title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Aorta Tissue; renlab.H3K27ac.STL003AO.01.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY46
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11865
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11864
****************
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: GSM906392_UCSD.Aorta.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003AO.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Aorta H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Aorta, Donor STL003, 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.13535
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,220,930
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.454
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4955
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9991
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5384
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906392_UCSD.Aorta.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003AO.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Aorta H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Aorta, Donor STL003, 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.13655
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 8
BROWSER_TRACK_NAME: Aorta H3K27ac 03 46
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Histone H3K27ac Donor STL003 Library AY46 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,220,930
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.454
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4955
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9991
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5384
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Aorta

value: Male

value: Caucasian

value: Biorupter

value: 5 micrograms


title: mRNA from mock-treated 35S:GR-RBE floral buds, biological replicate 2, techinical replicate 2

status: Public on Jul 12 2012

type: SRA

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

country: USA

institute: Yale University

library_source: transcriptomic

data_processing: We used Tophat v1.2.0 (Trapnell et al. 2009) to perform spliced alignments of the reads against the Arabidopsis thaliana TAIR10 reference genome. Only reads that mapped to a single unique location with in the genome with a maximum of two mismatches in the anchor region of the spliced alignment were reported in these results. We used the default settings for all other Tophat options. To obtain a tally of the number of the reads that overlapped the exons of a gene, we analyzed the aligned reads with HTSeq v0.4.5p6 and the gene structure annotation file for the reference genome (TAIR10). The tally for each sample was then processed with LOX v1.6 (Zhang et al. 2010) to statistically analyze the gene expression levels.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: floral buds, mock-treated 35S:GR-RBE

growth_protocol: Plants were grown at 22°C under 16-hour light/ 8-hour dark conditions

extract_protocol: Total RNA was extracted with Trizol (Invitrogen), treated with TURBO DNase (Applied Biosystems), purified using the Rneasy kit (Qiagen). Libraries were produced according to the standard Illumina protocols.Briefly, poly-A containing mRNA molecules were first purified from total RNA using poly-T attached magnetic beads and fragmented into small pieces using divalent cations. cDNA was synthesized from the fragmented mRNA, ligated with adapters and purified by Gel Extraction Kit (Qiagen). cDNA samples were amplified by PCR and purified with PCR purification Kit (Qiagen). Purified amplicons were run on an Illumina Genome Analyzer.

treatment_protocol: Floral buds were treated with DEX (10uM dexamethasone, 0.1% ethanol, 0.015% silwet) or mock (0.1% ethanol, 0.015% silwet) for four hours.

tag: strain

value: L er with 35S:GR-RBE transgene

tag: tissue

value: floral buds

tag: developmental stage

value: mixed stages


title: Reference Epigenome: ChIP-Seq Input from Human Adrenal Gland Tissue; renlab.Input.STL003AD.01.01

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK323
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11646
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11638
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM896167_UCSD.Adrenal_Gland.Input.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003AD.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Adrenal Gland Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Adrenal Gland, Donor STL003, 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.13531
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,898,051
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.0328
HOTSPOT_PERCENTILE: 37
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.199
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM896167_UCSD.Adrenal_Gland.Input.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL003AD.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Adrenal Gland Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Adrenal Gland, Donor STL003, 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.13651
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 8
BROWSER_TRACK_NAME: AG Input 03 23
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland ChIP-Seq Input Donor STL003 Library AK323 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,898,051
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.0328
HOTSPOT_PERCENTILE: 37
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.199
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Adrenal Gland tissue; renlab.Input.STL003AD.01.01

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

tag: sample alias

tag: sample common name

value: Adrenal Gland

tag: molecule

value: genomic DNA

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: ChIP-Seq Input

value: Input

value: 500 micrograms


title: mRNA from mock-treated 35S:GR-RBE floral buds, biological replicate 2, techinical replicate 1


