title: ChIP-Seq analysis of H3K4me1 in human CD34 cells, 30B1DAAXX090508-7-S

status: Public on May 11 2010

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1577
Library name: Solexa-11487
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1578
****************
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: GSM486707_BI.CD34_Primary_Cells.H3K4me1.CD34_39889.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30B1DAAXX090508-7-S-30ELUAAXX090512-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD34 Primary Cells, Donor CD34_39889 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.4796
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5514
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.5216
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.999
IROC_PERCENTILE: 93
POISSON_SCORE: 0.5856
POISSON_PERCENTILE: 63

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

ANALYSIS FILE NAME: GSM486707_BI.CD34_Primary_Cells.H3K4me1.CD34_39889.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30B1DAAXX090508-7-S-30ELUAAXX090512-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD34 Primary Cells, Donor CD34_39889 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.5070
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD34 H3K4me1 89
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells Histone H3K4me1 Donor CD34_39889 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5514
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.5216
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.999
IROC_PERCENTILE: 93
POISSON_SCORE: 0.5856
POISSON_PERCENTILE: 63

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

source_name: ChIP-Seq analysis ofH3K4me1 in human CD34 cells

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

value: genomic DNA

tag: disease

value: FHCRC

value: Primary Cell

value: CD34 Primary Cells

tag: markers

value: Unknown

value: Histone H3K4me1

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Abcam


title: Input_ChIPSeq

status: Public on May 06 2010

type: SRA

city: Chicago

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

country: USA

institute: University of Chicago

description: The sheared, non-precipitated DNA was used as Input control.

library_source: genomic

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.
Peak detection was performed using CCAT (Xu et al., manuscript under revision). The sequence tag density generated from the input library was used as background. Regions enriched in the Ebf1 ChIP sample were identified as peaks. Peaks with FDR <0.01 were considered significant. The peaks data is available in the 'GSE19971_EBF1_mm8_significant.peaks.txt' file, which is linked to the Series GSE19971 record as a supplementary file.

molecule: genomic DNA

organism: Mus musculus

source_name: pre B-cells, input

growth_protocol: RPMI 1640 + 10% fetal calf serum + 4µl/l 2-mercapto-ethanol + penicillin/streptomycin/glutamine, 37°C, 5% CO2.

extract_protocol: 10ng of Ebf1 ChIP material and input DNA, respectively, as per manufacturer's protocol. Briefly, using the Solexa ChIP Seq DNA sample preparation kit, universal linkers were added to the chromatin fragments and DNA was PCR amplified for 15 cycles. DNA was gel-purified and fragments between 200-300bp were selected for sequencing.

treatment_protocol: At a density of 10^6 per ml, the cells were crosslinked with 1% Formaldehyde for 5 minutes at 37°C. The reaction was stopped by the addition of 1/10 volumes of ice cold 1M glycine  solution. Cells were washed three times with ice cold PBS and lysed in 50mM Tris pH 8.0, 5mM EDTA, 1% (w/v) SDS (10^7 cell per ml). The chromatin was sheared to an average size of 500bp by sonication.

tag: cell line

tag: cell type

value: A-MuLV pre B-cells

tag: antibody


title: EBF1_ChIPSeq

description: ChIP was performed using custom-made polyclonal rabbit antibody against murine EBF1b.

source_name: pre B-cells, ChIP


title: Wild type testes

status: Public on May 04 2010

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

library_source: transcriptomic

data_processing: Illumina Genome Analyzer Pipeline version 1.0 produced an output containing sequences in seq and prb formats. First 30 bases of sequences were matched to both the dm3 Drosophila melanogaster genome and a library of (26+26)-nt exon junction sequences using ELAND. Exons sequences were retrieved from Ensembl database (version 50).

