title: Bisulfite-Seq analysis of RRBS528 derived from human WA-7 cells; 42TVLAAXX100212-1-S

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: NTR_0000837
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-17914
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2363
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2354
****************
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: GSM621353_BI.ES-WA7.RRBS.RRBS528-529.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS528-RRBS529.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of ES-WA7 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the ES-WA7 Cell Line, Libraries RRBS578-579 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6854
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: ESWA7 RRBS 28
BROWSER_TRACK_DESCRIPTION: BI ES-WA7 RRBS Libraries RRBS528-529 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.80

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

source_name: WA7 stem cells; 42TVLAAXX100212-1-S

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

value: genomic DNA

tag: disease

value: Harvard University

value: Cell Line

tag: line

tag: lineage

value: embrionic stem cell

value: undifferentiated

tag: passage

tag: medium

value: KSR

value: Female

tag: batch

value: DNA Methylation

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: 20 ng

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: T4 Ligase (2,000U/ul) 16C o/n

value: 2x5hrs Epitect Kit

value: Pfu Turbo Cx hot start

value: Smith et al., Methods 48, 226-232

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Gel size selection


title: Brd3_1H_plus

status: Public on Nov 10 2010

type: SRA

city: New York

first: Uwe

last: Schaefer

state: NY

address: 1230 York Ave.

country: USA

institute: Rockefeller University

description: Chromatin Immunoprecipitation against Brd3

library_source: genomic

data_processing: RTA 2.6, wig files contain alignments to mm9

molecule: genomic DNA

organism: Mus musculus

source_name: Macrophages

extract_protocol:
For ChIP experiments, BMDMs were pre-incubated with 1 mM of GSK-BET compound in DMSO or DMSO only for 30 minutes. Cells were stimulated with 100 ng/ml LPS for 1 hours by adding LPS directly to the culture medium. ChIP experiments were performed as described previously 22. Cells were crosslinked with 1% formaldehyde. DNA was sonicated using a Biorupter (Diagenode) to generate DNA-fragments of approximately 200 to 600 bp. The following antibodies were pre-bound to Invitogen Dynal magnetic beads in 0.5% BSA/PBS (Invitrogen Dynabeads anti-mouse M-280 or Dynabeads anti-rabbit M-280): H3 (Abcam, ab1791), H3K4me3 (Millipore, 17-614), H4Acet (Millipore, 06-866), BRD4 (Abcam, ab84776), CDK9 (Santa Cruz, sc-8338x), Pol II (Abcam, ab5408) and Pol II S2 (Abcam, ab5095). Regular ChIP was performed using 1x106 cells (for H3, H3K4me3, Pol II and Pol II S2) or 2x106 cells (for H4Acet, BRD4 and CDK9) and 2 mg antibody coupled to 20 mL beads. ChIP-Seq was performed using 1x107 cells and 7 mg antibody coupled to 70 mL magnetic beads (for H3, H3K4me3 and Pol II) or 2x107 cells and 14 mg antibody coupled to 140 mL beads (for Pol II S2, H4Acet, BRD4 and CDK9). Beads were added to the cell lysates and incubation was allowed to proceed overnight. Beads were washed 8x in modified RIPA wash buffer (50 mM HEPES [pH 7.6], 100 mM LiCl [for H4Acet, BRD4 and CDK9] or 300 mM LiCl [H3, H3K4me3, Pol II and Pol II S2], 1mM EDTA, 1% NP-40 and 0.7% Na-deoxycholate) and 1x in TE containing 50 mM NaCl. Elution of DNA was performed in TE buffer containing 1% SDS. After overnight cross-link reversal at 650C, RNase digestion and Proteinase K digestion, ChIP DNA and input DNA was purified using the QIAGEN Quiaquick PCR purification kit. For regular ChIP and for validation of ChIP-Seq, ChIP DNA was analyzed via qPCR using SYBR Green master mix (Roche) and the LightCycler480 (Roche).
For ChIP-Seq, 30 mL of remaining ChIP DNA was used to generate blunt-ended DNA using the Epicenter DNA ENDRepair kit (Epicenter Biotechnologies). The end-repaired DNA was purified using the QIAGEN Quiaquick PCR purification kit. Using Klenow Fragment (NEB) A bases were added to the DNA. DNA was purified using the QIAGEN MinElute kit. T4 DNA ligase (NEB) was used for ligation of Illumina/Solexa adapters to the DNA fragments. The adaptor-ligated DNA was purified with the QIAGEN MinElute kit. The DNA fragments were subjected to 18 cycles of PCR using the Illumina/Solexa primers 1.0 and 2.0 to generate the ChIP-Seq libraries. The ChIP-Seq libraries were purified with the QIAGEN MinElute kit. Samples were sequenced on the Illumina GAIIx platform for 36 cycles, and raw sequencing data was processed using the onboard SCS/RTA software version 2.6 yielding 36bp reads. Sequencing kits used were version 4 sequencing kits.

tag: strain

tag: cell type

value: Bone-marrow-derived macrophages

tag: treatment

tag: antibody

tag: antibody manufacturer

value: BETHYL

tag: antibody catalog #

tag: antibody lot #

tag: time


status: Public on Nov 11 2010

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: H3K9ac ChIP-Seq analysis of peripheral cd8 naive from TC001 (HS2282) using Illumina Genome Analyzer IIx
library name: HS2282
EXPERIMENT_TYPE: Histone H3K9ac
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 76-272 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K9ac
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9649S
CHIP_ANTIBODY_LOT: 1
****************
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: GSM613813_UCSF-UBC.CD8_Naive_Primary_Cells.H3K9ac.TC001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2282-1_61LH3AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on CD8 Naive Primary Cells, Donor TC001 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.4324
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0801
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1685
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9844
IROC_PERCENTILE: 51
POISSON_SCORE: 0.3042
POISSON_PERCENTILE: 14

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

ANALYSIS FILE NAME: GSM613813_UCSF-UBC.CD8_Naive_Primary_Cells.H3K9ac.TC001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2282-1_61LH3AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor TC001 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.4373
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD8N H3K9ac 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD8 Naive Primary Cells Histone H3K9ac Donor TC001 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0801
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1685
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9844
IROC_PERCENTILE: 51
POISSON_SCORE: 0.3042
POISSON_PERCENTILE: 14

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

organism: Homo sapiens

extract_protocol: library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Blood

tag: histological type

value: CD8 naive cell

tag: is tumor

value: No

value: primary cell


description:
design description: H3K9me3 ChIP-Seq analysis of peripheral cd8 naive from TC001 (HS2281) using Illumina Genome Analyzer IIx
library name: HS2281
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 248-571 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0012
****************
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: GSM613812_UCSF-UBC.CD8_Naive_Primary_Cells.H3K9me3.TC001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2281-1_61LH3AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD8 Naive Primary Cells, Donor TC001 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.4317
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0725
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.1293
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.7681
IROC_PERCENTILE: 32
POISSON_SCORE: 0.3839
POISSON_PERCENTILE: 53

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

ANALYSIS FILE NAME: GSM613812_UCSF-UBC.CD8_Naive_Primary_Cells.H3K9me3.TC001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2281-1_61LH3AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor TC001 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.4366
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD8N H3K9me3 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD8 Naive Primary Cells Histone H3K9me3 Donor TC001 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0725
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.1293
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.7681
IROC_PERCENTILE: 32
POISSON_SCORE: 0.3839
POISSON_PERCENTILE: 53

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


title: Brd3_1H_minus

treatment_protocol: For ChIP experiments, BMDMs were pre-incubated with 1 mM of GSK-BET compound in DMSO or DMSO only for 30 minutes. Cells were stimulated with 100 ng/ml LPS for 1 hours by adding LPS directly to the culture medium.


description:
design description: H3K4me3 ChIP-Seq analysis of breast myoepithelial cell from RM066 (HS2439) using Illumina Genome Analyzer IIx
library name: HS2439
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: 1 ug
SIZE_FRACTION: 80-180 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ug
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
****************

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

ANALYSIS FILE NAME: GSM613869_UCSF-UBC.Breast_Myoepithelial_Cells.H3K4me3.RM066.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2439-1_624UKAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Breast Myoepithelial Cells, Donor RM066 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.4320
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3354
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.3786
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3801
POISSON_PERCENTILE: 27

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

ANALYSIS FILE NAME: GSM613869_UCSF-UBC.Breast_Myoepithelial_Cells.H3K4me3.RM066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2439-1_624UKAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Breast Myoepithelial Cells, Donor RM066 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.4369
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC H3K4me3 66
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells Histone H3K4me3 Donor RM066 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3354
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.3786
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3801
POISSON_PERCENTILE: 27