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Adrenal Gland Tissue; renlab.H3K27ac.STL003AD.01.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK321
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11639
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11638
****************
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: GSM896163_UCSD.Adrenal_Gland.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003AD.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Adrenal Gland H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Adrenal Gland, Donor STL003, 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.13547
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,461,000
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.1143
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.2162
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9508
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3201
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM896163_UCSD.Adrenal_Gland.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003AD.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Adrenal Gland H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Adrenal Gland, Donor STL003, 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.13667
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 8
BROWSER_TRACK_NAME: AG H3K27ac 03 21
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland Histone H3K27ac Donor STL003 Library AK321 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,461,000
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.1143
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.2162
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9508
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3201
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Adrenal Gland tissue; renlab.H3K27ac.STL003AD.01.01

value: Histone H3K27ac

value: magnetic anti-rabbit

value: Active Motif


title: mRNA from DEX-treated 35S:GR-RBE floral buds, biological replicate 2, techinical replicate 2

source_name: floral buds, DEX-treated 35S:GR-RBE


title: mRNA from mock-treated 35S:GR-RBE floral buds, biological replicate 1, techinical replicate 1


title: mRNA from mock-treated 35S:GR-RBE floral buds, biological replicate 1, techinical replicate 2


title: mRNA from DEX-treated 35S:GR-RBE floral buds, biological replicate 2, techinical replicate 1


title: mRNA from DEX-treated 35S:GR-RBE floral buds, biological replicate 1, techinical replicate 1


title: Ago2VariantsIPSeq

city: Palo Alto

first: shuo

last: gu

address: 269 Campus Drive

department: Pediatrics

institute: Stanford University

data_processing:
Step 1. Fastq file was converted to Fasta file usying FASTX-toolkit
Step 2. Different samples were sorted by the barcode. ( Ago2 - CAAT; Ago2_D5 - TCGC; Ago2_PAZ - TATG; PAZ_D5 - GTTA; Ago2_PAZ8 - TTCT; PAZ8_D5 - ACTT; F181A - ATAC) Of note, this sequencing result contains additional samples non-related to this study under different barcodes.
Step 3. Custom Perl scripts were used to identify and remove the 4nt barcode from the 5’ end and linker sequences from the 3’end
Step 4.RNA sequences were then aligned to human miRNA library sequences (miRBase) by bowtie with command line " bowtie -f -n 0 -l 18 --best ref input output"
Step 5. Custom Perl scripts were used to identify miRNAs with both guide (mature) and passenger (*) strands detected and then caculated the percentageof its star strand to total reads
Genome_build: miRbase release 17
Supplementary_files_format_and_content: stat.txt files which list the abundance and star to total ratio of miRNAs of interests.

source_name: HEK293 Cells

extract_protocol: Total RNAs were extracted from Agos-IP samples by Trizol, and then ligated to Linker-1 (IDT) in the absence of ATP with T4 RNA ligase 1 (New England Biolabs). Ligated RNA was size selected (38-46nt DNA/RNA hybrid) on 12% PAGE. The 5’ ends RNA were ligated to barcoded adapters. Dual-ligated RNA was reverse transcribed; PCR amplified and size selected on 4% NuSieve (Lonza) agarose. All sequencing was performed on the Illumina/GAII platform.

treatment_protocol:
All mutant Flag-Ago2 constructs were created by PCR-based mutagenesis approaches based on the parental plasmids Flag-Ago2 which we obtained from Addgene. In brief, Ago2-D5 is slicer-defective mutant, Ago2-PAZ is PAZ domain deletion mutant and Paz-D5 is a combination of these two. Ago2-PAZ8 and PAZ8_D5 contain point mutations in the PAZ domain instead of domain deletion. F181A is a point mutation in the N domain of Ago2.
All transfection assays were done using TransIT-LT1 (MirusBio) following the manufacturer's protocol.  500ng plasmids expressing various Ago2 variants were transfected into HEK293 cells in 10cm dishes.
More detail can be found in accompanying paper " Slicing-independent RISC activation requires the Argonaute PAZ domain" in Current Biology.

