title: nlsSwi6KR25A_H3K9me2_ChIPSEQ_rep2

description: CCACTCT

data_processing:
All samples were barcoded at the 3'end of the 5'adapter using a hamming distance two code with a 3' CT (GTGCGCT, GCCACCT, AGAAGCT, ATCTTCT, TGCCACT, CACGGCT, CGGTCCT, CCACTCT) and sequenced (with other samples) in two lanes of an HiSeq 2000 instrument. Individual reads were assigned to their sample based on the first 7 nucleotides containing the barcode. The 3' adapter was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least 7 or 10 bases respectively. Low complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). All the reads that were shorter than 14 nucleotides were removed.
Genome_build: Initial identification of elements is based on the features described in the GFF file “pombe_09052011.gff” (downloaded from ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF).
Supplementary_files_format_and_content: wig file for multiple tracks

source_name: nlsSwi6KR25A H3K9me2 ChIPSEQ

growth_protocol: S.pombe strains were grown in YES media. ~150x10^7 cells were harvested from o/n cultures and processed for ChIP

extract_protocol:
Lysates were clarified from sonicated S. pombe cells and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using an Illumina-based protocol using custom reagents and barcoded adapters. Briefly, immunoprecipitated DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA fragments were size selected to remove excess adapters and adapter modified DNA fragments were enriched by PCR amplification with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified ChIP-seq libraries thus generated were validated and subsequently captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 system following the manufacturer's protocols.

tag: chip antibody

tag: chip antibody manufacturer

value: WAKO

tag: chip antibody catalog #

tag: chip antibody lot #


title: nlsSwi6_H3K9me2_ChIPSEQ_rep2

status: Public on Jul 20 2013

type: SRA

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

description: CACGGCT

library_source: genomic

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: nlsSwi6 H3K9me2 ChIPSEQ

tag: genotype


title: 36_s_6

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

country: USA

institute: Beckman Research Institute

description: 36_s_6 serum

library_source: transcriptomic

data_processing:
Sequenced reads from Solexa were first mapped onto human genome version hg18 using novoalign software and the expression level of mature miRNAs in the miRBase human miRNA database v15 was summarized.
Quantile normalization was applied to the counts data
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each miRNA

molecule: total RNA

organism: Homo sapiens

source_name: serum

extract_protocol:
TRIZOL LS reagent (Invitrogen) was used to extract total RNA from ~1.5 ml of serum, as described in the manufacturer’s protocol. RNA pellet was dissolved in 10 μl of RNase-free water, and subjected to library construction and deep sequencing.
Each serum sample was independently subjected to library preparation and deep sequencing. All small RNAs of 15–52 nts were selected and sequenced using the Solexa system, following the manufacturer’s protocol (Illumina Inc., San Diego, CA). Library preparation, as well as cluster generation and deep sequencing, was performed according to the 5' ligation-dependent (5′ monophosphate-dependent) manufacturer’s protocol (Digital Gene Expression for small RNA; Illumina). For each sample, 5 μl of total RNA extracted from serum was used for small RNA library preparation. Small RNAs were size-selected between 17 and 52 nt according to the single-stranded DNA marker in the small RNA sequencing kit (Illumina). The library was quantified using picoGreen and qPCR. Sequencing was performed on a Genome Analyzer IIx (Illumina), and image processing and base calling were conducted using Illumina’s pipeline.

treatment_protocol: Pre-treatment sera from BC patients were used.

tag: er status

value: neg

tag: pr status

tag: her2 status

value: pos

tag: inflammatory

value: Y

tag: Stage

tag: relapse

value: N

tag: molecule subtype

value: miRNA


title: nlsSwi6_H3K9me2_ChIPSEQ_rep1

description: TGCCACT


title: 19_s_5

description: 19_s_5 serum


title: 48_s_8

description: 48_s_8 serum


title: WT_H3K9me2_ChIPSEQ_rep1

description: GTGCGCT

source_name: WT H3K9me2 ChIPSEQ

value: WT


title: 32_s_6

description: 32_s_6 serum


title: 41_s_3

description: 41_s_3 serum


title: 437_s_5

description: 437_s_5 serum


title: 482_s_4

description: 482_s_4 serum


title: 28_s_5

description: 28_s_5 serum


title: WT_H3K9me2_ChIPSEQ_rep2

description: GCCACCT


title: clr4D_H3K9me2_ChIPSEQ_rep1

description: AGAAGCT

source_name: clr4D H3K9me2 ChIPSEQ


title: 862_s_6

description: 862_s_6 serum


title: 35_s_8

description: 35_s_8 serum


title: comb_55

description: comb_55 serum


title: 31_s_7

description: 31_s_7 serum


title: 27_s_6

description: 27_s_6 serum


title: 49_s_7

description: 49_s_7 serum


title: 848_s_7

description: 848_s_7 serum


title: 1766_s_3

description: 1766_s_3 serum


title: nlsSwi6KR25A_H3K9me2_ChIPSEQ_rep1

description: CGGTCCT


title: PN01679_s_8

description: PN01679_s_8 serum


title: PN41_s_8

description: PN41_s_8 serum


title: PN49_s_6

description: PN49_s_6 serum


title: clr4D_H3K9me2_ChIPSEQ_rep2

description: ATCTTCT


title: 50_s_6

description: 50_s_6 serum


title: 52_s_5

description: 52_s_5 serum


title: 59_s_2

description: 59_s_2 serum


title: 1512_s_4

description: 1512_s_4 serum


title: 56_s_3

description: 56_s_3 serum


title: comb_47

description: comb_47 serum


title: 436_s_5

description: 436_s_5 serum


title: 1613_s_8

description: 1613_s_8 serum


title: 42_s_1

description: 42_s_1 serum


title: acrylic acid rep 1

status: Public on Jul 19 2013

city: Madison

first: Brian

last: Pfleger

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

data_processing:
Ribsomal RNA genes were removed from the PCC 7002 genome (Genbank ID CP000951.1-CP000957.1)
Reads were trimmed of Ns
Aligment to genome was done allowing 2 mismatches
RPKM values were calculated using the CLC Workbench
Genome_build: ASM1948v1
Supplementary_files_format_and_content: RPKM values and fold change

