hr Replicate 2


title: trm44del tan1del (JMW119) 6 hr Replicate 6


title: trm44del tan1del (JMW119) 3 hr Replicate 1


title: trm44del tan1del (JMW119) 1.5 hr Replicate 3


title: trm44del tan1del (JMW119) 0 hr Replicate 6


title: trm44del tan1del (JMW119) 1.5 hr Replicate 1


title: trm44del tan1del (JMW119) 0 hr Replicate 7


title: trm44del tan1del (JMW119) 1.5 hr Replicate 2


title: trm44del tan1del (JMW119) 0 hr Replicate 5


title: trm44del tan1del (JMW119) 0 hr Replicate 4


title: trm44del tan1del (JMW119) 3 hr Replicate 7


title: trm44del tan1del (JMW119) 0 hr Replicate 3


title: trm44del tan1del (JMW119) 0 hr Replicate 1


title: WT(JMW007) 6 hr Replicate 1

source_name: Wild type strain


title: WT(JMW007) 6 hr Replicate 2


title: WT(JMW007) 6 hr Replicate 3


title: trm44del tan1del (JMW119) 0 hr Replicate 2


title: WT(JMW007) 3 hr Replicate 4


title: WT(JMW007) 3 hr Replicate 3


title: WT(JMW007) 3 hr Replicate 2


title: WT(JMW007) 1.5 hr Replicate 2


title: WT(JMW007) 3 hr Replicate 1


title: WT(JMW007) 1.5 hr Replicate 3


title: WT(JMW007) 1.5 hr Replicate 1


title: WT(JMW007) 0.5 hr Replicate 3


title: WT(JMW007) 0.5 hr Replicate 4


title: WT(JMW007) 0.5 hr Replicate 2


title: shield-2

city: Copenhagen E

first: Eivind

last: Valen

state: Select

address: Ole Maaloes Vej 4

department: Dep. of Biology

country: Denmark

institute: University of Copenhagen

description: RNA-Seq

data_processing: Th summary result files of he developmental transcriptome of all samples are  available as supplementary information with the paper.

molecule: polyA RNA

organism: Danio rerio

source_name: Shield RNA-Seq

growth_protocol: Zebrafish embryos were dechorionated at the 1-cell stage, followed by incubation at 28C.

extract_protocol: Total RNA was isolated using the standard Trizol (Invitrogen) protocol. Two rounds of PolyA+-RNA purification were performed for each sample, using the PolyA(Purist)TM-MAG kit (Ambion). The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bioanalyzer. Strand-specific libraries for 76 bp paired-end sequencing were prepared according to a modified UTP-method (Parkhomchuk et al. 2009), as detailed in (Levin et al. 2010).

tag: tissue

value: embryo

tag: developmental stage

value: embryogenesis:shield stage

tag: average insert size (fragment length)

tag: stdev for insert size


title: WT(JMW007) 0 hr Replicate 4


title: WT(JMW007) 0.5 hr Replicate 1


title: WT(JMW007) 0 hr Replicate 2


title: WT(JMW007) 0 hr Replicate 3


title: WT(JMW007) 0 hr Replicate 1


title: shield_ChIPSeq_WholeCellExtract

description: ChIP-Seq

data_processing: Reads were mapped to the Zv9 genome assembly using bowtie

growth_protocol: Zebrafish embryos were dechorionated at the 1-cell stage, followed by incubation at 28C until they reach the shield stage (about 6 hours post fertilization)

extract_protocol: ChIP was performed as previously described (Vastenhouw et al. 2010), using the following antibodies: H3K4me3 (millipore #07-473) and H3K27me3 (millipore #07-449). Sequencing libraries were prepared according to standard Illumina protocols.

tag: embryogenesis stage

value: shield


title: shield_ChIPSeq_H3K4me3

description: ChIP-Seq

tag: chip antibody

value: Anti-trimethyl-Histone H3 (Lys4)

tag: chip antibody vendor

value: Millipore

tag: chip antibody catalog number


title: shield_ChIPSeq_H3K27me3

description: ChIP-Seq

value: Anti-trimethyl-Histone H3 (Lys27)


title: 2dpf-2

description: RNA-Seq

source_name: 2 dpf RNA-Seq

value: embryogenesis:2 dpf stage


title: 5dpf-2

description: RNA-Seq

source_name: 5 dpf RNA-Seq

value: embryogenesis:5 dpf stage


title: 28hpf-2

description: RNA-Seq

source_name: 28 hpf RNA-Seq

value: embryogenesis:28 hpf stage


title: 2dpf-1

description: RNA-Seq


title: bud-1

description: RNA-Seq

source_name: Bud RNA-Seq

value: embryogenesis:bud stage


title: shield-3

description: RNA-Seq


title: shield-1

description: RNA-Seq


title: dome-2

description: RNA-Seq

source_name: Dome RNA-Seq

value: embryogenesis:dome stage


title: 28hpf-1

description: RNA-Seq


title: 1Kcell-2

description: RNA-Seq

source_name: 1K cell RNA-Seq

value: embryogenesis:1K cell stage


title: dome-1

description: RNA-Seq


title: 2-4cell-2

description: RNA-Seq

source_name: 2-4cell RNA-Seq

value: embryogenesis:2-4 cell stage


title: 2-4cell-1

description: RNA-Seq


title: 1Kcell-1

description: RNA-Seq


title: LNCaP Genomic Input sequencing

status: Public on Nov 16 2011

city: Singapore

first: Cheng Wei

last: Chang

address: Genome Institute of Singapore Genome #02-01 60 Biopolis Street

department: Computational and Mathematical Biology 1

country: Singapore

institute: GIS

description:
LNCaP Genomic Input DNA
LNCaP Genomic Input DNA Sequencing

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer II Pipeline. In-house (Genome Institute of Singapore) BATMAN program was used for mapping the sequence tags of 36 bp to the reference genome hg18. In order to avoid potential PCR amplification bias, tags that shared the same mapping location on the same strand were removed. The uniquely-mapped reads with at most 2-mismatches were kept for further processing.
Peak calling: Binding peaks were determined using in-house Control based ChIPSeq Analysis Tools (CCAT) program with reference to a set of genomic input reads as baseline control. Peaks with a stringent cut-off of FDR 0.05 were considered.
CCAT file format: chromosome, peakcenter, regionstart, regionend, tagcount, bgcount, zscore, fdr

source_name: LNCaP prostate cancer cells

growth_protocol: Human LNCaP prostate cancer cells were maintained in RPMI Medium 1640 (Gibco) supplemented with 10% fetal bovine serum (FBS), 1 mM sodium pyruvate, 100 units/ml penicillin, 100 Âµg/ml streptomycin, and 30 Âµg/ml gentamycin in a 37Â°C incubator with 5% CO2. Prior to vehicle/drug stimulation, ~4 millions cells were seeded into 150 mm dish and starved with phenol red-free RPMI Medium 1640 containing 5% charcoal-dextran treated FBS (Hyclone) and the same amount of sodium pyruvate, penicillin, streptomycin and gentamycin as mentioned earlier for at least 72 hrs to ~80% confluence.