tag: cell line

value: HEK293 cell line

tag: passages

tag: ip antibody

value: Anti-FLAG (Sigma, Catalog# A2220, Lot# SLBB7030)


title: Colon_cdiffinfected_rep3

status: Public on Jul 11 2012

city: Blacksburg

first: Pawel

last: Michalak

state: VA

institute: Virginia Bioinformatics Institute

data_processing:
Adapter trimming
BWA alignment
RPKM-normalization
MiRNA quantification against miRBAse r. 18 with Partek Genomics Suite 6.12
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values for miRNAs in the samples

organism: Mus musculus

source_name: Colon; Clostridium difficile infected WT mice; replicate 3

growth_protocol: Colons from uninfected and C.difficile-infected C57BL6/J wild-type mice were collected in RNA Later prior to RNA isolation

extract_protocol:
After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
Illumina Small RNA Sample Preparation Kit

treatment_protocol: Following an antibiotic pre-treatment to ensure infection, C57BL6/J WT mice were challenged intragastrically with 107 cfu/mouse Clostridium difficile strain VPI 10463 (ATCC 43255). Colons were collected at day 4 post-infection. The antibiotic mixture consisted of colistin 850 U/mL (which corresponds to 4.2 mg/kg), gentamicin 0.035 mg/mL (which corresponds to 3.5 mg/kg), metronidazole 0.215 mg/mL (which corresponds to 21.5 mg/kg) and vancomycin 0.045 mg/mL (which corresponds to 4.5 mg/kg). The mixture was prepared and added to the drinking water for a 3-day pre-treatment period. A control group that received no antibiotics was also included. Following the treatment all mice were given regular autoclaved water for 2 days and all mice including the control group received a single dose of clindamycin (32 mg/kg) intraperitoneally 1 day before C. difficile challenge.

value: colon

tag: genotype

value: Wild-type

tag: infection

value: C. difficile-infected (107 cfu/mouse)

tag: sampling day


title: mRNA from DEX-treated 35S:GR-RBE floral buds, biological replicate 1, techinical replicate 2

value: L er with 35S:GR-RBE transgene

value: floral buds

value: mixed stages


title: Colon_cdiffinfected_rep2

source_name: Colon; Clostridium difficile infected WT mice; replicate 2


title: Colon_cdiffinfected_rep1

source_name: Colon; Clostridium difficile infected WT mice; replicate 1


title: Colon_uninfected_rep3

source_name: Colon; uninfected WT mice; replicate 3

value: Negative control (uninfected)


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Pancreas Tissue; renlab.H3K27ac.STL003PA.01.01

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK342
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11848
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11847
****************
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: GSM906397_UCSD.Pancreas.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003PA.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Pancreas H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Pancreas, Donor STL003, 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.13536
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,025,083
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.2162
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.317
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9841
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3446
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM906397_UCSD.Pancreas.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003PA.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Pancreas, Donor STL003, 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.13656
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 8
BROWSER_TRACK_NAME: Pancreas H3K27ac 03 42
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas Histone H3K27ac Donor STL003 Library AK342 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,025,083
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.2162
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.317
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9841
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3446
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Pancreas

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Male

value: Caucasian

value: Biorupter

value: 5 micrograms


title: Colon_uninfected_rep1

source_name: Colon; uninfected WT mice; replicate 1


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Left Ventricle Tissue; renlab.H3K27ac.STL003LV.01.01

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Left Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY50
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11891
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11885
****************
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: GSM906396_UCSD.Left_Ventricle.H3K27ac.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003LV.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Left Ventricle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Left Ventricle, Donor STL003, 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.13454
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,619,533
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.6255
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.6545
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9985
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6692
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM906396_UCSD.Left_Ventricle.H3K27ac.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL003LV.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Left Ventricle, Donor STL003, 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.13574
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 8
BROWSER_TRACK_NAME: LV H3K27ac 03 50
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Histone H3K27ac Donor STL003 Library AY50 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,619,533
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
FINDPEAKS_SCORE: 0.6255
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.6545
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9985
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6692
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Left Ventricle tissue; renlab.H3K27ac.STL003LV.01.01