organism: Picosynechococcus sp. PCC 7002

source_name: acrylic acid rep 1

growth_protocol: 50 mL volumes at a light intensity of 140 µE/m2/s at 35 °C with no agitation

extract_protocol: Trizol at 95C. Samples cleaned up with Rneasy Kit

treatment_protocol: Acrylic acid samples were treated with 5mM acrylic acid at pH 8.0

tag: condition

value: 5mM acrylic acid

tag: strain


title: control rep 2

source_name: control rep 2

value: control


title: control rep 1

source_name: control rep 1


title: TSW491

status: Public on Jul 18 2013

city: Cambridge

first: Christopher

last: Ng

state: Massachusetts

address: 77 Massachusetts Ave.

institute: Massachusetts Institute of Technology

description:
Strand-specific paired-end mRNA-Seq.
Summary processed data file: TSrpkms.txt

data_processing:
Reads were mapped to mm9 with the Bowtie alignment program with settings -m 1 -v 2 --best.
Differentially expressed genes were identified with the R package DESeq, using a 10% FDR cutoff and log2 difference of 0.5 between wild-type and mutant conditions.Outliers were further excluded by restricting the residual variance quotients to less than 10.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: MGSCv37
Supplementary_files_format_and_content: RPKM files are tab-delimited text files with the following four fields: NCBI Gene IDs, raw counts, #positions in gene, and RPKMs. Summary text files list the RPKMs for each sample in a condition (8wk cortex, 8wk striatum, 12wk cortex, 12wk striatum).

organism: Mus musculus

source_name: R6/2 wildtype littermate, striatum, 12 weeks

extract_protocol:
Flash-frozen tissues were homogenized and RNA extracted with TRIzol Reagent and purified with RNeasy columns (Qiagen), all samples with RINs greater than 7. Oligo d(T)25 Magnetic Beads (New England BioLabs) were used to isolate mRNA from 1-3μg of total RNA. Purified mRNA was fragmented with Ambion's RNA fragmentation kit for 5 minutes at 70°C.
Library construction was adapted from the dUTP strand-specific protocol of Levin et al. 2010. mRNA was ethanol precipitated, concentrated in 5μl of water, and pre-mixed with 3μg of random hexamers for 5 minutes at 65°C before chilling on ice. First-strand cDNA was synthesized as described, but incubated as follows: 10 minutes at 25°C, 50 minutes at 42°C, and 15 minutes at 70°C. First-strand cDNA was purified by PCI extraction, ethanol precipitated with 0.1 volume 3M ammonium acetate to remove dNTPs, and resuspended in 104μl H2O. Second-strand cDNA was synthesized as described, but incubated for 2.5 hours. Paired-end libraries for Illumina sequencing were then prepared from the cDNA as previously published except adaptor-ligated cDNA was size-selected to 200-400bp, and we performed PCR using Phusion High-Fidelity DNA polymerase with HF buffer (New England BioLabs) and 10ul of Q Solution (Qiagen). These paired-end, strand-specific cDNA libraries were then sequenced on the Illumina Genome Analzyer (36 bp reads) or HiSeq (40 bp reads).

tag: strain/background

value: C57Bl/6 / CBA

tag: genotype/variation

value: wild type

tag: tissue

value: brain striatum

tag: age

value: 12 weeks


title: TSW479


title: TSW478


title: TCW9457

description:
Strand-specific paired-end mRNA-Seq.
Summary processed data file: TCrpkms.txt

source_name: R6/2 wildtype littermate, cortex, 12 weeks

value: brain cortex


title: TCW9451


title: TSM490

source_name: R6/2, striatum, 12 weeks

value: R6/2 transgenic (Mangiarini et al., Cell 87:493-506,1996)


title: TSM482


title: TCW9469


title: PN05_s_5

description: PN05_s_5 serum


title: TCM9453

source_name: R6/2, cortex, 12 weeks


title: TCM9450


title: 29_s_8

description: 29_s_8 serum


title: 37_s_7

description: 37_s_7 serum


title: ESW183

description:
Strand-specific paired-end mRNA-Seq.
Summary processed data file: ESrpkms.txt

source_name: R6/2 wildtype littermate, striatum, 8 weeks

value: 8 weeks


title: ESW180


title: ESM192

source_name: R6/2, striatum, 8 weeks


title: ESM184


title: ESM181


title: ESW176


title: ECW180

description:
Strand-specific paired-end mRNA-Seq.
Summary processed data file: ECrpkms.txt

source_name: R6/2 wildtype littermate, cortex, 8 weeks


title: acrylic acid rep 2

source_name: acrylic acid rep 2


title: ECW178


title: ECW176


title: ECM181

source_name: R6/2, cortex, 8 weeks


title: ChIP_WT_H3K4me3_12wks_str_rep1_rep2

description: This Sample represents 2 replicates.

data_processing:
ChIP-Seq reads were aligned to the reference mouse genome (mm9) using Bowtie (v0.12.7).
Reads from biological replicates were concatenated for each condition.
Positive and negative strand reads were shifted according to a peak shift model built by the MACS algorithm (v1.4.0rc2) with parameters: effective genome size = 2.11e+09, band width = 300, p-value cutoff 1e-5.
Genome_build: MGSCv37
Supplementary_files_format_and_content: bigwig file contains peak-shifted read counts in 10 base pair windows for each chromosome.