extract_protocol: All DNA samples were processed as per Illumina Solexa ChIP-seq sample processing methods.  5 to15 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An A base was added to the polished DNA fragments followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification with Phusion or Pfx DNA polymerase (Invitrogen) and Illumina primers. 200-300 bp DNA size fractions were selectively excised from the 2% ultra low range agarose gel purified using the Qiagen gel extraction kit. The extracted DNA was quantified using Agilent bioanalyzer and subjected to Solexa sequencing according to the manufacturerâs instruction.

treatment_protocol: Androgen-deprived cells were treated with DHT to a final concentration of 100 nM for 2 hrs prior to the ChIP procedure. Cells cross-linked with 1% formaldehyde and harvested for sonication. ChIP was performed with specific antibody against AP-4 (catalog number: sc-18593 (N-17); lot number: D2903)

value: androgen-dependent prostate cancer cells


title: FoxA1 ChIP sequencing in Et (ethanol) treated LNCaP cells

city: singapore

first: Peck Yean

last: TAN

address: 60 Biopolis Street #02-01 Genome

institute: Genome Institute of Singapore (GIS)

description:
FoxA1 ChIP sequencing after 2 hrs Et (ethanol) treatment in LNCaP cells
FoxA1 Et

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer II Pipeline. In-house (Genome Institute of Singapore) BATMAN program was used for mapping the sequence tags of 36 bp to the reference genome hg18. In order to avoid potential PCR amplification bias, tags that shared the same mapping location on the same strand were removed. The uniquely-mapped reads with at most 2-mismatches were kept for further processing.

Peak calling: Binding peaks were determined using in-house Control based ChIPSeq Analysis Tools (CCAT) program with reference to a set of genomic input reads as baseline control. Peaks with a stringent cut-off of FDR 0.05 were considered.  CCAT file format: chromosome, peakcenter, regionstart, regionend, tagcount, bgcount, zscore, fdr.

growth_protocol: Human LNCaP prostate cancer cells were maintained in RPMI Medium 1640 (Gibco) supplemented with 10% fetal bovine serum (FBS), 1 mM sodium pyruvate, 100 units/ml penicillin, 100 µg/ml streptomycin, and 30 µg/ml gentamycin in a 37°C incubator with 5% CO2. Prior to vehicle/drug stimulation, ~4 millions cells were seeded into 150 mm dish and starved with phenol red-free RPMI Medium 1640 containing 5% charcoal-dextran treated FBS (Hyclone) and the same amount of sodium pyruvate, penicillin, streptomycin and gentamycin as mentioned earlier for at least 72 hrs to ~80% confluence.

treatment_protocol: Androgen-deprived cells were treated with DHT to a final concentration of 100 nM for 2 hrs prior to the ChIP procedure.  Cells treated with an equal volume of vehicle, Et, for 2 hrs, served as controls.

tag: cell line

value: LNCaP androgen-dependent prostate cancer cell line

tag: agent

value: ethanol

value: FoxA1 antibody

value: Abcam

tag: chip antibody lot#

tag: chip antibody catalog#


title: FoxA1 ChIP sequencing in DHT (5alpha-dihydrotestosterone) treated LNCaP cells

description:
FoxA1 ChIP sequencing after 2 hrs DHT (5alpha-dihydrotestosterone) treatment in LNCaP cells
FoxA1 DHT

value: DHT


title: PolII ChIP sequencing in Et (ethanol) treated LNCaP cells

description:
PolII ChIP sequencing after 2 hrs Et (ethanol) treatment in LNCaP cells
PolII Ethanol

value: PolII antibody


title: PolII ChIP sequencing in DHT (5alpha-dihydrotestosterone) treated LNCaP cells

description:
PolII ChIP sequencing after 2 hrs DHT (5alpha-dihydrotestosterone) treatment in LNCaP cells
PolII DHT


title: 5dpf-1

description: RNA-Seq

value: embryo


title: NKX3-1 ChIP sequencing in Et (ethanol) treated LNCaP cells

description:
NKX3-1 ChIP sequencing after 2 hrs Et (ethanol) treatment in LNCaP cells
NKX3-1 Et
Processed data file peaks_NKX31_ET_CHL013.significant.peak.txt did not meet our peak cut-off of FDR0.05, thus, no peak was called in this file though we did generate the chip-seq library.

value: NKX3-1 antibody

value: Santa Cruz


title: NKX3-1 ChIP sequencing in DHT (5alpha-dihydrotestosterone) treated LNCaP cells

description:
NKX3-1 ChIP sequencing after 2 hrs DHT (5alpha-dihydrotestosterone) treatment in LNCaP cells
NKX3-1 DHT


title: AR ChIP sequencing in DHT (5alpha-dihydrotestosterone) treated LNCaP cells

description:
AR ChIP sequencing after 2 hrs DHT (5alpha-dihydrotestosterone) treatment in LNCaP cells
AR DHT

value: AR antibody


title: bud-2

description: RNA-Seq


title: AR ChIP sequencing in Et (ethanol) treated LNCaP cells

description:
AR ChIP sequencing after 2 hrs Et (ethanol) treatment in LNCaP cells
AR Et


title: IL100003739

status: Public on Nov 15 2011

city: Knoxville

first: Kathleen

last: Cusick

state: TN

address: 1414 West Cumberland Ave

institute: Univ of Tenn

description: BB2000 harvested from broth 4.5h after inoculation (control of BB2204 broth)

data_processing: Primary image processing was done via the Illumina pipeline. Raw reads were mapped to the P. mirabilis HI4320 reference genome with the Mosaik aligner, allowing for 2 nt mismatches. Raw reads were normalized to  Reads Per Kilobase of gene/transcript per Million mapped reads (RPKM values) using an IGS in-house pipeline built around a combination of Burrows-Wheeler Aligner and TopHat/Cufflinks [Processed data is provided as a Series supplementary file.]