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

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/)

value: female

value: Breast

value: Myoepithelial cell

value: breast myoepithelial cell


title: Brd3_0H_minus


title: Brd3_0H_plus


title: new_H4K8Ac_0H_plus

description: Chromatin Immunoprecipitation against H4K8Ac

value: Millipore


title: Brd2_1H_plus

description: Chromatin Immunoprecipitation against Brd2


title: Brd2_1H_minus


title: Brd2_0H_plus


title: new_H4K5Ac_0H_plus

description: Chromatin Immunoprecipitation against H4K5Ac


title: H3_18_0H_minus redo

description: Chromatin Immunoprecipitation against H3

extract_protocol:
For ChIP experiments, BMDMs were pre-incubated with 1 mM of GSK-BET compound in DMSO or DMSO only for 30 minutes. Cells were stimulated with 100 ng/ml LPS for 1 or 4 hours by adding LPS directly to the culture medium. ChIP experiments were performed as described previously 22. Cells were crosslinked with 1% formaldehyde. DNA was sonicated using a Biorupter (Diagenode) to generate DNA-fragments of approximately 200 to 600 bp. The following antibodies were pre-bound to Invitogen Dynal magnetic beads in 0.5% BSA/PBS (Invitrogen Dynabeads anti-mouse M-280 or Dynabeads anti-rabbit M-280): H3 (Abcam, ab1791), H3K4me3 (Millipore, 17-614), H4Acet (Millipore, 06-866), BRD4 (Abcam, ab84776), CDK9 (Santa Cruz, sc-8338x), Pol II (Abcam, ab5408) and Pol II S2 (Abcam, ab5095). Regular ChIP was performed using 1x106 cells (for H3, H3K4me3, Pol II and Pol II S2) or 2x106 cells (for H4Acet, BRD4 and CDK9) and 2 mg antibody coupled to 20 mL beads. ChIP-Seq was performed using 1x107 cells and 7 mg antibody coupled to 70 mL magnetic beads (for H3, H3K4me3 and Pol II) or 2x107 cells and 14 mg antibody coupled to 140 mL beads (for Pol II S2, H4Acet, BRD4 and CDK9). Beads were added to the cell lysates and incubation was allowed to proceed overnight. Beads were washed 8x in modified RIPA wash buffer (50 mM HEPES [pH 7.6], 100 mM LiCl [for H4Acet, BRD4 and CDK9] or 300 mM LiCl [H3, H3K4me3, Pol II and Pol II S2], 1mM EDTA, 1% NP-40 and 0.7% Na-deoxycholate) and 1x in TE containing 50 mM NaCl. Elution of DNA was performed in TE buffer containing 1% SDS. After overnight cross-link reversal at 650C, RNase digestion and Proteinase K digestion, ChIP DNA and input DNA was purified using the QIAGEN Quiaquick PCR purification kit. For regular ChIP and for validation of ChIP-Seq, ChIP DNA was analyzed via qPCR using SYBR Green master mix (Roche) and the LightCycler480 (Roche).
For ChIP-Seq, 30 mL of remaining ChIP DNA was used to generate blunt-ended DNA using the Epicenter DNA ENDRepair kit (Epicenter Biotechnologies). The end-repaired DNA was purified using the QIAGEN Quiaquick PCR purification kit. Using Klenow Fragment (NEB) A bases were added to the DNA. DNA was purified using the QIAGEN MinElute kit. T4 DNA ligase (NEB) was used for ligation of Illumina/Solexa adapters to the DNA fragments. The adaptor-ligated DNA was purified with the QIAGEN MinElute kit. The DNA fragments were subjected to 18 cycles of PCR using the Illumina/Solexa primers 1.0 and 2.0 to generate the ChIP-Seq libraries. The ChIP-Seq libraries were purified with the QIAGEN MinElute kit. Samples were sequenced on the Illumina GAIIx platform for 36 cycles, and raw sequencing data was processed using the onboard SCS/RTA software version 2.6 yielding 36bp reads. Sequencing kits used were version 4 sequencing kits.

value: Abcam


title: H3_13_1H_plus redo

treatment_protocol: For ChIP experiments, BMDMs were pre-incubated with 1 mM of GSK-BET compound in DMSO or DMSO only for 30 minutes. Cells were stimulated with 100 ng/ml LPS for 1 or 4 hours by adding LPS directly to the culture medium.

tag: agent #1

value: GSK-BET

tag: agent #2

value: LPS


title: H3_14_1H_minus redo


title: H3_18_0H_minus


title: H3_14_1H_minus


title: PolII_total_1H_plus

description: Chromatin Immunoprecipitation against Pol II total

value: anti-Pol II total


title: H3_13_1H_plus


title: H3_17_0H_plus


title: PolII_total_0H_plus


title: PolII_total_1H_minus


title: PolII_total_0H_minus


title: Brd2_0H_minus


title: PolII_S2_1H_plus

description: Chromatin Immunoprecipitation against Pol II Serine 2 phosphorylated

value: anti-Pol II Serine 2 phosphorylated


title: PolII_S2_1H_minus

value: Bone-marrow-derived macrophages


title: PolII_S2_0H_minus


title: H3K4me3_24_0H_minus

description: Chromatin Immunoprecipitation against H3K4me3


title: 3_CDK_1H_minus

description: Chromatin Immunoprecipitation against CDK9 (P-TEFb)

value: anti-CDK9 (P-TEFb)

value: Santa Cruz

value: unknown


title: 4_CDK_1H_plus


title: H3K4me3_20_1H_minus


title: H3K4me3_23_0H_plus


title: 2_CDK_0H_plus


title: H3_17_0H_plus redo


title: ECR-WPP+12_GFP_INPUT_1

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

organism: Drosophila melanogaster

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  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 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No Treatment

tag: developmental stage


title: ECR-WPP+90_GFP_INPUT_1


title: H4ac_8_1H_minus

description: Chromatin Immunoprecipitation against H4Ac


title: H3K4me3_19_1H_plus


title: 1_CDK_0H_minus


title: ECR-WPP+90_GFP_ChIPSeq_1 and 2

tag: antibody name

value: GFP

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog

value: Custom


title: ECR-WPP+12_GFP_ChIPSeq_1 and 2


title: E16-24h_GFP_INPUT_1


title: E16-24h_GFP_ChIPSeq_1 and 2


title: H4ac_11_0H_plus

tag: strain

tag: cell type

tag: treatment

tag: antibody


title: PolII_S2_0H_plus

tag: antibody manufacturer

tag: antibody catalog #

tag: antibody lot #

tag: time


title: H4ac_12_0H_minus


title: 5T-0-6_GFP_ChIPSeq_1 and 2


title: H4ac_7_1H_plus


title: Brd4_2_1H_minus

description: Chromatin Immunoprecipitation against Brd4


title: Brd4_5_0H_plus


title: Chloronemata_200ng.ml-1 bleomycin_24hours

city: San Diego

first: John

middle: William

last: Whitaker

state: Ca

address: Gliam Drive

institute: UCSD

description: RNA from 3 independent replicates bulked

library_source: transcriptomic

data_processing: The reads from the two samples were pooled and mapped against the P. patens genome (version 1.2.1) using the read mapping program TopHat (version 1.0.11).

molecule: total RNA

organism: Physcomitrium patens

source_name: Chloronemal filaments

growth_protocol: Chloronemal tissue was grown on BCDAT agar medium overlain with cellophane for 6 days following subculture by homogenisation as detailed by Knight et al (2002)Molecular Plant Biology Vol. 2: pp. 285-299. Gilmartin PM, Bowler C (Eds) Oxford University Press.

extract_protocol:
RNA was isolated from a polyribosome-enriched fraction: protonemal tissue was harvested and residual liquid was squeezed from the tissue by pressing between two layers of Whatman 3MM chromatography paper. Squeeze-dried tissue was frozen in liquid nitrogen and homogenized.  Three replicates  of ca. 0.4g squeeze-dried protonemata, each corresponding to four 9cm Petri dish cultures were ground to a powder in liquid N2 in a mortar and pestle and homogenised in 30 ml 200mM sucrose - 200mM Tris-Cl, pH8.5 - 60mM KCl - 30mM MgCl2  - 1% (v/v) Triton X-100 - 5mM Ã¢-mercaptoethanol. The homogenates were centrifuged (20 min x 30,000 x g: Sorvall RC5B SS-34 rotor) and the supernatants aspirated and layered over 5ml sucrose cushions (1M sucrose - 40mM Tris-Cl, pH8.5 - 20mM KCl - 10mM MgCl2) and centrifuged at 150,000 x g (3h, Beckman Sw28 rotor).  Following centrifugation, the pellets were each resuspended in 0.5 ml RNA extraction buffer for isolation of RNA by phenol-chloroform extraction  Knight et al, 2002: Moss gene technology. In: Molecular Plant Biology Vol. 2: pp. 285-299. Gilmartin PM, Bowler C (Eds) Oxford University Press.)
Aliquots (1µg) of polysome-enriched RNA fraction from chloronemal tissue were used for cDNA synthesis using the Clontech SMART cDNA protocol (Clontech Protocol No. PT3041-1; Cat No. 634902). Libraries were prepared according to the Illumina protocol 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 the Illumina adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~375 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: Tissue was transferred into 5ml liquid BCDAT medium with or without 200ng.ml-1 bleomycin and harvested after 24 hours treatment

tag: cultivar

value: Villersexel K3

tag: tissue

value: 7d old chloronemata

tag: treatment group

value: 200ng.ml-1 bleomycin


title: Brd4_6_0H_minus


title: Chloronemata_untreated_24hours

value: untreated


title: Brd4_1_1H_plus

tag: agent #1


title: testes normal

city: Fort Collins

first: Stephen

middle: J

last: Coleman

state: CO

address: 1682 Campus Delivery

department: MIP

institute: Colorado State University

description: apparent normal gross morphology

data_processing: Sequencing tags were mapped to the reference equine genome sequence (EquCab2) using ELAND (efficient local alignment of nucleotide data – Illumina analysis pipeline version 0.3).  Mapping coordinates were assigned using Illumina’s default alignment parameters (best co-linear alignment, with no insertions or deletions, and an alignment score of 4 or greater).