extract_protocol:
Cortical and striatal tissues were crosslinked with 1% formaldehyde for ten minutes and the crosslinking was quenched by 0.125M final concentration of glycine. The crosslinked tissue was then homogenized, rinsed with PBS, pelleted, and frozen in liquid nitrogen for later use. Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibody (H3K4me3; Millipore, cat 17-614).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

tag: chip antibody

value: H3K4me3 (Millipore, cat 17-614)


title: ECM175


title: ChIP-Seq analysis of H3K36me3 in hN cells; Lib:RI:20101012:17--ChIP:MA:20100927:17:hN (ES H9 derived Neurons):H3K36Me3

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: CL_0000540
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:17--ChIP:MA:20100927:17:hN (ES H9 derived Neurons):H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8064
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8185
****************
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: GSM772803_BI.H9_Derived_Neuron_Cultured_Cells.H3K36me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:17--ChIP:MA:20100927:17:hN (ES H9 derived Neurons):H3K36Me3.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuron Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on the H9 Derived Neuron Cultured Cells, Library Lib:RI:20101012:17--ChIP:MA:20100927:17:hN (ES H9 derived Neurons):H3K36Me3, 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.17286
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,162,901
FINDPEAKS_SCORE: 0.4484
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.3712
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9941
IROC_PERCENTILE: 85
POISSON_SCORE: 0.6306
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772803_BI.H9_Derived_Neuron_Cultured_Cells.H3K36me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:17--ChIP:MA:20100927:17:hN (ES H9 derived Neurons):H3K36Me3.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuron Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from the H9 Derived Neuron Cultured Cells, Library Lib:RI:20101012:17--ChIP:MA:20100927:17:hN (ES H9 derived Neurons):H3K36Me3, 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.17469
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDN H3K36me3 e3
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuron Cultured Cells Histone H3K36me3 Library Lib:RI:20101012:17--ChIP:MA:20100927:17:hN (ES H9 derived Neurons):H3K36Me3 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,162,901
FINDPEAKS_SCORE: 0.4484
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.3712
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9941
IROC_PERCENTILE: 85
POISSON_SCORE: 0.6306
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neurons derived from H9 (WA09) human stem cells; Lib:RI:20101012:17--ChIP:MA:20100927:17:hN (ES H9 derived Neurons):H3K36Me3

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: H9 Derived Neuron Cultured Cells

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: >90% beta III tubulin(+) and >60% MAP2(+)

value: Medium:Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions - AB2+ANS+LIF on Matrigel (i.e., differentiation medium)

value: hN (ES H9 derived Neurons)

value: Female

value: Primary Cell Culture

value: ArunA Biomedical, Athens, GA

value: embryo

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: ChIP-Seq analysis H3K27me3 hNP; Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8062
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8184
****************
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: GSM772801_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3-Lib EpiLabSPL Row 1793.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuronal Progenitor Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3, 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.17303
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,111,982
FINDPEAKS_SCORE: 0.0929
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.1453
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9579
IROC_PERCENTILE: 78
POISSON_SCORE: 0.3482
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772801_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3-Lib EpiLabSPL Row 1793.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuronal Progenitor Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3, 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.17486
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP H3K27me3 e3
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,111,982
FINDPEAKS_SCORE: 0.0929
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.1453
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9579
IROC_PERCENTILE: 78
POISSON_SCORE: 0.3482
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neuronal progenitors derived from H9 (WA09) human stem cells; Lib:RI:20101012:10--ChIP:MA:20100927:10:hNP (ES H9 derived Nuronal Progenitors):H3K27Me3

value: Medium:Cultured in defined proliferation medium containing AB2+ANS plus FGF2 and LIF on Matrigel-coated surfaces.

value: hNP (ES H9 derived Nuronal Progenitors)

value: Unknown

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis H3K4me1: hNP; Lib:RI:20101012:07--ChIP:MA:20100927:07:hNP (ES H9 derived Nuronal Progenitors):H3K4Me1

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:07--ChIP:MA:20100927:07:hNP (ES H9 derived Nuronal Progenitors):H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8069
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8184
****************
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: GSM772808_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me1.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:07--ChIP:MA:20100927:07:hNP (ES H9 derived Nuronal Progenitors):H3K4Me1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuronal Progenitor Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:07--ChIP:MA:20100927:07:hNP (ES H9 derived Nuronal Progenitors):H3K4Me1, 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.17314
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,117,928
FINDPEAKS_SCORE: 0.2838
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3371
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9847
IROC_PERCENTILE: 65
POISSON_SCORE: 0.443
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772808_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me1.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:07--ChIP:MA:20100927:07:hNP (ES H9 derived Nuronal Progenitors):H3K4Me1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuronal Progenitor Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:07--ChIP:MA:20100927:07:hNP (ES H9 derived Nuronal Progenitors):H3K4Me1, 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.17497
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP H3K4me1 e1
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library Lib:RI:20101012:07--ChIP:MA:20100927:07:hNP (ES H9 derived Nuronal Progenitors):H3K4Me1 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,117,928
FINDPEAKS_SCORE: 0.2838
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3371
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9847
IROC_PERCENTILE: 65
POISSON_SCORE: 0.443
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neuronal progenitors derived from H9 (WA09) human stem cells; Lib:RI:20101012:07--ChIP:MA:20100927:07:hNP (ES H9 derived Nuronal Progenitors):H3K4Me1

value: genomic DNA

value: Histone H3K4me1


title: ChIP-Seq analysis of WCE in hNP; Lib:RI:20101012:12--ChIP:MA:20100927:12:hNP (ES H9 derived Nuronal Progenitors):WCE