organism: Proteus mirabilis

source_name: BB2000 broth (control for BB2204 broth)

growth_protocol: For RNA-Seq comparison between agar- (swarmer) and broth (swimmer)-grown BB2000, single colonies were grown overnight in 2 ml L broth. The next morning, cells were washed in LB broth. Samples defined as 'swimmer' were re-inoculated into fresh LB broth at a 1:10 dilution. Samples defined as 'swarmer' were serially diluted in 1x PBS, and 100ul f 10-2 dilution spread onto LB plates that had been dried for 30 min at 42C. Cells were harvested after 4.3h. For RNA-Seq analyses of the fliL mutant, single colonies of BB2204 and BB2000 were inoculated into 2 mL LB broth and incubated with agitation (200 rpm). Cells were harvested at 4.5h.

extract_protocol: cDNA library preparation and sequencing were performed at the University of Maryland, Baltimore Institute for Genomic Sciences (IGS) following standard protocols. Illumina RNAseq libraries were prepared with the mRNA-Seq Sample Prep Kit (Illumina, San Diego, CA) following a variation of the manufacturer's protocol. The DNA was purified between enzymatic reactions and the size selection of the library was performed with AMPure XT beads (Beckman Coulter Genomics, Danvers, MA). The median library fragment size (including adaptors totaling ~116bp) ranged from 402-419 bp, for an average of 300bp with a std dev of 25-40bp. One sample per lane was loaded onto the flow cell and sequenced in 50-nucleotide paired-end runs.

treatment_protocol: Cells were centrifuged at 10,000g for 5 min at room temperature, washed with 1x PBS, centrifuged, and pellets snap-frozen in a dry-ice/ethanol slurry. Cells were stored in RNase-free tubes at -80C until RNA extraction. Total RNA was extracted using the Ribopure Kit (Ambion) following manufacturer's instructions. The optional DNase treatment was included and incubation time extended to 1 hour.  mRNA enrichment was performed using the MICROBExpress kit (Ambion)

value: wild-type for swimming and swarming


title: ChIP-seq of H2BK5ac in IMR90; renlab.H2BK5ac.IMR90.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: NA
Library name: LL229
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10405
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
****************
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: GSM832837_UCSD.IMR90.H2BK5ac.LL229.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.IMR90.01.IMR90.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK5ac ChIP-Seq on IMR90 Cell Line, Library LL229, 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.12401
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,802,055
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.6835
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6779
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9988
IROC_PERCENTILE: 86
POISSON_SCORE: 0.7432
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM832837_UCSD.IMR90.H2BK5ac.LL229.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.IMR90.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK5ac ChIP-Seq read mappings from the IMR90 Cell Line, Library LL229, 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.12474
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 6
BROWSER_TRACK_NAME: IMR90 H2BK5ac 29
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK5ac Library LL229 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,802,055
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.6835
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6779
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9988
IROC_PERCENTILE: 86
POISSON_SCORE: 0.7432
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: IMR90 Cell Line, biological replicate 1 (r1); renlab.H2BK5ac.IMR90.01

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

tag: sample alias

tag: sample common name

value: IMR90 Cell Line

tag: molecule

value: genomic DNA

tag: disease

value: ATCC

value: Cell Line

tag: line

tag: lineage

tag: batch

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

tag: Sex

value: Female

value: Histone H2BK5ac

value: Bioruptor

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: IL100003740

description: BB2204 harvested from broth culture 4.5h after inoculation

source_name: BB2204 broth

tag: strain

tag: genotype/variation

value: BB2000 fliL::Tn5-Cm


title: IL100003743

description: BB200 harvested from broth cultures 4.3 h after inoculation (control of BB2000 agar)

source_name: BB2000 broth


title: ChIP-seq of H2BK5ac in IMR90; renlab.H2BK5ac.IMR90.02

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: NA
Library name: SK10
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10407
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM832838_UCSD.IMR90.H2BK5ac.SK10.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.IMR90.02.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK5ac ChIP-Seq on IMR90 Cell Line, Library SK10, 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.12388
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,816,239
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.6405
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.6216
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9991
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7149
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM832838_UCSD.IMR90.H2BK5ac.SK10.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.IMR90.02.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK5ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK10, 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.12461
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 6
BROWSER_TRACK_NAME: IMR90 H2BK5ac 10
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK5ac Library SK10 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,816,239
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.6405
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.6216
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9991
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7149
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK5ac.IMR90.02

value: Abcam


title: ChIP-seq Input in H9 cells; renlab.Input.hESC.H9.07

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: NA
Library name: SK338
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10409
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6940
****************
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: GSM832839_UCSD.H9.Input.SK338.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC.H9.07.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H9 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on H9 Cell Line, Library SK338, 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.12420
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,810,337
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0134
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.14
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.654
IROC_PERCENTILE: 27
POISSON_SCORE: 0.2578
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

ANALYSIS FILE NAME: GSM832839_UCSD.H9.Input.SK338.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC.H9.07.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H9 Cell Line, Library SK338, 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.12493
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 6
BROWSER_TRACK_NAME: H9 Input 38
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line ChIP-Seq Input Library SK338 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,810,337
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0134
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.14
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.654
IROC_PERCENTILE: 27
POISSON_SCORE: 0.2578
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.Input.hESC.H9.07

value: H9 Cell Line

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: mTeSER

value: ChIP-Seq Input

value: Input


title: trm44del tan1del tRNASer(CGA) U6:A67 (JMW561) 6 hr Replicate 3

source_name: trm44 tan1 deletion strain containing tRNASer(CGA) U6:A67 mutant

tag: hours at 37 degrees

tag: replicate number


title: IL100003738

description: BB2000 harvested from agar plates 4.3 h after plating

source_name: BB2000 agar

value: wild-type for swimming and swarming


title: H3K9ac2 Ikaros knockout chromatin preleukemic stage2

status: Public on Nov 13 2011

first: Jiangwen

last: Zhang

address: 7 Divinity Ave

department: FAS Center for Systems Biology

institute: Harvard University

description:
C57BL/6 x129S4/SvJae_Ikaros_knockoutpre-leukemic stageII
Chromatin IP against H3K9ac2