organism: Equus caballus

source_name: testes

extract_protocol: Messenger RNA was selected with PolyT capture beads from 3.5 to 10.0 mg of total RNA and fragmented by zinc metal ion hydrolysis.  RNA fragments were converted into cDNA using random hexamer primers and made double stranded using RNase H and DNA polymerase.  The cDNA fragments were ligated to sequencing adaptors using Illumina’s Genomic DNA sample prep.  Fragments between 100 and 300 basepairs were size selected by gel electrophoresis, applied to sequencing flow cells, and enriched by PCR to grow fragment clusters.  Sequencing was performed on an Illumina Genome Analyzer.

tag: sex

value: male

tag: breed

value: thoroughbred

tag: age

value: 4 years old

value: testes


title: synovial membrane LPS stimulated

description: joint received four 0.5ng LPS injections over eight days prior to collection

source_name: left carpal joint synovial membrane

value: pony

value: 3 years old

value: LPS

value: synovial membrane


title: full thickness articular cartilage LPS stimulated

source_name: left carpal joint articular cartilage

value: full thickness articular cartilage


title: 34-day embryo normal

description: apparent normal gross morphology

source_name: whole embryo

value: 34 days gestation

value: embryo


title: placental villous normal

description: apparent normal gross morphology

source_name: full term placental villous

value: female

value: full term

value: placental villous


title: full thickness articular cartilage normal

description: joint received four control PBS injections over eight days prior to collection

source_name: right carpal joint articular cartilage


title: synovial membrane normal

source_name: right carpal joint synovial membrane


title: cerebellum normal

description: apparent normal gross morphology

source_name: cerebellum

value: 2 years old

value: cerebellum


title: D5NP-CONTROL

status: Public on Nov 07 2010

city: Santa Cruz

first: Andrew

middle: V

last: Uzilov

address: 1156 High St, MS SOE3

institute: University of California, Santa Cruz

description:
nuclear RNA
library strategy: BARCODE
instrument model: ABI SOLiD3

data_processing:
Raw sequencing colorspace reads from the SOLiD3 run (10 barcodes) were split up by barcode using custom software to generate the 10 colospace FASTA files provided with this GEO submission. The same was done for the QUAL files in this submission.
We used the ABI Small RNA Analysis Pipeline (http://solidsoftwaretools.com), which takes as input sequencing reads in colorspace, filters out reads mapping to undesirable sequences, optionally maps unfiltered reads to a set of known canonical (small) RNA sequences, and maps the remaining unmapped reads to the genome. Our filtering database contained ABI SOLiD sequencing adapters and ribosomal RNA, including pre-rRNA (internally and externally transcribed spacer sequences); reads mapping to this database were removed. The remaining reads were mapped directly to the mm9 mouse genome assembly converted to SOLiD colorspace. The read sequence was inferred after the mapping process; that is, each colorspace read was converted to a sequence of bases that best satisfied the colorspace read as a match to a colorspace version of the reference genome. This accommodates the possibility that the reference genome sequence may be different from the RNA sequence. The resulting base-space sequences of every mapped read were output in the fourth column of a 6-column BED-format file, which are the "processed data" files in this GEO submission.
When mapping to the genome, the pipeline first creates "seed" mappings of the first 30 positions of each read (corresponding to the 5'-most bases in the cloned RNA fragment), allowing up to two colorspace mismatches in those regions. To determine how much, if any, of the remainder of the 50mer read sequence consists of the adapter (as opposed to RNA fragment), a set of local alignments of the entire read is made to the reference (at the seed mapping position) followed by each possible concatenation of a subset of adapter bases. The mapping among these alignments with the lowest number of mismatches determines the "extended" read length, excluding adapter sequence. The total number of color mismatches allowed in this extension step was six, to allow for the decay in accuracy towards the 3' end of SOLiD reads.
Note that we allowed each read to map to the genome multiple times, up to 15 loci per chromosome (each chromosome mapping was run as an independent computing job). A post-processing step (using custom code) summed those counts to determine the number of genome-wide read mappings for each read. These counts are in the suffix of each read name (4th column of BED file in the processed files in this GEO submission).

molecule: nuclear RNA

source_name: stem cell culture

growth_protocol: KH2 mouse embryonic stem cells (Open Biosystems) were cultured under standard conditions as in Beard et al (Genesis 2006), but on gelatin-coated dishes rather than feeder layers. UNDIFF CELLS: For the undifferentiated samples, cells were grown with leukemia inhibitory factor (LIF) in GMEM medium (Skarnes et al, Methods in Enzymology 2000). D5NP CELLS: To generate neural precursor cells, the KH2 cells were replated on fresh gelatin-coated dishes at a density of 1.5 x 104 cells/cm2 and the medium was switched to N2/B27 18 hours later (Ying et al, Nature Biotechnology 2003). The cultures were grown for 5 days under neural differentiation conditions before harvesting RNA.

extract_protocol: Adherent cells were washed twice with PBS and then mechanically dissociated from the dishes with PBS with 1 mM EDTA at 4°C. After pelleting at 500g, the cells were resuspended in lysis buffer minus NP40 (10 mM Tris-HCl pH 7.5, 75 mM NaCl and 1 mM MgCl2) and repelleted. The cells were then gently resuspended in the lysis buffer (same buffer above but with 0.3% NP40, mammalian protease inhibitor cocktail (Sigma) and Superase-In RNase inhibitor (Ambion, 200 U/ml)). After a 5-min incubation on ice, the lysates were spun at 900g for 5 min. The resulting supernatant was removed and transferred to TRIzol reagent (Invitrogen) for cytoplasmic RNA isolation. The nuclear pellet was gently resuspended and pelleted twice in lysis buffer to wash away contaminating cytoplasmic components. The resuspended nuclei were purified by sedimentation through a 25% sucrose cushion (dissolved in lysis buffer without NP40) spun at 16,000g for 15 min. Under these sedimentation conditions, the nuclei form a pellet. The resulting nuclei were disrupted by sonication in TRIzol, and the RNA was isolated by the standard reagent protocol, and treated with DNase I (Ambion) and acid-phenol-chloroform extraction to remove genomic DNA. The effectiveness of the cytoplasmic or nuclear enrichment strategy was qualitatively determined by reverse-transcription PCR against U2 or U6 snRNA (nuclear RNA-enriched) and spliced B-actin mRNA (cytoplasmic RNA-enriched) in the two samples. Nuclear RNA integrity was assayed by [32P]pCp 3' end labeling with pCp and RNA ligase (NEB) followed by 10% urea PAGE analysis to visualize the characteristic nuclear RNA mobilities of U1, U2 and U3 RNAs and tRNA.

treatment_protocol:
The "nuclease" samples were partially digested with P1 ssRNA-specific endonuclease. The "PNK" samples were treated with polynucleotide kinase.
Digestion was carried out using P1, which displays robust activity at high temperatures (~70°C) at acidic pH (~4.5) with little sequence specificity. We performed digests at buffer conditions close to physiological conditions and at 37°C, where P1 activity is less robust. All of the following steps were performed with two different input RNA samples in parallel: nuclear RNA from mouse undifferentiated embryonic stem cells (KH2) or the KH2 line differentiated into neural precursor cells. The two different nuclear RNA samples (500 ng) were suspended in a nuclease digestion buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl2, 5 mM MgCl2 and 0.01 mM Zn(OAc)2) at 1 ng/ul and denatured at 55°C for 5 min and then placed at 37°C for 10 min to facilitate refolding. Parallel reactions with no nuclease or P1 (Sigma) were then initiated from this master mix. For nuclease digestion, 1 ug of enzyme was added, reactions were incubated for 1 h at 37°C and then stopped by addition of 10 mM EDTA and acid-phenol-chloroform extraction. For the no-nuclease conditions, two samples (control and PNK treatment) were used in which half the material was treated with T4 PNK (30 U; USB) for 1 h in a buffer that favors both the 5' phosphorylation activity and the 3' phosphatase activity (50 mM imidazole-HCl, pH 6.0, 10 mM MgCl2 and 10 mM DTT).
RNA fragments (from each of "nuclease", "control", or "PNK" treatments) were size-selected to 20-100 bases, then cloned using the SOLiD Small RNA Expression Kit protocol (https://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_054973.pdf) and PCR-amplified. Equimolar quantities of each barcoded sample were mixed for the sequencing run.

value: neural precursor cells

tag: developmental stage

value: CONTROL


title: barcode09 (sample not used)

value: embryonic stem cells

value: UNDIFF


title: barcode06 (sample not used)


title: MacroH2A1 nucleosomes

city: Philadelphia

last: Pehrson

state: PA

address: 3800 Spruce Street

institute: University of Pennsylvania

description: mononucleosomal DNA

data_processing:
The .bed files and .graph files were prepared as described in Barski et al. Cell 129, 823-837 (2007). Sequence tags are mapped in 200 bp windows in the .graph files.
The sorted.txt file represents sequences mapped to mm8 using ELAND software.
For the relative macroH2A1 content file (see GSE18963 supplementary file), we used tools in the rna-seq workflow of Partek Genomics Suite (version 6.5b, 6.09.0806, Partek Inc.) to calculate the relative macroH2A1 content of individual genes. This program counts and normalizes hits in predefined regions specified in a refFlat file. The gene list was the Mouse build 8 version of refFlat.txt obtained from the UCSC Genome site. All exon information was stripped from the refFlat.txt file, which left only the start and stop sites for the genes. Normalized RPKM (reads per kilobase per million reads) values were compared to calculate fold change and FDR-adjusted p-values for each transcript.