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:12--ChIP:MA:20100927:12:hNP (ES H9 derived Nuronal Progenitors):WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8066
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8184
****************
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: GSM772805_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.Input.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:12--ChIP:MA:20100927:12:hNP (ES H9 derived Nuronal Progenitors):WCE-Lib EpiLabSPL Row 1795.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuronal Progenitor Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:12--ChIP:MA:20100927:12:hNP (ES H9 derived Nuronal Progenitors):WCE, 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.17240
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,439,011
FINDPEAKS_SCORE: 0.0027
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0031
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0318
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772805_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.Input.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:12--ChIP:MA:20100927:12:hNP (ES H9 derived Nuronal Progenitors):WCE-Lib EpiLabSPL Row 1795.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuronal Progenitor Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:12--ChIP:MA:20100927:12:hNP (ES H9 derived Nuronal Progenitors):WCE, 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.17423
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP Input CE
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Library Lib:RI:20101012:12--ChIP:MA:20100927:12:hNP (ES H9 derived Nuronal Progenitors):WCE EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,439,011
FINDPEAKS_SCORE: 0.0027
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0031
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0318
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neuronal progenitors derived from H9 (WA09) human stem cells; Lib:RI:20101012:12--ChIP:MA:20100927:12:hNP (ES H9 derived Nuronal Progenitors):WCE

value: Primary Cell Culture

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27me3 in human CD56+ ectoderm cells; DNA_Lib 3193

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 3193
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15384
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15412
****************
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: GSM1112827_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K27me3.DNA_Lib_3193.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3193.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 3193, 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.17288
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,131,042
FINDPEAKS_SCORE: 0.3582
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9807
IROC_PERCENTILE: 89
POISSON_SCORE: 0.4561
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.53

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

ANALYSIS FILE NAME: GSM1112827_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K27me3.DNA_Lib_3193.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3193.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 3193, 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.17471
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto H3K27me3 93
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K27me3 Library DNA_Lib 3193 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,131,042
FINDPEAKS_SCORE: 0.3582
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9807
IROC_PERCENTILE: 89
POISSON_SCORE: 0.4561
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.53

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 3193

value: BioSam 1247

tag: lineage

value: ectoderm

tag: medium

value: CD56 ectoderm - Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

value: presumed normal

tag: passage

tag: line

value: CD56+ ectoderm

value: adherence

tag: batch

value: BioSAli 1890

value: Cell Line

value: intermediate

tag: Sex

value: Male

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: Branson


title: ChIP-Seq analysis of WCE in human CD15 cells; Lib EpiLabSPL Row 623

description:
sample_term_id: CL_0000775
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 623
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8019
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2562
****************
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: GSM772758_BI.CD15_Primary_Cells.Input.23.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 623-Lib EpiLabSPL Row 1801.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD15 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD15 Primary Cells, Donor 23.0, 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.17234
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,226,851
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.0129
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.0406
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772758_BI.CD15_Primary_Cells.Input.23.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 623-Lib EpiLabSPL Row 1801.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD15 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD15 Primary Cells, Donor 23.0, 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.17417
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CD15 Input 23.0 23
BROWSER_TRACK_DESCRIPTION: BI CD15 Primary Cells ChIP-Seq Input Donor 23.0 Library Lib EpiLabSPL Row 623 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,226,851
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.0129
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.0406
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD15+ cells from cord blood; Lib EpiLabSPL Row 623

value: CD15 Primary Cells

value: genomic DNA

value: FHCRC

value: Primary Cell

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis: H3K4me3 in hN cells; Lib:RI:20101012:14--ChIP:MA:20100927:14:hN (ES H9 derived Neurons):H3K4Me3

description:
sample_term_id: CL_0000540
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:14--ChIP:MA:20100927:14:hN (ES H9 derived Neurons):H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8037
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8185
****************
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: GSM772776_BI.H9_Derived_Neuron_Cultured_Cells.H3K4me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1689-Lib:RI:20101012:14--ChIP:MA:20100927:14:hN (ES H9 derived Neurons):H3K4Me3.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuron Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on the H9 Derived Neuron Cultured Cells, Library Lib EpiLabSPL Row 1689, 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.17207
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 50,973,503
FINDPEAKS_SCORE: 0.5262
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5241
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.5268
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772776_BI.H9_Derived_Neuron_Cultured_Cells.H3K4me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1689-Lib:RI:20101012:14--ChIP:MA:20100927:14:hN (ES H9 derived Neurons):H3K4Me3.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuron Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the H9 Derived Neuron Cultured Cells, Library Lib EpiLabSPL Row 1689, 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.17390
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDN H3K4me3 89
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuron Cultured Cells Histone H3K4me3 Library Lib EpiLabSPL Row 1689 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 50,973,503
FINDPEAKS_SCORE: 0.5262
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5241
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.5268
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neurons derived from H9 (WA09) human stem cells; Lib:RI:20101012:14--ChIP:MA:20100927:14:hN (ES H9 derived Neurons):H3K4Me3

value: H9 Derived Neuron Cultured Cells

value: >90% beta III tubulin(+) and >60% MAP2(+)

value: Medium:Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions - AB2+ANS+LIF on Matrigel (i.e., differentiation medium)

value: hN (ES H9 derived Neurons)

value: Female

value: Primary Cell Culture

value: ArunA Biomedical, Athens, GA

value: embryo

value: 10 million cells

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3


title: TSM492

value: C57Bl/6 / CBA

value: R6/2 transgenic (Mangiarini et al., Cell 87:493-506,1996)

value: brain striatum

value: 12 weeks


title: ChIP-Seq analysis H3K9me3: hNP; Lib:RI:20101012:09--ChIP:MA:20100927:09:hNP (ES H9 derived Nuronal Progenitors):H3K9Me3