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 genomes using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: mouse Ik knockout DP thymocytes

growth_protocol: Ikaros dominant negative (IkDN) and WT strains were bred and housed under pathogen-free conditions

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

tag: genetic background

value: C57BL/6 x129S4/SvJae

tag: genotype

value: Ikaros knockout

tag: cell type

value: DP thymocytes

tag: developmental stage

value: pre-leukemic stage II

tag: chip antibody

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog number


title: input DNA Ikaros knockout chromatin preleukemic stage2

description:
C57BL/6 x129S4/SvJae_Ikaros_knockoutpre-leukemic stageII
input DNA


title: H3K36me3 Ikaros knockout chromatin preleukemic stage2

description:
C57BL/6 x129S4/SvJae_Ikaros_knockoutpre-leukemic stageII
Chromatin IP against H3K36me3


title: PolII Ikaros knockout chromatin preleukemic stage2

description:
C57BL/6 x129S4/SvJae_Ikaros_knockoutpre-leukemic stageII
Chromatin IP against PolII

value: PolII


title: input DNA Ikaros knockout chromatin preleukemic stage1

description:
C57BL/6 x129S4/SvJae_Ikaros_knockoutpre-leukemic stageI
input DNA

value: pre-leukemic stage I


title: H3K27me3 Ikaros knockout chromatin preleukemic stage2

description:
C57BL/6 x129S4/SvJae_Ikaros_knockoutpre-leukemic stageII
Chromatin IP against H3K27me3


title: H3K9ac2 Ikaros knockout chromatin stageI

description:
C57BL/6 x129S4/SvJae_Ikaros_knockoutpre-leukemic stageI
Chromatin IP against H3K9ac2


title: H3K4me3 Ikaros knockout chromatin preleukemic stage2

description:
C57BL/6 x129S4/SvJae_Ikaros_knockoutpre-leukemic stageII
Chromatin IP against H3K4me3

value: Abcam and Millipore


title: H3K27me3 Ikaros knockout chromatin stageI

description:
C57BL/6 x129S4/SvJae_Ikaros_knockoutpre-leukemic stageI
Chromatin IP against H3K27me3


title: H3K36me3 Ikaros knockout chromatin stageI

description:
C57BL/6 x129S4/SvJae_Ikaros_knockoutpre-leukemic stageI
Chromatin IP against H3K36me3


title: H3K4me3 Ikaros knockout chromatin stageI

description:
C57BL/6 x129S4/SvJae_Ikaros_knockout pre-leukemic stageI
Chromatin IP against H3K4me3


title: H3K9ac2 wildtype

description:
C57BL/6
Chromatin IP against H3K9ac2

source_name: mouse wt DP thymocytes

value: wt


title: Mi2beta wildtype 1and2

description:
C57BL/6
Chromatin IP against Mi2beta

value: homemade Mi2beta (Chd4)


title: Ikaros wildtype 1and2

description:
C57BL/6
Chromatin IP against Ikaros

value: homemade Ikaros (Ikzf1)


title: input wildtype 1and2

description:
C57BL/6
input DNA


title: input DNA Ikaros knockout chromatin

description:
C57BL/6 x129S4/SvJae_Ikaros_knockout
input DNA


title: H3K4me3 wildtype

description:
C57BL/6
Chromatin IP against H3K4me3


title: Aio Ikaros knockout chromatin

description:
C57BL/6 x129S4/SvJae_Ikaros_knockout
Chromatin IP against Aiolos

value: homemade Aiolos


title: PolII wildtype

description:
C57BL/6
Chromatin IP against PolII

value: Abcam


title: ChIP-seq analysis of inducible V5-tagged Olig2 (iOlig2-V5) in progenitor motor neurons (Day 4)

status: Public on Nov 12 2011

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: progenitor motor neurons (Day4 directed differentiation)

data_processing:
Alignment: Sequence reads were aligned to the mouse genome (version mm9) using Bowtie (Langmead, et al. Genome Biology 2009) version 0.12.5 with options "-q --best --strata -m 1 -p 4 --chunkmbs 1024". Only uniquely mapping reads were analyzed further. All alignment data is provided here in BAM format.
Peaks: Binding events were detected using GPS (Guo, et al. Bioinformatics 2010) version 1.0. In GPS, the scaling ratio between IP and control channels was estimated using the median ratio of all 10Kbp windows along the genome. The GPS binding model was initialized to the default and iteratively updated over up to 3 training rounds. In this study, we require that reported peaks contain a ChIP-seq enrichment level that is significantly greater than 1.5 times the control level with p-value <0.01 as tested using the Binomial distribution. Signal-to-noise ratios are estimated by comparing the ChIP-seq read count occurring at any peak found for a given transcription factor in any condition to the count of remaining reads in that experiment. Peaks are provided here in two formats, BED and GPS raw output. The BED format shows the GPS-predicted binding position, and the Q-value calculated by GPS is provided in the score field. The GPS raw output has the following fields (tab-separated): 1) Binding event coordinate, 2) IP read count assigned to event, 3) Control read count assigned to event, 4)Fold enrichment (IP/Control), 5) Q-value (multiple hypothesis corrected), 6) P-value, 7) Shape deviation from the empirical read distribution (log10(KL)), 8) Shape deviation between IP vs Control (log10(KL)).
WIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts.