source_name: Liver

growth_protocol: Frozen livers were obtained from Pel Freez Biologicals

extract_protocol: The preparation of solubilized chromatin and purification of macroH2A1 nucleosomes is described in Changolkar and Pehrson Mol. Cell Biol. 26, 4410 (2006). Briefly, mono- and oligonucleosomes were prepared by micrococcal nuclease digestion with solubilization facilitated by removing H1 with CM Sepharose. MacroH2A1 nucleosomes were purified by differential thio-affinity chromatography using Activated Thiol Sepharose (GE Healthcare), which does not bind macroH2A1, and Thiopropyl Sepharose (GE Healthcare), which binds macroH2A1 nucleosomes. The specificity of this approach was demonstrated by the absence of purified nucleosomes when macroH2A1 knockout livers were used. Mononucleosomal DNA from macroH2A1 and starting material nucleosomes was gel purified and sequenced using the Solexa 1G Genome Analyzer following manufacturer protocols (Barski et al. Cell 129, 823-837 (2007)).

tag: fraction

value: macroH2A1 nucleosomes

tag: gender

value: Female

value: 8 to 10 weeks


title: barcode10 (sample not used)

tag: strain

tag: cell type


title: Starting material

description: mononucleosomal DNA

value: bulk nucleosomes


title: UNDIFF-CONTROL


title: 5T-0-6_GFP_INPUT_1


title: D5NP-NUCLEASE

treatment_protocol:
RNA fragments (from each of "nuclease", "control", or "PNK" treatments) were size-selected to 20-100 bases, then cloned using the SOLiD Small RNA Expression Kit protocol (https://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_054973.pdf) and PCR-amplified. Equimolar quantities of each barcoded sample were mixed for the sequencing run.
The "nuclease" samples were partially digested with P1 ssRNA-specific endonuclease. The "PNK" samples were treated with polynucleotide kinase.
Digestion was carried out using P1, which displays robust activity at high temperatures (~70°C) at acidic pH (~4.5) with little sequence specificity. We performed digests at buffer conditions close to physiological conditions and at 37°C, where P1 activity is less robust. All of the following steps were performed with two different input RNA samples in parallel: nuclear RNA from mouse undifferentiated embryonic stem cells (KH2) or the KH2 line differentiated into neural precursor cells. The two different nuclear RNA samples (500 ng) were suspended in a nuclease digestion buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl2, 5 mM MgCl2 and 0.01 mM Zn(OAc)2) at 1 ng/ul and denatured at 55°C for 5 min and then placed at 37°C for 10 min to facilitate refolding. Parallel reactions with no nuclease or P1 (Sigma) were then initiated from this master mix. For nuclease digestion, 1 ug of enzyme was added, reactions were incubated for 1 h at 37°C and then stopped by addition of 10 mM EDTA and acid-phenol-chloroform extraction. For the no-nuclease conditions, two samples (control and PNK treatment) were used in which half the material was treated with T4 PNK (30 U; USB) for 1 h in a buffer that favors both the 5' phosphorylation activity and the 3' phosphatase activity (50 mM imidazole-HCl, pH 6.0, 10 mM MgCl2 and 10 mM DTT).
RNA fragments (from each of "nuclease", "control", or "PNK" treatments) were size-selected to 20-100 bases, then cloned using the SOLiD Small RNA Expression Kit protocol (https://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_054973.pdf) and PCR-amplified. Equimolar quantities of each barcoded sample were mixed for the sequencing run.

value: NUCLEASE


title: D5NP-PNK

treatment_protocol: The "nuclease" samples were partially digested with P1 ssRNA-specific endonuclease. The "PNK" samples were treated with polynucleotide kinase.

value: PNK


title: UNDIFF-PNK


title: UNDIFF-NUCLEASE


title: hnRNPH_CLIPSeq 1

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

description: UV cross-linking and immunoprecipitation against hnRNP H

data_processing: The 3' Illumina small RNA adapter was trimmed from the 3' end of reads.  All resulting sequences were collapsed and stripped of quality scores such that each sequence was represented exactly once.  The set of non-redundant sequences was mapped to the genome (hg18), a set of pre-computed splice junctions, and the ribosomal repeating subunit using Bowtie version 0.10.1 using options --best --strata -m 1 -n 2.  Uniquely mapping reads were then converted to SAM format.

molecule: other

source_name: HEK 293T

growth_protocol: HEK 293T cells were grown in Dulbecco's Modified Eagle's Medium supplemented with 10% FBS.

extract_protocol: We have adapted standard CLIP protocols to isolate RNA bound by hnRNP H in vivo. HEK 293T cells were grown to confluence and UV irradiated at 400 mJ/cm2. Total protein was isolated using RIPA buffer (50 mM Tris-HCl pH 7.4, 0.1% Na-deoxycholate, 1% NP-40). Lysate was treated with DNase I and dilute RNase A (Fermentas). Immunoprecipitation of hnRNP H was performed using rabbit polyclonal anti-hnRNP H antibodies (Bethyl labs, A300-511A) that were pre-conjugated to protein A beads (Invitrogen). IP’d protein-RNA complexes were washed with RIPA buffer, treated with alkaline phosphatase, and ligated to the Illumina 3’ end small RNA adapter. The complexes were subsequently radiolabeled with P32-ATP using T4 PNK, and electrophoresed on a NuPage Bis-Tris SDS-PAGE gel (Invitrogen). Protein-RNA complexes were transferred to nitrocellulose and exposed to film. Protein-RNA complexes from bands excised between 50 and 80 kD, in increments of ~7 kD, were proteinase K treated. RNA was eluted and precipitated, and RNA of length 40-60 nucleotides was ligated to the Illumina 5’ end small RNA adapter. Reverse transcription was performed using a primer complementary to the 3’ adapter, and 35 cycles of PCR was performed using the Illumina small RNA PCR primers. PCR products of length ~125-175 nucleotides were gel purified and sequenced on an Illumina 1G Genome Analyzer.

treatment_protocol: Cells grown in 10cm2 plates were washed with PBS, covered with 4 mL of PBS, and UV irradiated at 400 mJ/cm2 once in a Stratalinker 2400.

value: HEK 293T

tag: clip antibody

value: Rabbit polyclonal, Bethyl labs A300-511A


title: c2c12_lko_100

description: RNAseq of polyA+ RNA was performed on C2C12 cells transfected with empty pLKO.1 vector and selected with puromycin. After adaptor ligation, the library was agarose gel electrophoresed and a band of ~250 nucleotides was excised and subjected to 11 cycles of PCR, followed by a second round of size selection by gel electrophoresis.

data_processing: Reads were mapped to the genome (mm9), a set of pre-computed splice junctions, and the ribosomal repeating subunit using bowtie using options --best --strata -m 1 -n 2. Read pairs were mapped independently. Uniquely mapping reads were then converted to SAM format.

source_name: C2C12 with control shRNA vector

growth_protocol: C2C12 cells were grown in Dulbecco's Modified Eagle's Medium supplemented with 20% FBS at sub-confluent conditions.

extract_protocol: Total RNA was isolated from cells that were ~60% confluent by Trizol, followed by chloroform extraction, precipitation, and cleanup/Dnase treatment on RNeasy columns (Qiagen). PolyA+ RNA was selected using polyT Dynabeads (Invitrogen), fragmented with zinc acetate, and converted to cDNA by RT. Libraries were generated according to the Illumina Paired-end sample preparation protocol, with the following modifications: after adaptor ligation, samples were agarose gel electrophoresed. A band at ~250 nt and a band at ~400 nt were excised from the same lane of the gel, yielding library mean insert lengths of 98+/-15 and 99+/-15 for control and knockdown short libraries, respectively, and mean insert lengthso of 277+/-14 and 282+/-19 for control and knockdown long libraries, respectively. Nucleic acid was isolated from each band by column purification, and subjected to 11 cycles of PCR. A final round of size selection was performed by gel purification of the PCR products.

tag: insert length mean

tag: insert length standard deviation


title: hnRNPH_CLIPSeq 2


title: c2c12_cugbp1_280

description: RNAseq of polyA+ RNA was performed on C2C12 cells transfected with empty pLKO.1 vector and selected with puromycin. After adaptor ligation, the library was agarose gel electrophoresed and a band of ~400 nucleotides was excised and subjected to 11 cycles of PCR, followed by a second round of size selection by gel electrophoresis.

data_processing: Reads were mapped to the genome (mm9), a set of pre-computed splice junctions, and the ribosomal repeating subunit using Bowtie version 0.10.1 using options --best --strata -m 1 -n 2. Read pairs were mapped independently. Uniquely mapping reads were then converted to SAM format.

source_name: C2C12 with shRNA against CUGBP1


title: c2c12_cugbp1_100

description: RNAseq of polyA+ RNA was performed on C2C12 cells transfected with empty pLKO.1 vector and selected with puromycin. After adaptor ligation, the library was agarose gel electrophoresed and a band of ~280 nucleotides was excised and subjected to 11 cycles of PCR, followed by a second round of size selection by gel electrophoresis.


title: CTL RIP-seq

status: Public on Nov 04 2010

city: Worcester

first: Alper

last: Kucukural

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

description:
Non-specific antibody.
The non-specific IgG is protein A purified from rabbit preimmune serum. It was generated in house.

data_processing:
Alignment: Sequence reads were mapped to the rat (rn4: Nov, 2004 assembly) genome with Bowtie (release 0.12.6). All unique reads were mapped with two or fewer mismatches.