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:09--ChIP:MA:20100927:09:hNP (ES H9 derived Nuronal Progenitors):H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8071
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8184
****************
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: GSM772810_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1792-Lib:RI:20101012:09--ChIP:MA:20100927:09:hNP (ES H9 derived Nuronal Progenitors):H3K9Me3.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuronal Progenitor Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib EpiLabSPL Row 1792, 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.17217
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,908,005
FINDPEAKS_SCORE: 0.0326
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.1043
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8484
IROC_PERCENTILE: 60
POISSON_SCORE: 0.2907
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772810_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1792-Lib:RI:20101012:09--ChIP:MA:20100927:09:hNP (ES H9 derived Nuronal Progenitors):H3K9Me3.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuronal Progenitor Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib EpiLabSPL Row 1792, 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.17400
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP H3K9me3 92
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library Lib EpiLabSPL Row 1792 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,908,005
FINDPEAKS_SCORE: 0.0326
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.1043
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8484
IROC_PERCENTILE: 60
POISSON_SCORE: 0.2907
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neuronal progenitors derived from H9 (WA09) human stem cells; Lib:RI:20101012:09--ChIP:MA:20100927:09:hNP (ES H9 derived Nuronal Progenitors):H3K9Me3

value: genomic DNA

value: Medium:Cultured in defined proliferation medium containing AB2+ANS plus FGF2 and LIF on Matrigel-coated surfaces.

value: hNP (ES H9 derived Nuronal Progenitors)

value: Unknown

value: Protein A-Sepharose 4B

value: SDS lysis

value: Abcam

value: Histone H3K9me3

value: Bioruptor


title: ChIP_R6-2_H3K4me3_12wks_ctx_rep1_rep2_rep3

description: This Sample represents 3 replicates.

value: brain cortex

value: H3K4me3 (Millipore, cat 17-614)


title: ChIP-Seq analysis H3K36me3 hNP; Lib:RI:20101012:11--ChIP:MA:20100927:11:hNP (ES H9 derived Nuronal Progenitors):H3K36Me3

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:11--ChIP:MA:20100927:11:hNP (ES H9 derived Nuronal Progenitors):H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8056
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8184
****************
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: GSM772795_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K36me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:11--ChIP:MA:20100927:11:hNP (ES H9 derived Nuronal Progenitors):H3K36Me3-Lib EpiLabSPL Row 1794.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuronal Progenitor Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:11--ChIP:MA:20100927:11:hNP (ES H9 derived Nuronal Progenitors):H3K36Me3, 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.17298
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 64,319,157
FINDPEAKS_SCORE: 0.5731
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.398
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9979
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7198
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772795_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K36me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:11--ChIP:MA:20100927:11:hNP (ES H9 derived Nuronal Progenitors):H3K36Me3-Lib EpiLabSPL Row 1794.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuronal Progenitor Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:11--ChIP:MA:20100927:11:hNP (ES H9 derived Nuronal Progenitors):H3K36Me3, 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.17481
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP H3K36me3 e3
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library Lib:RI:20101012:11--ChIP:MA:20100927:11:hNP (ES H9 derived Nuronal Progenitors):H3K36Me3 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 64,319,157
FINDPEAKS_SCORE: 0.5731
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.398
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9979
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7198
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neuronal progenitors derived from H9 (WA09) human stem cells; Lib:RI:20101012:11--ChIP:MA:20100927:11:hNP (ES H9 derived Nuronal Progenitors):H3K36Me3

value: Primary Cell Culture

value: ArunA Biomedical, Athens, GA

value: 10 million cells

value: 70 ul bed volume

value: Histone H3K36me3


title: ChIP_R6-2_H3K4me3_8wks_str_rep1_rep2

description: This Sample represents 2 replicates.

value: C57Bl/6 / CBA

value: R6/2 transgenic (Mangiarini et al., Cell 87:493-506,1996)

value: brain striatum

value: 8 weeks

value: H3K4me3 (Millipore, cat 17-614, lot JBC1793805)


title: ChIP-Seq analysis of H3K9me3 in human CD56+ mesoderm cells; DNA_Lib 3197

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 3197
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15380
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15410
****************
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: GSM1112823_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_3197.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3197.hg19.level.1.release.9
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 3197, 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.17315
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,638,106
FINDPEAKS_SCORE: 0.0413
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.6868
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3546
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112823_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K9me3.DNA_Lib_3197.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3197.hg19.level.2.release.9
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 3197, 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.17498
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCM H3K9me3 97
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 3197 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,638,106
FINDPEAKS_SCORE: 0.0413
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.6868
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3546
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

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 3197

value: BioSam 1249

value: mesoderm

value: CD56 mesoderm - 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 1892

value: Cell Line

value: intermediate

value: Male

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: Branson


title: ChIP_WT_H3K4me3_12wks_ctx_rep1_rep2_rep3

description: This Sample represents 3 replicates.

source_name: R6/2 wildtype littermate, cortex, 12 weeks

value: C57Bl/6 / CBA

value: wild type

value: brain cortex

value: 12 weeks

value: H3K4me3 (Millipore, cat 17-614)


title: ChIP_WT_H3K4me3_8wks_str_rep1_rep2

description: This Sample represents 2 replicates.

value: brain striatum

value: 8 weeks

value: H3K4me3 (Millipore, cat 17-614, lot JBC1793805)


title: ECM184

value: R6/2 transgenic (Mangiarini et al., Cell 87:493-506,1996)


title: ChIP-Seq analysis of H3K4me1 in hN cells; Lib:RI:20101012:13--ChIP:MA:20100927:13:hN (ES H9 derived Neurons):H3K4Me1