source_name: Chromatin IP against V5

growth_protocol: ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described (Wichterle, et al. Cell 2002).  Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x105 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 1, Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 ÂµM all-trans-Retinoic acid (RA, Sigma) and 0.5 ÂµM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0. Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

extract_protocol: Differentiating embryoid bodies were washed with PBS and then dissociated by mild Trypsinization (Invitrogen) followed by mechanical dissociation until single-cell suspension was obtained. Cells were fixed with 1% formaldehyde for 15 minutes at room temperature. Pellets containing ~40 x106 cells were flash frozen and stored at -80 oC. Cells were thawed on ice, resuspended in 5ml of Lysis Buffer A and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 5ml Lysis Buffer B and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 3ml of Sonication Buffer (SB). Nuclear extracts were sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp. Sonicated chromatin was incubated for 16 hours at 4C with Protein-G beads (Invitrogen) conjugated with either rabbit anti-V5 (Abcam), mouse anti-Flag M2 (Sigma) or rabbit anti-Olig2 (Millipore). After incubation and with the aid of a magnetic device, beads were washed once with SB+500nM NaCl, once with LiCl Wash Buffer (LiClB) and 1ml of TE. Then, beads were centrifugated at 950g for 3 min and remove residual TE with a pipette. 210ul of Elution Buffer was added to the beads followed by incubation at 65 oC for 45 minutes with a brief pulse of vortex every 10 minutes. 200ul of supernatant was removed after a 1 minute centrifugation at 16,000g. The crosslink was reversed by 16 hours incubation at 65 oC.  RNA was digested by the addition of 200ul of TE and RNAseA (Sigma) at a final concentration of 0.2mg/ml and incubated for 2 hours at 37C.  Protein was digested by the addition of Proteinase K (0.2 mg/ml final, Invitrogen) supplemented with CaCl2 followed by a 30 minutes incubation at 55 oC. DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and then recovered with an ethanol precipitation with glycogens as carrier. The pellets were suspended in 70ul of water. Purified DNA fragments were processed according to the Illumina/Solexa sequencing protocol using a Genome Analyzer II (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 ÂµM all-trans-Retinoic acid (RA, Sigma) and 0.5 ÂµM agonist of hedgehog signaling (SAG, Calbiochem). Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

tag: cell line

value: Ainv15 (ATCC SCRC-1029) with inducible V5-tagged Olig2

tag: treatment

value: +Dox

tag: cell stage

value: anti-V5 (Abcam, ab15828)


title: ChIP-seq analysis of Olig2 using native antibody in progenitor motor neurons (Day 4)

source_name: Chromatin IP against Olig2

value: progenitor motor neurons (Day4 directed differentiation)

value: Olig2 (Millipore, ab9610)


title: ChIP-seq analysis of inducible Flag-tagged Hoxc9 (iFlag-Hoxc9) in progenitor motor neurons (Day 5)

description: progenitor motor neurons (Day5 directed differentiation)

source_name: Chromatin IP against Flag

value: Ainv15 (ATCC SCRC-1029) with inducible Flag-tagged Hoxc9

value: anti-Flag (Sigma, F1804-200UG)


title: ChIP-seq analysis of inducible V5-tagged Hoxc9 (iHoxc9-V5) in progenitor motor neurons (Day 5)

value: Ainv15 (ATCC SCRC-1029) with inducible V5-tagged Hoxc9

value: progenitor motor neurons (Day5 directed differentiation)


title: Pseudo-ChIP control using anti-V5 in progenitor motor neurons (Day 4)

source_name: Pseudo IP against V5


title: Large TSC2 WT + Rapa (3hr)

city: Ithaca

first: Shu-Bing

last: Qian

state: NY

address: 301 Biotech Bldg.

department: Division of Nutritional Sciences

institute: Cornell University

description: supplementary file: Ribosome Protected RNA Fragments

data_processing: Each run file contains 3 barcoded samples. The fastq files were first splited into different groups so that each barcoded sample ends up with a dedicated run file based on the barcode sequences (raw files). Then,  reads were cleaned by filtering out reads with less than 10 nt polyA (allowing one nt mismatch of polyA). After removing poly-A tails, only reads which are longer than 20bp were retained for further process. The first 3 nucleotides (2 nt barcodes + 1st nt) were removed because the first nucleotide showed the highest rate of mismatch. Finally, the sequences of ribosome protected fragments were obtained(processed files).

source_name: Embryonic Fibroblast

growth_protocol: TSC2+/+ MEFs were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol: The library construction protocol is described in the accompanying manucript (under review). Briefly, ribosome profiling was performed to separate the lysates into three fractions, including small (1 ribosome), medium(2-4 ribosomes) and large(≥5 ribosomes). RNAs were digested by RNAse I and extracted from each fraction. Then, ribosome protected mRNA fragments were selected and purifed. Next, Poly-(A) tails were added to the framents and then the framents were converted to cDNA with barcodes by reverse transcription reaction. Furthermore, the cDNA was circulated and re-linealized. Finally, cDNA was PCR amplified and library fragments were isolated. Libraries were sequenced on the Illumina Genome Analyzer following the manufacturer's protocols.

treatment_protocol: TSC2+/+ MEFs were kepted in DMEM with 20 nM Rapamycin(Sigma) at 37℃ for 3 hours

value: 20nM Rapamycin 3hrs

tag: sample type

value: Large (≥5 ribosomes)

value: TSC2 Wild Type

value: mouse embryonic fibroblast

value: 129S4/SvJae, C57BL/6, CBA


title: H3K36me3 wildtype

description:
C57BL/6
Chromatin IP against H3K36me3

value: wt

value: DP thymocytes


title: H3K27me3 wildtype

description:
C57BL/6
Chromatin IP against H3K27me3

value: Millipore


title: Small TSC2 WT + Rapa (3hr)

value: Small (1 ribosome)


title: Medium TSC2 KO

growth_protocol: TSC2 -/- MEFs were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

treatment_protocol: No Treatment

value: No Treatment

value: Medium (2-4 ribosomes)

value: TSC2 Knock Out


title: Large TSC2 KO


title: Small TSC2 KO

growth_protocol: TSC2-/- MEFs were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).