value: Left Ventricle

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Histone H3K27ac

value: 500 micrograms

value: magnetic anti-rabbit

value: Active Motif


title: Colon_uninfected_rep2

source_name: Colon; uninfected WT mice; replicate 2

value: colon

value: Wild-type


title: ChIP-Seq analysis of H3K36me3 in human CD56+ mesoderm cells; DNA_Lib 1277

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1277
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11700
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11767
****************
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: GSM916072_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K36me3.DNA_Lib_1277.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1277-DNA_Lib 1277.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1277, 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.13390
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,028,380
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.6206
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.4981
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9958
IROC_PERCENTILE: 83
POISSON_SCORE: 0.7352
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM916072_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K36me3.DNA_Lib_1277.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1277-DNA_Lib 1277.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1277, 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.13410
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 8
BROWSER_TRACK_NAME: hDCM H3K36me3 77
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1277 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,028,380
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.6206
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.4981
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9958
IROC_PERCENTILE: 83
POISSON_SCORE: 0.7352
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 1277

extract_protocol: Library construction protocol: Single read - Illumina

value: BioSam 575

tag: lineage

value: mesoderm

tag: medium

value: Day 0-1:DMEM F12, 0.5% FBS, Activin A (100ng/mL) BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL). Days 1-5:DMEM F12, 0.5% FBS, BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL)

value: presumed normal

tag: passage

tag: line

value: CD56+ mesoderm

value: adherence

tag: batch

value: BioSAli 712

value: Cell Line

value: intermediate

tag: Sex

value: Harvard

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human CD56+ mesoderm cells; DNA_Lib 1276

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1276
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11701
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11767
****************
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: GSM916073_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_1276.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1276-DNA_Lib 1276.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1276, 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.13383
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,663,619
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.2346
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2693
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9269
IROC_PERCENTILE: 75
POISSON_SCORE: 0.4698
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM916073_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_1276.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1276-DNA_Lib 1276.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1276, 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.13403
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 8
BROWSER_TRACK_NAME: hDCM H3K9me3 76
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1276 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,663,619
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.2346
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2693
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9269
IROC_PERCENTILE: 75
POISSON_SCORE: 0.4698
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 1276

value: BioSam 575

value: mesoderm

value: genomic DNA

value: Male

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me3 in human CD56+ mesoderm cells; DNA_Lib 1273

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1273
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11697
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11767
****************
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: GSM916069_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K4me3.DNA_Lib_1273.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1273-DNA_Lib 1273.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1273, 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.13395
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,874,078
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.7889
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.7952
HOTSPOT_PERCENTILE: 93
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.7969
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.56

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

ANALYSIS FILE NAME: GSM916069_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K4me3.DNA_Lib_1273.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1273-DNA_Lib 1273.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1273, 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.13415
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 8
BROWSER_TRACK_NAME: hDCM H3K4me3 73
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1273 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,874,078
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.7889
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.7952
HOTSPOT_PERCENTILE: 93
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.7969
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.56

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 1273

value: Day 0-1:DMEM F12, 0.5% FBS, Activin A (100ng/mL) BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL). Days 1-5:DMEM F12, 0.5% FBS, BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL)

value: presumed normal

value: CD56+ mesoderm

value: adherence

value: BioSAli 712

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K36me3 in human CD56+ mesoderm cells; DNA_Lib 1283

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1283
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11696
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11768
****************
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: GSM916068_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K36me3.DNA_Lib_1283.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1283-DNA_Lib 1283.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1283, 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.13391
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,222,595
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.6528
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5411
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.997
IROC_PERCENTILE: 92
POISSON_SCORE: 0.7528
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM916068_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K36me3.DNA_Lib_1283.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1283-DNA_Lib 1283.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1283, 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.13411
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 8
BROWSER_TRACK_NAME: hDCM H3K36me3 83
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1283 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,222,595
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.6528
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5411
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.997
IROC_PERCENTILE: 92
POISSON_SCORE: 0.7528
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 1283

value: BioSam 577

value: BioSAli 713

value: Cell Line

value: intermediate

value: Harvard

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug


title: ChIP-Seq analysis of H3K4me3 in human CD25- IL17- Th stim MACS cells; DNA_Lib 712