description:
sample_term_id: CL_0000540
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:13--ChIP:MA:20100927:13:hN (ES H9 derived Neurons):H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8046
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8185
****************
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: GSM772785_BI.H9_Derived_Neuron_Cultured_Cells.H3K4me1.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:13--ChIP:MA:20100927:13:hN (ES H9 derived Neurons):H3K4Me1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuron Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the H9 Derived Neuron Cultured Cells, Library Lib:RI:20101012:13--ChIP:MA:20100927:13:hN (ES H9 derived Neurons):H3K4Me1, 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.17206
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,134,916
FINDPEAKS_SCORE: 0.4328
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4672
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.996
IROC_PERCENTILE: 85
POISSON_SCORE: 0.5632
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772785_BI.H9_Derived_Neuron_Cultured_Cells.H3K4me1.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:13--ChIP:MA:20100927:13:hN (ES H9 derived Neurons):H3K4Me1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuron Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the H9 Derived Neuron Cultured Cells, Library Lib:RI:20101012:13--ChIP:MA:20100927:13:hN (ES H9 derived Neurons):H3K4Me1, 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.17389
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDN H3K4me1 e1
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuron Cultured Cells Histone H3K4me1 Library Lib:RI:20101012:13--ChIP:MA:20100927:13:hN (ES H9 derived Neurons):H3K4Me1 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,134,916
FINDPEAKS_SCORE: 0.4328
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4672
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.996
IROC_PERCENTILE: 85
POISSON_SCORE: 0.5632
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neurons derived from H9 (WA09) human stem cells; Lib:RI:20101012:13--ChIP:MA:20100927:13:hN (ES H9 derived Neurons):H3K4Me1

value: H9 Derived Neuron Cultured Cells

value: genomic DNA

value: >90% beta III tubulin(+) and >60% MAP2(+)

value: Medium:Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions - AB2+ANS+LIF on Matrigel (i.e., differentiation medium)

value: hN (ES H9 derived Neurons)

value: Female

value: Primary Cell Culture

value: ArunA Biomedical, Athens, GA

value: embryo

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: TCM9452

source_name: R6/2, cortex, 12 weeks

value: C57Bl/6 / CBA

value: brain cortex

value: 12 weeks


title: ChIP-Seq analysis of WCE in human hN (ES H9 derived Neurons) cells; Lib EpiLabSPL Row 1693

description:
sample_term_id: CL_0000540
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1693
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7998
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8185
****************
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: GSM772737_BI.H9_Derived_Neuron_Cultured_Cells.Input.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1693-Lib:RI:20101012:18--ChIP:MA:20100927:18:hN (ES H9 derived Neurons):WCE.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuron Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on the H9 Derived Neuron Cultured Cells, Library Lib EpiLabSPL Row 1693, 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.17323
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,220,883
FINDPEAKS_SCORE: 0.0036
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0128
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0625
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772737_BI.H9_Derived_Neuron_Cultured_Cells.Input.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1693-Lib:RI:20101012:18--ChIP:MA:20100927:18:hN (ES H9 derived Neurons):WCE.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuron Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the H9 Derived Neuron Cultured Cells, Library Lib EpiLabSPL Row 1693, 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.17506
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDN Input 93
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuron Cultured Cells ChIP-Seq Input Library Lib EpiLabSPL Row 1693 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,220,883
FINDPEAKS_SCORE: 0.0036
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0128
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0625
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neurons derived from H9 (WA09) human stem cells; Lib EpiLabSPL Row 1693

value: H9 Derived Neuron Cultured Cells

value: genomic DNA

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP_R6-2_H3K4me3_8wks_ctx_rep1_rep2

description: This Sample represents 2 replicates.

value: R6/2 transgenic (Mangiarini et al., Cell 87:493-506,1996)

value: 8 weeks

value: H3K4me3 (Millipore, cat 17-614, lot JBC1793805)


title: ChIP-Seq analysis of WCE in human angular gyrus cells; DNA_Lib 708

description:
sample_term_id: UBERON_0002686
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 708
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8621
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9456
****************
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: GSM772931_BI.Brain_Angular_Gyrus.Input.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 635-DNA_Lib 708.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Brain Angular Gyrus, Donor 149, 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.17305
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,076,686
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.0064
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0428
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772931_BI.Brain_Angular_Gyrus.Input.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 635-DNA_Lib 708.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Brain Angular Gyrus, Donor 149, 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.17488
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BAG Input 49 35
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus ChIP-Seq Input Donor 149 Library DNA_Lib 635 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,076,686
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.0064
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0428
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 708

value: Brain, Angular Gyrus

value: Post-Mortem

value: no AD evident at demise

value: Angular gyrus

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: cell/nuclei lysis

value: Branson


title: ChIP_R6-2_H3K4me3_12wks_str_rep1_rep2

description: This Sample represents 2 replicates.

source_name: R6/2, striatum, 12 weeks

value: C57Bl/6 / CBA

value: brain striatum

value: 12 weeks

value: H3K4me3 (Millipore, cat 17-614)


title: ChIP_WT_H3K4me3_8wks_ctx_rep1_rep2

description: This Sample represents 2 replicates.

source_name: R6/2 wildtype littermate, cortex, 8 weeks

value: wild type

value: brain cortex

value: 8 weeks


title: ChIP-Seq analysis of H3K4me3 in human hNP (ES H9 derived Nuronal Progenitors) cells; Lib EpiLabSPL Row 1695

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1695
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7997
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8184
****************
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: GSM772736_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:08--ChIP:MA:20100927:08:hNP (ES H9 derived Nuronal Progenitors):H3K4Me3-Lib EpiLabSPL Row 1695.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuronal Progenitor Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:08--ChIP:MA:20100927:08:hNP (ES H9 derived Nuronal Progenitors):H3K4Me3, 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.17316
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,455,257
FINDPEAKS_SCORE: 0.4843
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.4824
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4849
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772736_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:08--ChIP:MA:20100927:08:hNP (ES H9 derived Nuronal Progenitors):H3K4Me3-Lib EpiLabSPL Row 1695.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuronal Progenitor Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the H9 Derived Neuronal Progenitor Cultured Cells, Library Lib:RI:20101012:08--ChIP:MA:20100927:08:hNP (ES H9 derived Nuronal Progenitors):H3K4Me3, 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.17499
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP H3K4me3 e3
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuronal Progenitor Cultured Cells Histone H3K4me3 Library Lib:RI:20101012:08--ChIP:MA:20100927:08:hNP (ES H9 derived Nuronal Progenitors):H3K4Me3 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,455,257
FINDPEAKS_SCORE: 0.4843
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.4824
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4849
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neuronal progenitors derived from H9 (WA09) human stem cells; Lib EpiLabSPL Row 1695

value: genomic DNA

value: Medium:Cultured in defined proliferation medium containing AB2+ANS plus FGF2 and LIF on Matrigel-coated surfaces.