Mapped data were processed with in-house softwares to determine the number of uniquely mapped reads to a particular region (intron/exon, 5’UTR, 3’UTR, CDS) of each gene. The softwares used are available upon request.

organism: Rattus norvegicus

source_name: rat cortical neurons, control

growth_protocol: Rat cortical neurons were dissected from E18 rat brains and cultured in vitro for 14 days. All cultures were maintained in neuroblasal medium supplemented with 2% B27 and 1% L-glutamine.

extract_protocol: Cortical neuronal lysates were sonicated and precleared. TDP-43-RNA complexes were isolated using a TDP-43-specific antibody. Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 1004898). Briefly, RNA was fragmented using fragmentation buffer and first strand cDNA was generated using SuperScript II followed by second strand synthesis using DNA Pol I. The cDNA 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 (3’ to 5’ 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, cDNA 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 cDNA was used to produce a DNA sequencing library according to protocols provided by Illumina. DNA fragments from the sequencing library were captured onto single-end flow cells and 36 bp single end sequences were produced using an Illumina GAIIx genome analyzer following standard sequencing protocols provided by the manufacturer.

value: Sprague-Dawley

value: embryonic day 18 (E18)

value: brain

value: cultured primary neurons

tag: passages

tag: rip antibody

value: non-specific rabbit IgG


title: TDP-43 RIP-seq

description:
RNA IP against TDP-43.
The TDP-43 (748C) antibody is a peptide antibody generated against: NQGNMQREPNQAFGSGNN. It was generated in house.

source_name: rat cortical neurons, TDP-43 RIP


title: 1n Sc_mid log_repA

first: Alex

last: Rolfe

address: 77 Massachusetts Ave, 32-G538

department: CSAIL

institute: Massachusetts Institute of Technology

data_processing: Reads were mapped to the Sigma1278b genome with bowtie (--best --strata --strandfix -m 100 -k 100); the reads are not strand-specific. Count is the number of weighted hits that map to each ORF. Weight is 1/(total number of hits for the read).

organism: Saccharomyces cerevisiae

source_name: budding yeast, haploid

growth_protocol: Mid-log phase cultures grown at 30C in synthetic complete (SC) medium + 2% glucose.

extract_protocol: Total RNA was extracted using acid phenol and glass beads. Poly(A) RNA was purified from total RNA using Qiagen Oligotex mRNA kit. The poly(A) RNA was then processed for cDNA library construction as described in Mortazavi et al., Nature Methods 5, 2008 and in instructions for Illumina DNA Sample Prep Kit. The libraries were sequenced for 36 cycles on Illumina Genome Analyzer 2 using the standard protocol.

treatment_protocol: Cells were collected by centrifugation at 4C, frozen in liquid nitrogen and stored at -80C until RNA extraction.

value: Sigma 1278b

tag: ploidy

value: haploid (MATa)


title: 4n Sc_mid log_repB

source_name: budding yeast, tetraploid

value: tetraploid (MATaaaa)


title: 1n Sc_mid log_repB


title: 4n Sc_mid log_repA


title: Islet6_Input

status: Public on Nov 02 2010

city: Bethesda

first: Francis

middle: S

last: Collins

state: MD

address: 1 Center Drive, Rm 126

department: Genome Technology Branch

institute: NHGRI

description: Islet 6 (UGA076) input DNA

data_processing: wig: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. Reads mapping with two or fewer mismatches were used; duplicate reads (same start, strand) were excluded; reads were extended by 250bp. Reads overlapping 100bp (1000bp for H3K79me2) bins were counted to create wiggle file. wig_n6: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. Reads mapping with two or fewer mismatches were used; no more than six reads with the same start position and strand were retained. Reads overlapping 100bp bins were counted to create wiggle file.

source_name: Pancreatic islets

growth_protocol: Human islet shipments obtained from islet distribution centers were warmed to 37 C and washed with calcium- and magensium-free Dulbecco's Phosphate Buffered Saline

extract_protocol: Libraries were constructed according to Illumina's standard protocol. ChIP DNA samples underwent reverse crosslinking, proteinase K and Rnase treatment, phenol-chloroform extraction, and ethanol precipitation prior to library preparation.

tag: tissue

value: Pancreatic islets

tag: chip antibody

value: anti-Input

tag: antibody manufacturer

tag: antibody catalog #

tag: antibody lot #

tag: sonication cycles


title: Islet9_DNase

description: ISLET9 DNAse I hypersensitivity

extract_protocol: Song, L., and Crawford, G.E. (2010). DNase-Seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements across the Genome from Mammalian Cells. Cold Spring Harb Protoc 2010, pdb.prot5384-.


title: Islet6_CTCF_Abcam

description: Islet 6 (UGA076) chromatin IP using anti-CTCF (Abcam)

value: anti-CTCF (Abcam)

value: AbCam


title: Islet7_DNase

description: ISLET7 DNAse I hypersensitivity


title: Islet5_K4me3

description: Islet 5 (WBB020) chromatin IP using anti-H3K4me3


title: Islet5_K79me2

description: Islet 5 (WBB020) chromatin IP using anti-H3K79me2


title: barcode03 (sample not used)

value: embryonic stem cells

tag: developmental stage

value: UNDIFF


title: Islet8_DNase

description: ISLET8 DNAse I hypersensitivity


title: Islet6_CTCF_Millipore

description: Islet 6 (UGA076) chromatin IP using anti-CTCF(Millipore)

value: anti-CTCF (Millipore)

value: Millipore


title: c2c12_lko_280


title: Islet5_GFP

description: Islet 5 (WBB020) chromatin IP using anti- GFP

value: anti-GFP

value: Santa Cruz


title: Islet5_K4me1

description: Islet 5 (WBB020) chromatin IP using anti-H3K4me1


title: Islet6_GFP

description: Islet 6 (UGA076) chromatin IP using anti-GFP


title: Islet5_Input

description: Islet 5 (WBB020) input DNA


title: Islet4_K79me2

description: Islet 4 (UFK467) chromatin IP using anti-H3K79me2


title: Islet4_K4me3

description: Islet 4 (UFK467) chromatin IP using anti-H3K4me3


title: Islet3_K4me1

description: Islet 3 (UG3360) chromatin IP using anti-H3K4me1


title: Islet3_GFP

description: Islet 3 (UG3360) chromatin IP using anti- GFP


title: Islet3_Input

description: Islet 3 (UG3360) input DNA


title: Islet2_Input

description: Islet 2 (VAD335) input DNA


title: larval fat body

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing: mRNA-Seq reads were aligned to BDGP Release 5/DM3 using ELAND, using the first 25 bases of a read as a seed.  Each matched seed was then extended up to 36 bases and scored to break any ties between multi-matches.  For mRNA expression counts, unique reads in the genome that landed within any known exons were counted.  The counts were normalized by the mRNA length to get the final RPKM values (reads per KB per million reads).

molecule: polyA RNA

source_name: third instar larval fat body

growth_protocol: Drosophila larvae were grown on standard cornmeal, molasses agar media

extract_protocol: Tissues were lysed by homogenization in TRIzol reagent and RNA was prepared as indicated in the manufactures protocol. PolyA-selected RNA from 5ug of total RNA was used to generate a cDNA library for Illumina based mRNA-sequencing according to the manufactures protocol.

treatment_protocol: Not applicable

value: fat body

value: OregonR

value: third instar larva


title: Islet4_K4me1

description: Islet 4 (UFK467) chromatin IP using anti-H3K4me1


title: larval midgut

source_name: third instar larval midgut

value: midgut


title: Islet2_K4me3_rep1

description: Islet 2 (VAD335) chromatin IP using anti-H3K4me3


title: Islet1_K4me3

description: Islet 1 (UKI217) chromatin IP using anti-H3K4me3


title: Islet2_K4me3_rep2


title: Shoot_BS-Seq

status: Public on Nov 01 2010

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

description: Bisulfite sequencing

data_processing:
Alignment: We used Perl scripts to convert all the Cs in the ‘forward’ reads (and in the scaffold) to Ts, and all the Gs in the ‘reverse’ reads and scaffold to As, and aligned the converted reads to the converted  scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases. Each half of the read was aligned independently using bowtie. allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).

organism: Oryza sativa

source_name: Seedling Shoots

growth_protocol: 14 days post germination, grown in MS media under 16/8 light/dark cycles at 25oC

extract_protocol:
Genomic DNA was extracted using the CTAB protocol. 1 gram of tissue was ground in liquid nitrogen, resuspended in CTAB buffer (2 % CTAB, 100 mM Tris pH 8.0, 20 mM EDTA, 1.4 M NaCl, 2 % PVP 40) and incubated for 2 hrs at 65C. Following centrifugation, DNA samples were treated with RNase A and DNA was purified from the supernatant using chloroform. DNA was precipitated with ethanol, and resuspended in TE prior to sonication.