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 712
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11699
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9445
****************
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: GSM916071_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K4me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 712-DNA_Lib 712-DNA_Lib 712.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 62, 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.13399
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,637,381
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.2381
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.2538
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9996
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2972
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916071_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K4me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 712-DNA_Lib 712-DNA_Lib 712.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 62, 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.13419
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 8
BROWSER_TRACK_NAME: CCIPsMpT H3K4me3 62 12
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 712 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,637,381
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.2381
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.2538
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9996
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2972
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- IL17- Th stim MACS is one of  CD4+  T cell subsets  that purified by microbeads, LS column  ; DNA_Lib 712

value: BioSam 135

value: genomic DNA

tag: markers

value: CD4+ T cell

value: CD25- IL17- Th stim MACS

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: 10 ul bed volume

value: Branson


title: ChIP-Seq analysis of H3K4me3 in human CD56+ mesoderm cells; DNA_Lib 1279

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1279
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11691
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11768
****************
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: GSM916063_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K4me3.DNA_Lib_1279.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1279-DNA_Lib 1279.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1279, 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.13396
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,732,213
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.8252
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.8359
HOTSPOT_PERCENTILE: 100
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.8298
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.56

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

ANALYSIS FILE NAME: GSM916063_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K4me3.DNA_Lib_1279.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1279-DNA_Lib 1279.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1279, 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.13416
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 8
BROWSER_TRACK_NAME: hDCM H3K4me3 79
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1279 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,732,213
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.8252
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.8359
HOTSPOT_PERCENTILE: 100
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.8298
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.56

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 1279

tag: sample alias

value: BioSam 577

value: mesoderm

value: Day 0-1:DMEM F12, 0.5% FBS, Activin A (100ng/mL) BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL). Days 1-5:DMEM F12, 0.5% FBS, BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL)

value: presumed normal

value: CD56+ mesoderm

value: adherence

value: BioSAli 713

value: Cell Line

value: Male

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K9me3 in human CD56+ mesoderm cells; DNA_Lib 1282

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1282
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11695
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11768
****************
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: GSM916067_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_1282.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1282-DNA_Lib 1282.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1282, 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.13384
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,346,886
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.3402
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.3493
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.963
IROC_PERCENTILE: 88
POISSON_SCORE: 0.5316
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM916067_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_1282.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1282-DNA_Lib 1282.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1282, 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.13404
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 8
BROWSER_TRACK_NAME: hDCM H3K9me3 82
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1282 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,346,886
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.3402
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.3493
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.963
IROC_PERCENTILE: 88
POISSON_SCORE: 0.5316
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 1282

tag: sample common name

value: genomic DNA

value: intermediate

value: Harvard

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1 in human CD56+ mesoderm cells; DNA_Lib 1272

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1272
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11698
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11767
****************
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: GSM916070_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K4me1.DNA_Lib_1272.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1272-DNA_Lib 1272.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1272, 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.13393
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,195,925
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.5301
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.5589
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9907
IROC_PERCENTILE: 75
POISSON_SCORE: 0.653
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916070_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K4me1.DNA_Lib_1272.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1272-DNA_Lib 1272.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1272, 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.13413
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 8
BROWSER_TRACK_NAME: hDCM H3K4me1 72
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 1272 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,195,925
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.5301
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.5589
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9907
IROC_PERCENTILE: 75
POISSON_SCORE: 0.653
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 1272

value: BioSam 575

value: mesoderm

value: Day 0-1:DMEM F12, 0.5% FBS, Activin A (100ng/mL) BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL). Days 1-5:DMEM F12, 0.5% FBS, BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL)

tag: molecule

value: presumed normal

value: BioSAli 712

value: 10 ul bed volume

value: Histone H3K4me1

value: Branson


title: Eri1_knockout

city: San Francisco

first: Molly

middle: Fisher

last: Thomas

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: University of California San Francisco

description:
15 - 30 nt RNA
small RNA-seq

data_processing: Processed BED and .txt File Generation: For all reads, the 5' end of the read was treated as the small RNA 5' nucleotide, and the 3' end of the small RNA was determined by the 3'-most perfect match to the first 6 nt of the 3' adaptor. Reads without a perfect 6-nt adapter match were discarded. All adapter-extrated reads 15-30 nt in length were mapped the the University of California at Santa Cruz mm8 assembly of the mouse genome by searching for exact matches over the entire sequence. .txt files contain sequences 15-30 nt long that have been trimmed of adapter sequences. .BED files contain a subset of sequences from the .txt files that map uniquely to the mouse genome (mm8) with no more than two mismatches.