value: hNP (ES H9 derived Nuronal Progenitors)

value: Unknown

value: Primary Cell Culture

value: ArunA Biomedical, Athens, GA

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in human hN (ES H9 derived Neurons) cells; Lib EpiLabSPL Row 1690

description:
sample_term_id: CL_0000540
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1690
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7999
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8185
****************
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: GSM772738_BI.H9_Derived_Neuron_Cultured_Cells.H3K9me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:15--ChIP:MA:20100927:15:hN (ES H9 derived Neurons):H3K9Me3-Lib EpiLabSPL Row 1690.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuron Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the H9 Derived Neuron Cultured Cells, Library Lib:RI:20101012:15--ChIP:MA:20100927:15:hN (ES H9 derived Neurons):H3K9Me3, 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.17299
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,237,826
FINDPEAKS_SCORE: 0.0148
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0825
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.8105
IROC_PERCENTILE: 48
POISSON_SCORE: 0.2236
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772738_BI.H9_Derived_Neuron_Cultured_Cells.H3K9me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:15--ChIP:MA:20100927:15:hN (ES H9 derived Neurons):H3K9Me3-Lib EpiLabSPL Row 1690.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuron Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the H9 Derived Neuron Cultured Cells, Library Lib:RI:20101012:15--ChIP:MA:20100927:15:hN (ES H9 derived Neurons):H3K9Me3, 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.17482
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDN H3K9me3 e3
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuron Cultured Cells Histone H3K9me3 Library Lib:RI:20101012:15--ChIP:MA:20100927:15:hN (ES H9 derived Neurons):H3K9Me3 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,237,826
FINDPEAKS_SCORE: 0.0148
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0825
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.8105
IROC_PERCENTILE: 48
POISSON_SCORE: 0.2236
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neurons derived from H9 (WA09) human stem cells; Lib EpiLabSPL Row 1690

value: H9 Derived Neuron Cultured Cells

value: >90% beta III tubulin(+) and >60% MAP2(+)

value: Medium:Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions - AB2+ANS+LIF on Matrigel (i.e., differentiation medium)

value: hN (ES H9 derived Neurons)

value: Female

value: embryo

value: Abcam

value: Histone H3K9me3


title: Brf1 - Input - repeat

status: Public on Jul 17 2013

city: Bethesda

first: Nagarajavel

last: Vivekananthan

state: Maryland

address: 9500 Rockville Pike, Buld 6A/Rm 2A14

department: NICHD

institute: National Institutes of Health

description:
MNase digested DNA
415-input-2

data_processing:
Nucleosomes: For wild type - experiment, ELAND was used to align the reads to the NCBI Saccharomyces cerevisiae genome sequence Build 2.1
Nucleosomes: For wild type repeat sample,  BWA was used to align the reads to Saccharomyces cerevisiae genome sequence
Samples were aligned with either BWA (413-Input, 413-IP, 416-1-Input, 416-1-IP, 415-1-Input, 415-1-IP)  or Bowtie 2 (416-1-Input, 416-3-IP, 415-2-Input, 415-2-IP)  to the Saccharomyces cerevisiae genome sequence (SacCer2).

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium.

extract_protocol:
Nuclei were digested with micrococcal nuclease. Nucleosomes: mono-nucleosomal DNA was gel-purified. IP experiments: DNA was extracted from a fraction of the MNase digest (Input) for paired-end sequencing. The rest of the digest was immunoprecipitated using anti-FLAG antibody and eluted with 3-FLAG peptide (IP) and the DNA was extracted and sequenced.
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

tag: strain

tag: genotype

value: MATalpha ADE2 can1 his3 leu2 lys2delta trp1 ura3 BRF1:3XFLAG:KanMX

tag: antibody


title: Brf1 - IP -repeat

description:
Immuno-purified MNase digested DNA
415-IP-2

value: anti-FLAG


title: ChIP-Seq analysis of H3K27me3 in hN cells; Lib:RI:20101012:16--ChIP:MA:20100927:16:hN (ES H9 derived Neurons):H3K27Me3

description:
sample_term_id: CL_0000540
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20101012:16--ChIP:MA:20100927:16:hN (ES H9 derived Neurons):H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8048
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8185
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For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
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data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772787_BI.H9_Derived_Neuron_Cultured_Cells.H3K27me3.113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:16--ChIP:MA:20100927:16:hN (ES H9 derived Neurons):H3K27Me3.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H9 Derived Neuron Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on the H9 Derived Neuron Cultured Cells, Library Lib:RI:20101012:16--ChIP:MA:20100927:16:hN (ES H9 derived Neurons):H3K27Me3, 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.17224
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,648,054
FINDPEAKS_SCORE: 0.1131
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.1944
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9058
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4146
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772787_BI.H9_Derived_Neuron_Cultured_Cells.H3K27me3.113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:16--ChIP:MA:20100927:16:hN (ES H9 derived Neurons):H3K27Me3.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuron Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the H9 Derived Neuron Cultured Cells, Library Lib:RI:20101012:16--ChIP:MA:20100927:16:hN (ES H9 derived Neurons):H3K27Me3, 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.17407
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDN H3K27me3 e3
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuron Cultured Cells Histone H3K27me3 Library Lib:RI:20101012:16--ChIP:MA:20100927:16:hN (ES H9 derived Neurons):H3K27Me3 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,648,054
FINDPEAKS_SCORE: 0.1131
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.1944
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9058
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4146
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neurons derived from H9 (WA09) human stem cells; Lib:RI:20101012:16--ChIP:MA:20100927:16:hN (ES H9 derived Neurons):H3K27Me3