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

value: japonica

tag: cultivar

value: Nipponbare

value: seedling shoots


title: Endosperm_BS-Seq

description: Bisulfite sequencing

source_name: Endosperm

growth_protocol: isolated at the milky stage

value: endosperm


title: Islet2_GFP

description: Islet 2 (VAD335) chromatin IP using anti- GFP

value: Pancreatic islets


title: Embryo_BS-Seq

description: Bisulfite sequencing

source_name: Embryo

value: embryo


title: negative2

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

description: input DNA

data_processing: Sequencing reads were quality trimmed by clipping at 3 consecutive nucleotides with quality score less than 10. Reads shorter than 18 nucleotides were discarded and the remaining reads were mapped against the human reference genome (hg18 assembly, NCBI build 36) using SHRiMP package (Rumble et al, 2009)  with default settings, which allows mapping in SOLiD color space corresponding to dinucleotide encoding of the sequenced DNA. For analysis we used only uniquely placed reads, which were defined as reads having at least two additional mismatches in the second best hit compared to the best hit. The Cisgenome software package (Ji et al, 2008) was used for the identification of binding peaks from the ChIP-seq data. Two-sample analysis mode was used to compare samples with control input data. The parameters for peak discovery were set as follows: window size 100, step size 25, maximum gap 200, active single strand filtering with forward and reverse reads cutoff 4, minimum peak with 225 and minimum reads per window was set to obtain < 0.1 or 0.01 false positive rate (FDR).

source_name: cell line

extract_protocol: Immunoprecipitated chromatin was sheared for a second time for 6 minutes using Covaris sonicator (6 x 16 mm AFA fiber Tube, duty cycle: 20%, intensity: 5, cycles/burst: 200, frequency sweeping) to obtain suitable shorter fragments (75-125 bp). To exclude a shearing bias as a possible source of binding site ultrastructure, partial digestion using DNaseI was used as an alternative to shorten the fragments for one control ChIP-seq library and one input library. For DNaseI treatment, chromatin was resuspended in 45 µl of freshly prepared reaction buffer (10mM MnCl2, 0.1mM CaCl2, 10mM Tris, pH 7.5) and digested with 0.5mU of DNaseI for 5 minutes at room temperature. The reaction was stopped by adding EDTA to a final concentration of 50mM. Chromatin was immediately extracted using phenol/chloroform procedure and precipitated. After fragmentation, fragments were blunt-ended and phosophorylated at the 5'-prime end using the End-it Kit (Epicentre) according to the manufacturer’s instructions. Ligation of double stranded adapters compatible with SOLiD sequencing was performed using Quick ligation kit (New England Biolabs) with 750 mM P1 ds and P2 ds adaptor (Applied Biosystems), 11.7 µl of 2x Quick ligation buffer, 1 µl Quick Ligase in total volume of 23.4 µl. Samples were purified using Ampure beads (Agencourt) and run on a native 6% polyacrylamide gel. Fragments ranging from 140 to 180 bp were excised; the piece of gel containing DNA fragments was shredded and dispersed into 400 µl of Platinum PCR Supermix with 750 mM of each P1 and P2 PCR primer, 2,5 U of Pfu (Stratagene) and 5 U Taq (Bioline). Prior to ligation-mediated PCR the sample was incubated at 72˚C for 20 minutes in PCR mix to let the DNA diffuse out of the gel and to perform nick translation on non ligated 3'-ends of DNA fragments. After 17 cycles of amplification the library was purified using Ampure beads and was quality checked on 2100 Bioanalyzer (Agilent) for the absence of possible adapter dimers and heterodimers.

tag: cell line


title: Tcf4_3.nonsh

description: ChIP DNA


title: Hom2_PD_(20091104_7)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Homotypic H2Av (H2Av/H2Av) Sequential Affinity Purification, replicate 2
average length of the paired end segments (Mean): 125.70
average length of the paired end segments (SD): 57.03

data_processing: 1. Ran Eland to map 35bp paired-end reads to release 5 of the unmasked Drosophila melanogaster reference sequence obtained from FlyBase. 2. Worked from the *export.txt files which have the uniquely mapped paired end reads. 3. Made a location file for all paired-end segments with chromsome, strand, start and end positions. 4. Counted the number of times each genomic position was read in 10bp intervals along the entire genome. 5. Normalized the 10bp interval counts by dividing by the total number of counts, which is approximately the total number of base pairs included in all the paired-end reads. 6. Rescaled by multiplying each interval count by one billion.

source_name: Homotypic H2Av (H2Av/H2Av) pull-down DNA

extract_protocol: Protocol included in file SequentialAffinityPurification.rtf


title: Hom1_PD_(20091104_6)

description:
Homotypic H2Av (H2Av/H2Av) Sequential Affinity Purification, replicate 1
average length of the paired end segments (Mean): 139.73
average length of the paired end segments (SD): 54.70


title: Tcf4_1.1

description: ChIP DNA


title: Islet3_K79me2

description: Islet 3 (UG3360) chromatin IP using anti-H3K79me2

value: AbCam


title: Islet4_Input

description: Islet 4 (UFK467) input DNA

value: anti-Input


title: Root_BS-Seq

description: Bisulfite sequencing

source_name: Seedling Roots

tag: strain

value: seedling roots


title: Tcf4_2

description: ChIP DNA


title: Tcf4_1.2

description: ChIP DNA


title: Hom1_IN_(20091104_4)

description:
Input to sequential affinity purification, replicate 1.
average length of the paired end segments (Mean): 117.21
average length of the paired end segments (SD): 42.21

source_name: Homotypic H2Av input


title: Het2_IN_(20091104_1)

description:
Input to sequential affinity purification, replicate 2
average length of the paired end segments (Mean): 120.45
average length of the paired end segments (SD): 42.73

source_name: Heterotypic H2Av input


title: Het1_PD_(20091104_3)

description:
Heterotypic H2Av (H2A/H2Av) Sequential Affinity Purification, replicate 1. Stably
average length of the paired end segments (Mean): 125.22
average length of the paired end segments (SD): 48.55

source_name: Heterotypic H2Av (H2A/H2Av) pull-down DNA


title: Het2_PD_(20091104_2)

description:
Heterotypic H2Av (H2A/H2Av) Sequential Affinity Purification, replicate 2
average length of the paired end segments (Mean): 145.11
average length of the paired end segments (SD): 62.14


title: FAv_PD_(20091104_8)

description:
Single H2Av pulldown
average length of the paired end segments (Mean): 98.66
average length of the paired end segments (SD): 42.74

source_name: single H2Av pull-down DNA


title: 80mM_salt_paired_(20100623)

description:
80mM NaCl soluble
n = 409,901 pairs
mean insert size = 124.667
standard deviation = 37.975

data_processing: 1. Ran Eland to map 35bp paired-end reads to release 5 of the unmasked Drosophila melanogaster reference sequence obtained from FlyBase. 2. Worked from the 80mM_salt_paired_x_eland_export.txt files, which have the uniquely mapped paired end reads, or from 80mM_salt_paired_Novoalign.txt, which includes reads with one mis-match. 3. Made a location file for all paired-end segments with chromsome, strand, start and end positions. 4. Counted the number of times each genomic position was read in 10bp intervals along the entire genome. 5. Normalized the 10bp interval counts by dividing by the total number of counts, which is approximately the total number of base pairs included in all the paired-end reads. 6. Rescaled by multiplying each interval count by one billion.

source_name: 80mM NaCl soluble pull-down DNA

extract_protocol: Protocol included in file Salt+EDTA_extraction_20080522.rtf


title: 80mM_salt_(20081216_8)

description: 80mM NaCl soluble

data_processing: 1. Ran Eland to map 35bp single-end reads to release 5 of the unmasked Drosophila melanogaster reference sequence obtained from FlyBase.  2. Worked from the 80mM_salt_eland_extended.txt file which has one row per read with multiple mapped positions. 3. If a read was mapped to multiple locations, one location was picked at random and a file of locations for each read was made with chromosome, strand, start and end positions. 4. Moved the location of each read to the middle of a 150bp fragment including the read at the 5' or 3' end depending on the strand. 5. Fitted a Gaussian kernel with bandwidth=20 and interval width=10bp and normalized it to the number of reads. 6. Repeated step 5 for each strand separately without moving the location. Results are in the supplementary wiggle files.


title: ChIP-Seq for p300 in ES (129JAE-C57/B6) cells 2

status: Public on Oct 31 2010

city: Rotterdam

first: Menno

middle: P

last: Creyghton

address: Doctor Molewaterplein 40

institute: Erasmus MC

description: Chromatin IP against p301

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using MAQ (phred score 50).
For all samples aligned sequences were extended 600bp upstream and 400bp downstream (with respect to read strand) for transcription histone marks and and 200bp upstream and 0bp downstream (with respect to read strand) for transcription factors, allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Embyonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 200 and 350bp (representing shear fragments between 100 and 250nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number

value: Santa Cruz s.c. 585

tag: cell type

value: embryonic stem cells


title: Seq for whole cell extract from ES (129JAE-C56/B6) cells

description: Whole Cell Extract


title: ChIP-Seq for p300 in ES (129JAE-C57/B6) cells 1

description: Chromatin IP against p300


title: ChIP-Seq for H3K4me1 in mefs

description: Chromatin IP against H3K4me1

source_name: mouse embryonic fibroblasts

growth_protocol: mefs were grown under typical culture conditions

value: Abcam AB8895

value: mefs


title: GM06990_Input_seq

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description:
Input DNA
Alignment, peak, and wig files were generated from two lanes of sequencing.