growth_protocol: CD4+ T cells from spleen and lymph nodes (superficial cervical, facial, axillary, brachial, and inguinal) were purified and stimulated in vitro for 44 hours with anti-CD3 (2C11) and anti-CD28 (37.51) antibodies in Th2 conditions (1000 U/ml IL-4 and 5Âµg/ml anti-IFN-gamma)

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen) and small (18-30 nt) RNA was size fractionated by gel extraction. 3' linkers (5'P-TCGTATGCCGTCTTCTGCTTGidT) were ligated to small RNAs by the Rnl2 (1-249) enzyme (NEB) followed by 5' linker ligation (GUUCAGAGUUCUACAGUCCGACGAUC) by Rnl1 (NEB). RNA was then reverse transcribed using SS III and amplified by PCR for 15 cycles. Amplified cDNA was purified by gel-extraction. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: CD4+ T cell

tag: strain


title: ChIP-Seq analysis of H3K27me3 in human CD56+ mesoderm cells; DNA_Lib 1274

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1274
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11690
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11767
****************
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: GSM916062_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K27me3.DNA_Lib_1274.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1274-DNA_Lib 1274.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1274, 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.13386
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,352,094
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1821
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.3108
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.97
IROC_PERCENTILE: 93
POISSON_SCORE: 0.4229
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916062_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K27me3.DNA_Lib_1274.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1274-DNA_Lib 1274.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1274, 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.13406
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 8
BROWSER_TRACK_NAME: hDCM H3K27me3 74
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K27me3 Library DNA_Lib 1274 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,352,094
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1821
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.3108
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.97
IROC_PERCENTILE: 93
POISSON_SCORE: 0.4229
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 1274

value: genomic DNA

tag: disease

value: CD56+ mesoderm

value: adherence

value: Cell Line

value: intermediate

value: Male

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K27me3 in human fetal brain cells; DNA_Lib 385

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 385
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11689
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7163
****************
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: GSM916061_BI.Fetal_Brain.H3K27me3.UW_H22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 385-DNA_Lib 385-DNA_Lib 385-DNA_Lib 385.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Fetal Brain H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Fetal Brain, Donor UW H22676, 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.13387
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,238,255
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2435
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.2851
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9651
IROC_PERCENTILE: 80
POISSON_SCORE: 0.453
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM916061_BI.Fetal_Brain.H3K27me3.UW_H22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 385-DNA_Lib 385-DNA_Lib 385-DNA_Lib 385.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Fetal Brain, Donor UW H22676, 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.13407
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 8
BROWSER_TRACK_NAME: FB H3K27me3 76 85
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain Histone H3K27me3 Donor UW H22676 Library DNA_Lib 385 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,238,255
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2435
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.2851
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9651
IROC_PERCENTILE: 80
POISSON_SCORE: 0.453
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Primary fetal brain tissue; DNA_Lib 385

value: BioSAli 186

value: Fetal Brain

value: Post-Mortem

value: Unknown

value: Primary Tissue

value: Brain

value: University of Washington

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug


title: ChIP-Seq analysis of H3K27me3 in human CD25- IL17+ Th17 stim cells; DNA_Lib 738

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 738
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11687
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9446
****************
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: GSM916059_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K27me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 738-DNA_Lib 738-DNA_Lib 738.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 62, 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.13398
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,125,811
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.024
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.1502
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.6758
IROC_PERCENTILE: 7
POISSON_SCORE: 0.2413
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916059_BI.CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells.H3K27me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 738-DNA_Lib 738-DNA_Lib 738.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells, Donor Donor 62, 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.13418
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 8
BROWSER_TRACK_NAME: CCIPsT H3K27me3 62 38
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K27me3 Donor 62 Library DNA_Lib 738 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,125,811
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.024
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.1502
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.6758
IROC_PERCENTILE: 7
POISSON_SCORE: 0.2413
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- IL17+ Th17 stim is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 738

value: BioSam 134

value: presumed normal

value: genomic DNA

value: CD4+ T cell

value: CD25- IL17+ Th17 stim

value: Primary Cell

value: Donor 62

value: Dana Farber

value: 10 ul bed volume

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human fetal brain cells; DNA_Lib 386