title: Small TSC2 WT


title: Medium TSC2 WT


title: Large TSC2 WT + Rapa (30min)

treatment_protocol: TSC2+/+ MEFs were kepted in DMEM with 20 nM Rapamycin(Sigma) at 37℃ for 30 minutes

value: 20nM Rapamycin 40min


title: Medium TSC2 WT + Rapa (30min)


title: Small TSC2 WT + Rapa (30min)


title: Medium TSC2 KO + DMSO

treatment_protocol: DMSO as the control


title: Large TSC2 KO + DMSO


title: Mi2beta Ikaros knockout chromatin

description:
C57BL/6 x129S4/SvJae_Ikaros_knockout
Chromatin IP against Mi2beta

value: C57BL/6 x129S4/SvJae

value: Ikaros knockout

value: homemade Mi2beta (Chd4)


title: Small TSC2 KO + DMSO


title: Large TSC2 WT + DMSO


title: Small TSC2 WT + DMSO


title: Medium TSC2 WT + DMSO


title: hESC_D3_Smad_XL_rep2

status: Public on Nov 11 2011

first: Matthew

last: Trotter

address: West Forvie Building, Forvie Site, Robinson Way

department: Department of Surgery

country: United Kingdom

institute: University of Cambridge

description: Chromatin IP for Smad2/3: DNA cross linked with formaldehyde plus extra chemical linkers.

data_processing:
Read Filtering: Read sequences were quality filtered and aligned to the human genome (hg18) by the Illumina ELAND pipeline with default settings ([Reads were filtered to include only those that a) aligned to human chromosomes 1-22, X & Y with at most 2 mismatches, and b) lay outside repeat regions as defined by hg18 RepeatMasker information obtained from the UCSC Genome Bioinformatics website (http://genome.ucsc.edu/).
Bound Region Detection (GFF format) Smad2/3-bound regions were identified using the Model-based analyiss of ChIP-Seq (MACS) algorithm (http://liulab/dfci.harvard.edu/MACS/) as described in [Brown et al. Stem Cells, 2011 (epub doi: 10.1002/stem.666. PMID: 21630377)].

source_name: Endoderm progenitor

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: hESCs were induced to differentiate into endoderm using CDM-PVA supplemented with Activin (100 ng/ml)+BMP4 (10 ng/ml)+FGF2 (20ng/ml) for three days

value: endoderm progenitor derived from H9 hESC

tag: chip antibody vendor

value: Santa Cruz Biotechnology Inc

tag: chip antibody cat. number


title: Medium TSC2 WT + Rapa (3hr)

value: 20nM Rapamycin 3hrs


title: Large TSC2 WT

value: Large (≥5 ribosomes)

value: TSC2 Wild Type


title: smRNA_infected_72h

status: Public on Nov 10 2011

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing: Adapter-trimmed sequencing libraries were mapped against an index composed of both the human (UCSC hg19, http://genome.ucsc.edu) and HCMV Towne (Genbank FJ616285.1) genomes, using Bowtie software (version 0.12.7, with parameters -k 1 -m 10 -l 25 --best). Custom Perl scripts were used to overlap mapped coordinates with smRNA annotations, which were obtained from miRBase 16.0 (http://www.mirbase.org) and the UCSC Table Browser.

growth_protocol: Primary human foreskin fibroblasts were cultured as previously described (Sanders J Virol 2008) and maintained within passages 16 to 20.

extract_protocol: The Illumina Small RNA Sample Prep v1.5 kit was used to prepare smRNA-seq samples and CLIP-seq libraries were generated as described (Yeo Nat Struct Mol Biol 2008; Zisoulis Nat Struct Mol Biol 2010).

treatment_protocol: For infections, G0-synchronized cells were trypsinized, re-suspended in the presence of HCMV, and plated at near confluence. All infections were performed with the wild-type Towne strain at an MOI of 3. For mock infections, tissue culture supernatant (spent media from 3 days of culture) containing 1% DMSO was used in place of virus stock.

value: human foreskin fibroblasts (HFF)

value: HCMV infected


title: smRNA_mock_72h

value: mock infected


title: smRNA_mock_24h


title: smRNA_infected_24h


title: hESC_D3_Smad_XL_rep1


title: hESC_D0_Smad_XL_rep2

source_name: Pluripotent hESC (H9)

growth_protocol: H9 hESCs were grown in Chemically Defined Medium, as described in Vallier et al., Stem Cells, 2009, supplemented with 10ng/mL activin (R&D systems) and 12ng/mL FGF2

value: H9 hESC


title: hESC_Input_XL

description: Input control for ChIP-Seq: DNA cross linked with formaldehyde plus extra chemical linkers.


title: hESC_D0_Smad_XL_rep1


title: HDAC3KO No Treat H3K9Ac

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description: Sample 5

data_processing: Sequencing was performed by the Functional Genomics Core at the University of Pennsylvania.  Sequence reads of 36 bp were obtained using the Solexa Analysis Pipeline, and were mapped to the mouse genome (mm8).   All but one of the identically aligning reads were removed to minimize PCR bias.  Regions that overlapped with peaks in the input data were discarded.

source_name: HDAC3KO No Treat H3K9Ac

growth_protocol: Bone marrow derived macrophages were obtained by culturing bone marrow from 12-16 week old male C57Bl/6J mice in 30% L929 conditioned medium for six days, changing the media on the fourth day of culture.  Cells were replated on day 6, allowed to rest overnight and then treated accordingly.  Control macrophages were from mice with exons 4-7 of HDAC3 floxed with loxP sites (HDAC3 floxed).  HDAC3 KO macrophages were from mice expressing Cre recombinase under the control of the lysozyme M promoter and with floxed HDAC3.

extract_protocol: Cells were fixed in 1% PFA for 15 minutes and quenched with glycine.  Nuclei were harvested and lysed.  Extracts were sonicated using a Bioruptor (Diagenode). Immunoprecipiation using anti-HDAC3 (Abcam, ab7030) and anti-H3K9Ac (Upstate Biotechnologies, 06-942) were performed and resulting chromatin was isolated.  Control Input DNA for comparison with the H3K9Ac ChIP was generated by pooling equal amounts of nuclear extract from Control and HDAC3 KO macrophages with and without IL-4 treatment prior to immunoprecipitation.  ChIP and Input DNA was prepared from bone marrow derived macrophages for sequencing according to the amplification protocol from Illumina. DNA for the HDAC3 ChIP-seq was obtained by pooling DNA from two independent ChIPs each using a pool of four mice for each condition while the DNA for the H3K9Ac ChIP-seq was obtained from a pool of four mice for each condition.

treatment_protocol: Macrophages were treated with either control vehicle, 0.1% bovine serum albumin (BSA) or 10ng/mL of IL-4 for 24 hours.