Raw files:
20ERRAAXX_1.prb.txt
20ERRAAXX_1.seq.txt
20ER2AAXX_4.prb.txt
20ER2AAXX_4.seq.txt

data_processing: Illumina sequencing generated 23-32 base pair short reads from the ends of ChIP-enriched DNA fragments. These short reads were mapped back to the hg18 genome using the ELAND algorithm. Peaks were identified using a Parzen window based algorithm as described previously with minor modifications (Shivaswamy et al. 2008. PLoS Biol 6: e65. ). Wig file was generated with a fixed step based on the Wiggle format (WIG), displaying continuous-valued data in a track format. A value in a wig file represents how many reads are overlapped in a fixed step.

source_name: Peripheral vein

growth_protocol: The lymphoblastoid (GM06990) cell line was purchased from Coriell and cultured in RPMI medium containing 15% fetal bovine serum (FBS) and 1% antibiotics (penicillin/streptomycin).

extract_protocol: CHIP and input DNA were used for library construction by following Illumina's instructions with Chip-seq DNA Sample Prep Kit

value: Epstein-Barr Virus transformed lymphoblastoid

tag: antibody


title: ChIP-Seq for H3K4me3 in proB cells

description: Chromatin IP against H3K4me3

source_name: proB cells

growth_protocol: CD19+ pro–B cells were isolated from bone marrow by MACS cell separation (Miltenyibiotech) following manufacturer's protocol. Purified B cell subsets were resuspended in IMDM with 15% FCS as well as IL-4, IL-7, SCF (10 ng ml−1 each; Peprotech) and plated on OP9 bone marrow stromal cells (ATCC).

value: Abcam AB8580

value: CD19+ proB cells


title: ChIP-Seq for H3 in proB cells

description: Chromatin IP against H3

value: Abcam AB1791


title: Seq for whole cell extract from proB cells

description: Whole Cell Extract

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were purified and prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 200 and 350bp (representing shear fragments between 100 and 250nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.


title: Seq for whole cell extract from whole liver

description: Whole Cell Extract

source_name: Whole Liver

growth_protocol: Liver was dissected away from surrounding tissues and dissociated in 10 ml DAG media (phenol-red free DMEM Gibco and BSA 1g per 0.5 l) and filtered two times through a sterile 100 μM cell strainer. Liver cell preparations were centrifuged at 30g for 3 min at 4 °C and the cells were washed two times in PBS.

value: perfused Whole Liver


title: ChIP-Seq for H3K27ac in proB cells

description: Chromatin IP against H3K27ac

value: Abcam AB4729


title: ChIP-Seq for H3K4me1 in mefs derived iPS cells

description: Chromatin IP against H3K4me1

source_name: iPS cells

growth_protocol: (O6) murine iPS cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

value: iPS cells


title: ChIP-Seq for H3 in whole liver

description: Chromatin IP against H3


title: ChIP-Seq for H3K4me3 in whole liver

description: Chromatin IP against H3K4me3


title: ChIP-Seq for H3K4me1 in proB cells

description: Chromatin IP against H3K4me1


title: ChIP-Seq for H3K27ac in whole liver

description: Chromatin IP against H3K27ac


title: Tcf4_3.DNaseI

description: ChIP DNA


title: ChIP-Seq for H3K4me1 in whole liver

description: Chromatin IP against H3K4me1


title: ChIP-Seq for H3 in mefs

description: Chromatin IP against H3


title: GM06990_E2F4_ChIP_seq

description:
Chromatin IP against E2F4
We unfortunately lost our FC6413_1.seq.txt file recently. So, it is not submitted.
Alignment, peak, and wig files were generated from two lanes of sequencing.

Raw files:
FC6413_1.prb.txt
FC11853_4.seq.txt
FC11853_4.prb.txt :

value: Santa Cruz Biotech


title: ChIP-Seq for Rfx1 in neural progenitors (129JAE-C57/B6 derived)

description: Chromatin IP against Rfx1

source_name: Neural progenitors

growth_protocol: Neural progenitors were derived by plating 4 day-old embryoid bodies and selection for 5-7 days in chemically defined ITSFn media. Neural precursor cells were isolated, and cultured on polyornithine-coated cell culture dishes in N3 media containing FGF and EGF

value: Santa Cruz s.c. 10562X

value: Neural progenitors


title: ChIP-Seq for H3K4me1 in ES (129JAE-C57/B6) cells containing the dox inducible 4f2a transgene (carey et al.,2010)

description: Chromatin IP against H3K4me1

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates.


title: ChIP-Seq for H3K4me1 in ES (C57/B6 inbred) cells

description: Chromatin IP against H3K4me1

growth_protocol: j21 (C57BL/6) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates.


title: ChIP-Seq for H3 in ES (129JAE-C57/B6) cells

description: Chromatin IP against H3


title: ChIP-Seq for H3K4me3 in ES (129JAE-C57/B6) cells

description: Chromatin IP against H3K4me3


title: ChIP-Seq for H3K27ac in neural progenitors (129JAE-C57/B6 derived)

description: Chromatin IP against H3K27ac


title: ChIP-Seq for H3K4me1 in ES (129JAE-C57/B6) cells

description: Chromatin IP against H3K4me1


title: CG8478_E16-24h_INPUT_2

status: Public on Oct 30 2010

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  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 3â 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.


title: Jurkat

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

description: Jurkat cells were cultured in RPMI 1640 supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100mg/ml streptomycin and 20µg/ml blasticidin.

data_processing: Sequence reads were obtained using the Illumina Genome Analyzer II. Reads were aligned to human genome (hg18) using MAQ (version 0.6.6) .

source_name: Leukemic T-cell line originally derived from a T-ALL patient

extract_protocol: ChIPed DNA was prepared according to the Illumina protocol with two modifications: 1) DNA fragments ranging from 150bp to 300bp were selected at the gel selection step; 2) 21 instead of 18 cycles of PCR were done at the amplification step.

value: Leukemic T-cell

value: anti-TAL1 Ab (Santa Cruz sc-12984)


title: Jurkat preimmune

treatment_protocol: Jurkat cells were cultured in RPMI 1640 supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100mg/ml streptomycin and 20µg/ml blasticidin.

value: normal IgG (Santa Cruz sc-2028)


title: Trl_INPUT_2


title: Trl_E0-8h_INPUT_1


title: CG8478_E16-24h_ChIPSeq_1 and 2

tag: antibody name

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog

value: Custom


title: Trl_E0-8h_ChIPSeq_1 and 2

value: Trl


title: Starving cells (t2) exp2

status: Public on Oct 29 2010

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

description: polyA RNA high-throughput sequencing

data_processing: RPKM values were calculated based on alignment. Mapping was done against all annotated transcripts from Polysphondylium pallidum PN500, whole genome shotgun sequence project (NCBI AccNo.: ADBJ00000000) using the Illumina-supplied tool ELAND (Bentley et al, 2008) with standard parameters. Expression  values (RPKMs) were calculated by counting the number of unique mappable reads per transcript and normalizing these to the total number of mappable reads and length of the respective transcript (adapted from Mortazavi et al, 2008).

organism: Heterostelium pallidum

source_name: Cell culture, starving cells (t2) exp2

growth_protocol: Cells grown on lawns of Klebsiella planticola, harvested before complete consumption of food bacteria, no signs of multicellular development

extract_protocol: Illumina mRNA-Seq sample prep kit following the manufacturer's instructions. PolyA RNA purification is part of the Illumina library preparation protocol. In detail, polyA RNA was separated from total RNA using magnetic oligo-dT beads. Total RNA was prepared from frozen cell pellets as described previously (Lucas et al, 2009).

tag: growth condition

value: Starving cells

tag: time

tag: agent

value: untreated


title: Starving cells (t3) exp2

description: polyA RNA high-throughput sequencing

source_name: Cell culture, starving cells (t3) exp2


title: Starving cells, glorin treated (t2+) exp2

description: polyA RNA high-throughput sequencing

source_name: Cell culture, starving cells, glorin treated (t2+) exp2

value: glorin


title: Starving cells, glorin treated (t3+) exp2

description: polyA RNA high-throughput sequencing

source_name: Cell culture, starving cells, glorin treated (t3+) exp2


title: Starving cells (t3) exp1

description: polyA RNA high-throughput sequencing

source_name: Cell culture, starving cells (t3) exp1


title: Starving cells, glorin treated (t3+) exp1

description: polyA RNA high-throughput sequencing

source_name: Cell culture, starving cells, glorin treated (t3+) exp1


title: Growing cells (t0) exp2

description: polyA RNA high-throughput sequencing

source_name: Cell culture, growing cells (t0) exp2

value: Growing cells


title: Starving cells (t2) exp1

description: polyA RNA high-throughput sequencing

source_name: Cell culture, starving cells (t2) exp1


title: ChIP-Seq for H3K27ac in ES (129JAE-C57/B6) cells 1

description: Chromatin IP against H3K27ac

tag: chip antibody

value: embryonic stem cells


title: ChIP-Seq for H3K27ac in ES (129JAE-C57/B6) cells 2

description: Chromatin IP against H3K27ac


title: Growing cells (t0) exp1

description: polyA RNA high-throughput sequencing

source_name: Cell culture, growing cells (t0) exp1


title: P.falciparum_3D7_genomicDNA_T7ampflication

status: Public on Oct 28 2010

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

data_processing: Reads (76 bp) were aligned to the P.falciparum (3D7) genome (PlasmoDB v6.1) using BWA. Datasets for different methods were equalized for the total number of uniquely mapped tags  by random removal of sequenced tags. GFF files were generated from these BED files.

organism: Plasmodium falciparum 3D7

source_name: Ring stage

growth_protocol: Parasites were cultured in standard RPMI medium supplemented with 10% human serum and 0.2% NaHCO3 in 20ml per 250ml tissue culture flasks and candle jars. The culture was synchronised with sorbitol treatments.