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 386
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11682
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7163
****************
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: GSM916054_BI.Fetal_Brain.H3K9me3.UW_H22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 386-DNA_Lib 386-DNA_Lib 386-DNA_Lib 386.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Fetal Brain H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Brain, Donor UW H22676, 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.13394
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,012,613
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.1004
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1768
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.8106
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3201
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM916054_BI.Fetal_Brain.H3K9me3.UW_H22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 386-DNA_Lib 386-DNA_Lib 386-DNA_Lib 386.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Brain, Donor UW H22676, 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.13414
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 8
BROWSER_TRACK_NAME: FB H3K9me3 76 86
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain Histone H3K9me3 Donor UW H22676 Library DNA_Lib 386 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,012,613
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.1004
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1768
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.8106
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3201
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Primary fetal brain tissue; DNA_Lib 386

value: BioSAli 186

value: Fetal Brain

value: Post-Mortem

value: Unknown

value: Primary Tissue

value: Abcam

value: Histone H3K9me3


title: 21Usensor(RNAe)

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: Small RNA sequence data

data_processing:
Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads. 3' adapter seqeunce starts with 'TCGTATG'.
Reads were mapped to C.elegans genome assembly using megablast software.
Genome_build: WS220

organism: Caenorhabditis elegans

source_name: Complete worms

growth_protocol: Animals were grown on standard agar plates and fed with E. coli

extract_protocol: Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. 5' and 3' adapttors were ligated. RNA was not treated with any enzymes before ligation steps.

value: Bristol N2 background

tag: age

value: adult stage

value: transgene not reactivated by RNAi against prg-1

tag: treatment

value: RNA was not treated with any enzyme before ligation procedures


title: 21Usensor(+)

description: Small RNA sequence data

value: transgene reactivates upon RNAi against prg-1


title: ChIP-Seq analysis of H3K4me1 in human CD19 cells; DNA_Lib 1261

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1261
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11681
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11766
****************
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: GSM916053_BI.CD19_Primary_Cells.H3K4me1.130.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1261-DNA_Lib 1261.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of CD19 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD19 Primary Cells, Donor 130, 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.13388
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,061,820
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.7899
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7606
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9999
IROC_PERCENTILE: 100
POISSON_SCORE: 0.8231
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916053_BI.CD19_Primary_Cells.H3K4me1.130.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1261-DNA_Lib 1261.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD19 Primary Cells, Donor 130, 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.13408
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 8
BROWSER_TRACK_NAME: CD19 H3K4me1 30 61
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells Histone H3K4me1 Donor 130 Library DNA_Lib 1261 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,061,820
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.7899
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7606
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9999
IROC_PERCENTILE: 100
POISSON_SCORE: 0.8231
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Bulk lymphocytes were purified from cord blood and further selected by flow cytometry; DNA_Lib 1261

value: CD19 Primary Cells

value: presumed normal

value: genomic DNA

value: Female

value: Primary Cell

value: FHCRC

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9me3 in human HUES64 derived CD184+ cells; DNA_Lib 242

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 242
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11685
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9460
****************
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: GSM916057_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9me3.DNA_Lib_242.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 242-DNA_Lib 242-DNA_Lib 242-DNA_Lib 242-DNA_Lib 242.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 242, 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.13380
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,942,234
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.1738
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.22
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9273
IROC_PERCENTILE: 81
POISSON_SCORE: 0.4252
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM916057_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9me3.DNA_Lib_242.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 242-DNA_Lib 242-DNA_Lib 242-DNA_Lib 242-DNA_Lib 242.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 242, 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.13400
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 8
BROWSER_TRACK_NAME: hDCE H3K9me3 42
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 242 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,942,234
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.1738
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.22
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9273
IROC_PERCENTILE: 81
POISSON_SCORE: 0.4252
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 242

value: CD184+ endoderm cultured cells

value: RPMI 100ng/mL Activin A 50ng/mL Wnt3a

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 137

value: Cell Line

value: differentiated

value: Male

value: Harvard University

value: 10 ul bed volume

value: Abcam

value: Histone H3K9me3

value: Branson