value: genomic DNA

value: Primary Cell Culture

value: ArunA Biomedical, Athens, GA

value: Protein A-Sepharose 4B

value: Histone H3K27me3


title: Brf1 - Input

description:
MNase digested DNA
415-input-1


title: Tfc1 - IP -repeat

description:
Immuno-purified MNase digested DNA
416-IP-3

value: MATalpha ADE2 his3 leu2 lys2delta trp1 ura3 TFC1:3XFLAG:KanMX


title: Control - IP

description:
Immuno-purified MNase digested DNA
413-IP-1

value: MATalpha ADE2 his3-11 leu2-3,112  lys2delta  trp1-1  ura3-1


title: Tfc1 - Input

description:
MNase digested DNA
416-input-1


title: Tfc1 - Input - repeat

description:
MNase digested DNA
416-input-3


title: Tfc1 - IP

description:
Immuno-purified MNase digested DNA
416-IP-1


title: s04_MCF7_SPDEF_rep1

first: Mauro

middle: Antonio

last: Alves Castro

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

description: In-house id: mf025_MCF7_SPDEF_CRI01

data_processing:
ChIP-Seq reads were aligned to genome build hg18 and filtered by removing reads either with quality less than 5 or overlapping "signal artefact" regions (regions obtained from http://hgdownload-test.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeMapability/). Peaks were called using model-based analysis for ChIP-Seq (MACS) (Zhang et al., Genome Biology, 9(9):R137, 2008), run using default parameters. Quality control of the raw sequenced data was conducted using the FastQC software (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and good quality scores across all bases were observed.
To evaluate the consistency of signal between replicates we measured the read coverage over all genomic regions covering peak regions that were called in at least two of the three replicates. There is a good correlation between pairs of replicates, with Spearman’s correlation coefficients ranging from 0.51 to 0.74
Genome_build: hg18
Supplementary_files_format_and_content: Files produced by MACS that report peak positons, summit and statistics. The files named NAME_peaks.bed are in BED format which contains the peak locations and in the 5th column is the -10*log10pvalue of peak region. The files names NAME_summits.bed is in BED format, which contains the peak summits locations for every peaks, and in the 5th column in this file is the summit height of fragment pileup.

source_name: MCF-7 breast cancer cell line

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10% heat-inactivated foetal calf serum and 1% penicillin-streptomycin.

extract_protocol:
ChIP of DNA was performed as described in Schmidt et al., Methods (2009) doi: 10.1016/j.ymeth.2009.03.001
Illumina sequencing libraries were prepared as described in Schmidt et al., Methods (2009) doi: 10.1016/j.ymeth.2009.03.001

treatment_protocol: Cells growing asynchronously in full media were fixed for ChIP.

tag: cell type

value: MCF-7 breast cancer cell line

value: SPDEF (sc67022; Santa Cruz Biotechnology)

tag: chip treatment conditions

value: Full media


title: s03_MCF7_ER_rep3

description: In-house id: mf006_MCF7_ERa_E2_45min_CRI01

tag: chip antibody

value: ERα (sc543; Santa Cruz Biotechnology)

value: 10nM E2, 45 minutes


title: s06_MCF7_SPDEF_rep3

description: In-house id: mf027_MCF7_SPDEF_CRI01


title: s05_MCF7_SPDEF_rep2

description: In-house id: mf026_MCF7_SPDEF_CRI01


title: s01_MCF7_ER_rep1

description: In-house id: jc780_MCF7_ER_E2_rep1_CRI01


title: EGDe WT Rhamnose-2

city: Bedford Park

first: Joelle

middle: K

last: Salazar

state: IL

address: 6502 S Archer Rd

institute: Illinois Institute of Technololgy

description:
mRNA-seq
purified mRNA

data_processing:
Deep RNA sequencing was conducted on an Illumina HiSeq 2000 instrument (12.5 filter-passed 50 + 50 nt paired-end reads) (Illumina Inc., San Diego, CA).
Reads were mapped to the L. monocytogenes 10403S sequence available at the Broad Institute using GSNAP3.
Gene and transcript expressions were computed using Cufflinks, FPKM.
Quality control of transcripts was performed using FastQC.
Genome_build: Listeria monocytogenes 10403S Supercontig 6.1, Broad Institute
Supplementary_files_format_and_content: GSE47721_Gene_FPMK.txt.gz: Tab-delimited text file includes gene symbols and FPKMs.

organism: Listeria monocytogenes

source_name: Bacterial culture, WT

growth_protocol: L. monocytogenes cultures were grown overnight in BHI at 37°C, washed three times with PBS, and sub-cultured 1:100 into 100-ml phenol-red broth containing rhamnose as the sole carbon source. Bacteria were grown at 37C for 4 h to mid-log phase.

extract_protocol:
Total RNA was extracted using Ambion RiboPure Bacterial Kit (Life Technologies Corporation, Carlsbad, CA). Total RNA from two biological replicates was prepared from independent cultures on different days to ensure the reproducibility of RNA-seq data.
mRNA was purified using the NuGEN Prokaryotic RNA-Seq system (NuGEN, San Carlos, CA).

tag: strain/background

value: EGDe

value: LII

tag: genotype/variation

value: wild-type

tag: carbon source

value: L-rhamnose

tag: media

value: phenol-red broth


title: EGDe 0753 Rhamnose-2

description:
mRNA-seq
purified mRNA

source_name: Bacterial culture, lmo0753 deletion