extract_protocol: Genomic DNA was isolated with standard phenol-chlorophorm methods following ProtK diggestion. Genomic DNA was sheared to 100-600bp using a Bioruptor (Diagenode) and processed for sequencing by different methods.

tag: library preparation

value: T7 polymerase based method


title: P.falciparum_3D7_genomicDNA_12cyclePCR

value: standard illumina with 12 cycles of PCR


title: P.falciparum_3D7_genomicDNA_amplificationfree

value: Amplification free (Kozerawa et al. 2009)


title: Erythroid

description: Human primary proerythroblasts were obtained by ex vivo differentiation from CD34+ hematopoietic stem cells. Briefly, light-density mononuclear cells were isolated by ficoll density gradient centrifugation from G-CSF-mobilized adult blood from donors without hematological malignancies (Ottawa Hospital Research Ethics Board #2007804-01H). CD34+ cells were enriched through positive immunomagnetic selection using the CD34 MicroBead Kit (Miltenyi Biotec Inc.) (purity > 95 ± 3%) and differentiated ex vivo as described in (Giarratana et al., 2005) except that we used 20% BIT (StemCell Technologies). Cells at day 10 of differentiation (corresponding to the proerythroblast stage) were used for chromatin immunoprecipitation

source_name: Primary pro-erythroblasts derived ex vivo from CD34+ multipotential hematopoietic progenitors

value: Pro-erythroblasts


title: Starving cells, glorin treated (t2+) exp1

description: polyA RNA high-throughput sequencing

source_name: Cell culture, starving cells, glorin treated (t2+) exp1


title: P.falciparum_3D7_genomicDNA_6cyclePCR

value: standard illumina with 6 cycles of PCR


title: P.falciparum_3D7_ChIPseq_input_10hpi

description: MNase-seq

data_processing: Reads (76 bp) were aligned to the P.falciparum (3D7) genome (PlasmoDB v6.1) using BWA. Datasets for different stages were equalized for the total number of uniquely mapped tags (5,5M for ChIP-seq and 11M for MNase-seq) by random removal of sequenced tags. GFF files were generated from these BED files.

source_name: Asexual stages

growth_protocol: Parasites were cultured in standard RPMI medium supplemented with 10% human serum and 0.2% NaHCO3 in 20ml per 250ml tissue culture flasks and candle jars. The culture was synchronised with multiple rounds of sorbitol treatments and Percoll gradient centrifugation.

extract_protocol: Native chromatin was diggested with MNase and immunoprecipitated using the indicated antisera. Immunoprecipitated DNA fragments were purified and sequenced using a T7- polymerase based library preparation protocol.

tag: develpmental stage


title: P.falciparum_3D7_ChIPseq_input_20hpi

description: MNase-seq


title: P.falciparum_3D7_ChIPseq_input_40hpi

description: MNase-seq


title: P.falciparum_3D7_ChIPseq_input_30hpi

description: MNase-seq


title: P.falciparum_3D7_ChIPseq_H3K4me3_20hpi

description: native ChIP-seq

tag: antibody manufacturer

value: AbCam


title: P.falciparum_3D7_ChIPseq_H3K4me3_10hpi

description: native ChIP-seq


title: RNA-seq seed

status: Public on Nov 06 2010

city: Qingdao

first: Naihao

last: Ye

address: Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences, Qingdao, 266071, China

country: China

data_processing: Filtering: Illumina high-throughput sequencing technology was employed to sequence the small RNA libraries from safflower seed, leaf and petal. After filtering the low quality reads, adaptor and contaminant sequences , the clean reads are aquired for seed, leaf and petal respectively.

organism: Carthamus tinctorius

source_name: seed

extract_protocol: For deep sequencing, the samples were firstly processed by 15% denaturing polyacryl amide gel electrophoresis (PAGE). After that, the small RNA fragments in the range of 10–30nt were isolated from the gel and purified. Then, the 5’and 3’ termini of the small RNA were linked with proprietary adapters sequentially and RT-PCR was used to amplify RNA to DNA, which can be used as templates to produce sequencing libraries. At last, approximately 20μg sequencing libraries were produced and Illumina Solexa Genome Analyzer was employed to sequence the generated libraries.

treatment_protocol: Safflowers were cultivated in the growth chamber with the temperature of day at 26°C and night at 20°C with the humidiy controlled at 80%. Collected mature seeds and petals in full bloom and flourish leaves were stored at -80°C until further use. Total RNA were extracted from the seeds, leaves and petals of safflower cultures separately using Trizol (Invitrogen) following the manufacturer’s protocol. The quality of total RNA samples was checked using the NanoDrop Spectrometer (ND-1000 Spectrophotometer, Peqlab) as well as the Agilent 2100 Bioanalyzer (RNA Nano Chip, Agilent).

tag: tissue

value: seed


title: P.falciparum_3D7_ChIPseq_H3K9ac_30hpi

description: native ChIP-seq

value: Diagenode

tag: antibody lot number


title: P.falciparum_3D7_ChIPseq_H3K4me3_30hpi

description: native ChIP-seq


title: P.falciparum_3D7_ChIPseq_H3K9ac_40hpi

description: native ChIP-seq


title: P.falciparum_3D7_ChIPseq_H2A_40hpi

description: native ChIP-seq

tag: strain

value: antiTy

value: a mouse monoclonal antibody named BB2, which we received from Prof Keith Gull. Ref:Bastin, P., Bagherzadeh, A., Matthews, K. R. and Gull, K. (1996b). A novel epitope tag system to study protein targeting and organelle biogenesis in Trypanosoma brucei. Mol. Biochem. Parasitol. 77, 235-239.


title: P.falciparum_3D7_ChIPseq_H3K9ac_10hpi

description: native ChIP-seq

tag: antibody catalog number


title: P.falciparum_3D7_ChIPseq_H3K9ac_20hpi

description: native ChIP-seq


title: P.falciparum_3D7_ChIPseq_H2A.Z_40hpi

description: native ChIP-seq

value: homemade rabbit polyclonal antibody against an N terminal peptide of histone H2A.Z of Plasmodium falciparum


title: P.falciparum_3D7_ChIPseq_H2A.Z_20hpi

description: native ChIP-seq


title: RNA-seq leaf

institute: Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences, Qingdao, 266071, China

source_name: leaf

value: leaf


title: P.falciparum_3D7_ChIPseq_H2A.Z_10hpi

description: native ChIP-seq


title: P.falciparum_3D7_ChIPseq_H2A.Z_30hpi

description: native ChIP-seq


title: P.falciparum_3D7_ChIPseq_H3K4me3_40hpi

description: native ChIP-seq


title: P.falciparum_3D7_RNAseq_5hpi

description: RNA-seq

data_processing: Reads (76 bp) were aligned to the P.falciparum (3D7) transcriptome (PlasmoDB v6.1) using BWA. Datasets for different stages were equalized for the total number of uniquely mapped tags (8,2M) by random removal of sequenced tags and BED files were generated from those files. Tags/kb of CDS were calculated for each gene and corrected for each stage by a correction factor (based on the amount of RNA per parasites nucleus present in each stage  - as described in more detail in Bartfai et al 2010). GFF files were generated on these stage-corrected values.

extract_protocol: total RNA was isolated using RNeasy Mini Kit (Qiagen) combined with on-column DNase treatment, was cleaned once more over an RNeasy (Qiagen) collumn with additional on-column DNase treatment and was subjected to polyA-selection (Qiagen, Oligotex mRNA Mini Kit).  mRNA was fragmented by hydrolysis and converted to double-stranded cDNA using AT(76%)-corrected nonamer primers. ~ 40 ng cDNA sample ranging in size from 100bp–1kb was used for sequencing using a T7-based polymerase based library preparation protocol.


title: P.falciparum_3D7_RNAseq_20hpi

description: RNA-seq


title: P.falciparum_3D7_RNAseq_10hpi

description: RNA-seq


title: RNA-seq petal

source_name: petal

value: petal


title: P.falciparum_3D7_RNAseq_15hpi

description: RNA-seq


title: P.falciparum_3D7_RNAseq_25hpi

description: RNA-seq


title: P.falciparum_3D7_RNAseq_30hpi

description: RNA-seq


title: P.falciparum_3D7_RNAseq_35hpi

description: RNA-seq


title: P.falciparum_3D7_RNAseq_40hpi

description: RNA-seq


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: MRE-Seq analysis of peripheral cd8 naive from TC009 (HS2749) using Illumina Genome Analyzer IIx
library name: HS2749
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 149-393 bp
****************
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: GSM613923_UCSF-UBC.CD8_Naive_Primary_Cells.MRE-Seq.TC009.bed
ANALYSIS ALIAS: HS2749-1_7095NAAXX-HS2749-1_62A09AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on CD8 Naive Primary Cells, Donor TC009 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.4198
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.51
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 89

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

ANALYSIS FILE NAME: GSM613923_UCSF-UBC.CD8_Naive_Primary_Cells.MRE-Seq.TC009.wig
ANALYSIS ALIAS: HS2749-1_7095NAAXX-HS2749-1_62A09AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from CD8 Naive Primary Cells, Donor TC009 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.4170
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD8N MRE 09
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD8 Naive Primary Cells MRE-Seq Donor TC009 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 99.51
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 89

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

extract_protocol: library construction protocol: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab 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: Blood

tag: histological type

value: CD8 naive cell

tag: is tumor

value: No

value: primary cell