tag: strain

tag: tissue

value: Bone Marrow

tag: cell-type

value: Macrophage

tag: mutation

value: LysM Cre+, HDAC3 floxed

value: BSA


title: Saccharomyces_bayanus_nucleosomes

city: Toronto

first: Kyle

last: Tsui

address: 160 College Street

country: Canada

institute: University of Toronto

data_processing: The genome sequences were retrieved using SGD. Reads were mapped using Maq and only unique reads were further processed.  Reads correspond to fragments of 36 bps in size but they were extended to 147 bp to represent nucleosome fragments.

organism: Saccharomyces bayanus

source_name: Saccharomyces bayanus

growth_protocol: Cells were grown in YPD (2% peptone, 1% yeast extract, 2% dextrose) starting from a overnight culture until they reached mid-log phase (0.8 OD).

extract_protocol: Mono-nucleosomes were extracted by treating the cell spheroplast with Mnase.  Samples representing mono-nucleosomes were gel extracted, end repaired and adapter ligated.

treatment_protocol: Cells were then cross-linked with formaldehyde and mono-nucleosomes were isolated according to modified protocols from Lee, Tillo., et al. Nature Genetics (2007)


title: Control IL4 H3K9Ac

description: Sample 4

source_name: Control IL4 H3K9Ac

value: HDAC3 floxed

value: H3K9Ac (Upstate Biotechnologies, 06-942)


title: HDAC3KO IL4 H3K9Ac

description: Sample 6

source_name: HDAC3KO IL4 H3K9Ac


title: Input Macrophage Pool

description: Sample 7

source_name: Input Macrophage Pool

value: equal mix of Sample 3-6

value: input


title: GIS_RnaPet_K562_cytosol_longPolyA

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

extract_protocol: For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisRnaPet

tag: datatype

value: RnaPet

tag: datatype description

value: RNA Paired-End Tags

tag: rnaextract

value: longPolyA

tag: rnaextract description

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

tag: biorep

tag: labexpid

tag: labversion

value: clone-free

tag: readtype

tag: readtype description

value: Paired 36 nt reads

tag: cell sex

value: F

tag: localization

value: cytosol

tag: localization description

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

tag: replicate

tag: replicate description

value: tier 1


title: Control No Treat H3K9Ac

description: Sample 3

source_name: Control No Treat H3K9Ac

tag: strain

tag: tissue

value: Bone Marrow

value: Macrophage

tag: treatment

tag: chip antibody


title: IL4 HDAC3

description: Sample 2

source_name: IL4 HDAC3

tag: cell-type

tag: mutation

value: None/WT

value: HDAC3 (Abcam, ab7030)


title: BSA HDAC3

description: Sample 1

source_name: BSA HDAC3

value: BSA


title: GIS_RnaPet_K562_chromatin_total

molecule: nuclear RNA

tag: datatype

tag: datatype description

tag: rnaextract

value: total

tag: rnaextract description

value: Total RNA extract (longer than 200 nt)

value: clone-based

value: chromatin

value: Nuclear DNA and associated proteins


title: GIS_RnaPet_NHEK_cytosol_longPolyA

source_name: NHEK

value: RnaPet

value: RNA Paired-End Tags

value: longPolyA

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

tag: biorep

tag: labexpid

tag: labversion

tag: readtype

value: U


title: GIS_RnaPet_NHEK_nucleus_longPolyA

value: clone-free

tag: readtype description

value: Paired 36 nt reads

tag: cell sex

tag: localization

value: nucleus

tag: localization description

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


title: GIS_RnaPet_H1-hESC_cell_longPolyA

value: M

value: cell

value: Whole cell

tag: replicate

tag: replicate description

value: tier 1


title: GIS_RnaPet_HeLa-S3_cytosol_longPolyA

value: F

value: cytosol

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


title: GIS_RnaPet_GM12878_nucleus_longPolyA

tag: cell description

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

value: clone-based


title: GIS_RnaPet_HepG2_nucleus_longPolyA

value: RnaPet

value: RNA Paired-End Tags

value: hepatocellular carcinoma


title: GIS_RnaPet_K562_nucleus_longPolyA

value: longPolyA

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


title: GIS_RnaPet_K562_nucleolus_total

value: total

value: Total RNA extract (longer than 200 nt)

value: Paired 36 nt reads

value: nucleolus

value: The part of the nucleus where ribosomal RNA is actively transcribed


title: GIS_RnaPet_HepG2_cytosol_longPolyA


title: GIS_RnaPet_prostate_cell_longPolyA

source_name: prostate

value: cell

value: Whole cell


title: GIS_RnaPet_HUVEC_nucleus_longPolyA

source_name: HUVEC

value: clone-free

value: U

value: nucleus

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

value: tier 1


title: Rice-Seedling-H3K36me3

status: Public on Nov 09 2011

city: Madison

first: Yufeng

last: Wu

state: WI

address: 1575 Linden Drive

institute: UW-Madison

data_processing: The reads from ChIP-seq were aligned to rice genome (TIGR release 5) with 1 bp mismatch allowed using MAQ program.  Only the reads mapped to a unique position of rice genome were included in the analysis.

organism: Oryza sativa

growth_protocol: Rice cultivar ‘Nipponbare’ seedlings grown in green house for two weeks.

extract_protocol: Commercial antibodies against H3K4me2 (07-030, Upstate), H3K36me3 (ab9050, Abcam) and H4K12ac (ab1762, Abcam) were used in ChIP experiments.  Construction of ChIP-seq libraries was according to the protocol of “preparing samples for ChIP sequencing of DNA” provided by Illumina.  Briefly, ChIPed DNA was end repaired using ‘End-It DNA End Repair Kit’ (Epicentre, ER0720).  The ‘dA’ base was then added to the 3’ ends of the blunt-ended DNA fragments using Klenow fragment (3’-5’exo-) (NEB, M0212S).  Linker for single read was ligated to the DNA molecules with ‘dA’ overhang using LigaFast kit (Promega, M8221).  After 2% agarose gel running with TAE buffer, the gel region containing about 150-300 bp DNA was excised for adapter ligated DNA size selection.  The adapter modified DNA fragments were enriched by PCR and purified by running 2% agarose gel in TAE buffer for isolation of DNA fragments in the range of 200-300 bp.  The purified DNA sample was ready for Illumina sequencing after quality validation.

treatment_protocol: Leaves of two-week old rice cultivar ‘Nipponbare’ seedlings grown in green house were collected and ground into fine powder in liquid nitrogen.  The resulting powder was suspended in nuclear isolation buffer (NIB: 20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermine, 0.1% mercaptoethanol, 40% Glycerol, pH 7.5) and followed the standard protocol for nuclei isolation. The prepared nuclei pellet was suspended in RSB buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2) for DNase I (Roche) digestion with increasing concentrations (0-4 units) for 10 min at 37°C.

tag: cultivar

value: Nipponbare

tag: tissue

value: Seedling

tag: antibody

value: H3K36me3 (ab9050, Abcam)


title: Rice-Seedling-H3K4me2


title: Rice-Seedling-H4K12ac

value: H4K12ac (ab1762, Abcam)


title: Callus_RNAseq_BiologicalReplicate2

data_processing: We used TopHat software to align the sequence reads to reference genome (Tigr release 5) and used Cufflink to call the expression values (FPKM, Fragments Per Kilobase of exon model per Million mapped fragments) of annotated rice genes and to detect differentially expressed genes.

source_name: Callus

growth_protocol: Rice cultivar ‘Nipponbare’ seedlings grown in green house for two weeks. Rice callus tissue was induced from sterilized ‘Nipponbare’ seeds in rice calli induction medium (NB basal medium plus vitamin, glutamine, proline, casein hydrolysate, sucrose and phytogel as well as 3 mg/L 2,4-D, pH 5.8) under 28-29°C with dark condition.

extract_protocol: Approximately 10 μg total RNA was converted to cDNA using the mRNA-seq kit from Illumina and barcoded cDNA library was sequenced on an Illumina Genome Analyzer 2 platform.

treatment_protocol: Leaves of two-week old rice cultivar ‘Nipponbare’ seedlings grown in green house and three-week old calli were collected and ground into fine powder in liquid nitrogen.Total RNA was extracted using a RNeasy Plant Kit (Qiagen Cat. NO. 74904). High-quality (RNA integrity number >8) was used for down-stream DNase I treatment to remove genomic DNA.

value: Callus


title: Seedling_RNAseq_BiologicalReplicate2

source_name: Seedling


title: Callus_RNAseq_BiologicalReplicate1


title: Seedling_RNAseq_BiologicalReplicate1


title: Rice-DH-seedling

description: DH sites region

data_processing: The reads from DNase-seq or ChIP-seq were filtered out the primer sequences and then aligned to rice genome (TIGR release 5) with 1 bp mismatch allowed using MAQ program.  Only the reads mapped to a unique position of rice genome were used to identify DH sites.  We used F-seq to identify DH sites with 200 bp bandwidth.  To detect the FDR of identified DH sites, we randomly generated 10 data sets, of which amount of reads is as same as the data sets from DNase-seq.  The FDR was calculated as ratio of DH sites identified from random data sets to DH sites from DNase-seq.  We set a cutoff in F-seq to control the FDR less than 0.05.  To investigate the saturation of DNase-seq data, we simulated the correlation between sequencing depth (the number of reads) and the total length of all DH sites identified.  We randomly sampled the reads from our dataset.  For callus, we sampled ~2%, ~4%, ~6% …98%, 100% reads from callus DNase-seq dataset, consisting of 50 data points in Figure 1b.  For seedling, we sampled ~3%, ~6%, ~9%..., ~96%, ~99% reads from seedling DNase-seq dataset.  We identified DH sites based on these randomly sampled data and examined the correlation between the read number and the total length of DH sites for each data point.  For each data point, we sampled 10 times and averaged the total length of DH sites.  We fitted the data into logarithmic growth model for the regression analysis.  We used DESeq  to identify the change of DNase I sensitivity in DH sites shared between callus and seedling (FDR=0.01).  The variance used in DESeq was estimated based on three replicates of DNase-seq in seedling and two lanes data from replicate 1 of callus.

extract_protocol: The degree of DNase I digestion was assessed by pulsed-field gel electrophoresis (PFGE: 20–60 switch time, 18 h, 6 V/cm; Bio-Rad).  High molecular weight (HMW) DNA after DNase I digestion was isolated, blunt ended with T4 DNA polymerase.  Biotinylated adaptor I (5’ Bio ACAGGTTCAGAGTTCTACAGTCCGAC and 5’ P- GTCG GACTGTAGAACTCTGAAC) was ligated to the DNA molecules.  Dynal M-280 beads (Invitrogen) were used for enriching DNase I digested DNA ends after MmeI digestion.  Adaptor II (5’ P-TCGTATGCCGTCTTCTGCTTG and 5’ CAAGCAGAAGACGGCATACGANN) was then ligated to the MmeI treated ends.  The DNA sample was amplified by PCR using linker-specific primers (5’ CAAGCAGAAGACGG CATACGA and 5’AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA), and purified by PAGE for isolation of DNA fragments with about 90 bp in size.  The final Illumina sequencing was performed using a primer specific to linker I (5’CCACCGACAGGTTCAGAGTTCTACAGTCCGAC).

treatment_protocol: Leaves of two-week old rice cultivar ‘Nipponbare’ seedlings grown in green house were collected and ground into fine powder in liquid nitrogen.  The resulting powder was suspended in nuclear isolation buffer (NIB: 20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermine, 0.1% mercaptoethanol, 40% Glycerol, pH 7.5) and followed the standard protocol for nuclei isolation.Three-week old calli were collected for nuclei isolation using the same method for leave tissue.  The prepared nuclei pellet was suspended in RSB buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2) for DNase I (Roche) digestion with increasing concentrations (0-4 units) for 10 min at 37°C.


title: Rice-DH-callus

description: DH sites region


title: GIS_RnaPet_K562_polysome_longPolyA

tag: datatype

value: RnaPet

tag: datatype description

value: RNA Paired-End Tags

value: longPolyA

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

value: clone-based

value: F

value: polysome

value: Strand of mRNA with ribosomes attached


title: GIS_RnaPet_K562_nucleoplasm_total

tag: rnaextract

value: total

tag: rnaextract description

value: Total RNA extract (longer than 200 nt)

value: Paired 36 nt reads

value: nucleoplasm

value: That part of the nuclear content other than the chromosomes or the nucleolus