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: mRNA from wild-type y,w male fly testis

extract_protocol: polyA RNA purified from total RNA

tag: tissue

value: testis


title: Bam mutant testes

source_name: mRNA from bam[1]/bam[114] mutant males testis


title: pilot4_lane2

status: Public on May 02 2010

city: Wildau

first: Peter

last: Beyerlein

state: Brandenburg

address: Bahnhofstraße 1

department: Bioinformatics

country: Germany

institute: Technische Hochschule Wildau

description:
mRNA from rat dorsal root ganglion
Illumina instrument model used was GA IIx.
Chemical fragmentation of pA-RNA; non-stranded

data_processing:
WIOS (Wildau In-Silico Sequence) Analysis Pipeline  [www.th-wildau.de/bioinformatics/wios] : Read Preprocessing (Quality Check and Read Splitting), Eland Alignment and Read Recombination, Known Gene/Exon/SpliceJunction Expression Estimation, Gene-Level Fold Change Analysis, De-Novo Gene Discovery.

processed data file build: RGSC3.4.50

processed data file types:
*18-cut_right.eland [exon alignment, right fragment]
*32-cut_left.eland [exon alignment, left fragment]
*25-cut_left.eland [splice junction alignment, left fragment]
*25-cut_right.eland [splice junction alignment, right fragment]

organism: Rattus norvegicus

source_name: L4 DRG

extract_protocol: Libraries were prepared according to Mortazavi et al., Nat Meth, 2008 [PMID: 18516045].

treatment_protocol: In vivo pain model -  L5 spinal nerve ligation (SNL) model of neuropathic pain according to Chung et al., Methods Mol Med, 2004

tag: strain

value: Sprague Dawley

tag: protocol

value: pilot


title: pilot4_lane1


title: pilot4_lane3


title: pilot1_lane1


title: 2 months SNL2_lane1

tag: time

value: 2 months

value: L5 SNL


title: U2OS_ERb_DoxyE2_specificAntibody_rep1

status: Public on May 12 2010

city: Emeryville

first: Xiaoyue

last: Zhao

state: CA

address: 5858 Horton St

institute: Bionovo Inc.

description: Chromatin IP against ERbeta

data_processing: Alignment: Sequence reads were obtained and mapped to the human genomes (hg18) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

organism: Homo sapiens

source_name: U2OS cells, ERb vector transfected with Doxycycline added and E2 treatment

extract_protocol: Amplified ChIP DNA samples were prepared utilizing the ChIP-Seq DNA-Sample Prep Kit per manufacturers’ protocol (Illumina, San Diego), with the following modifications. Following gel purification and clean-up of the adapter ligated ChIP DNAs, PCR amplification was performed as described for 20 cycles. Final amplified ChIP DNA libraries were analyzed using the Experion capillary electrophoresis system and 1K DNA chips (Bio-Rad, Hercules).

tag: chip antibody

value: ER beta


title: pilot2_lane1


title: 2 months SNL1_lane1


title: pilot3_lane1


title: Bam mutant ovaries

source_name: mRNA from bam[1]/bam[delta86] mutant female ovaries

value: ovary


title: ChIP-Seq analysis of H3K9me3 in human hES I3 TESR cells; 30DRPAAXX090625-2-S

status: Public on May 03 2010

city: Cambridge

state: MA

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12683/Solexa-16494
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2182
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2181
****************
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: GSM537625_BI.ES-I3.H3K9me3.Solexa-12683-16494.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DRPAAXX090625-2-S-42NF9AAXX091210-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the ES-I3 Cell Line, Library Solexa-12683-16494 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.4769
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0695
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.0703
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.5427
IROC_PERCENTILE: 3
POISSON_SCORE: 0.2905
POISSON_PERCENTILE: 14

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

ANALYSIS FILE NAME: GSM537625_BI.ES-I3.H3K9me3.Solexa-12683-16494.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DRPAAXX090625-2-S-42NF9AAXX091210-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-12683-16494 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.5043
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K9me3 94
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K9me3 Library Solexa-12683 and Solexa-16494 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0695
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.0703
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.5427
IROC_PERCENTILE: 3
POISSON_SCORE: 0.2905
POISSON_PERCENTILE: 14

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

source_name: I3(eye three) stem cells; 30DRPAAXX090625-2-S

value: genomic DNA

value: Harvard University

value: Cell Line

tag: line

value: hES I3 TESR

tag: lineage

value: embrionic stem cell

value: undifferentiated

tag: passage

tag: medium

value: TESR

tag: Sex

value: Female

tag: batch

value: Histone H3K9me3


title: Wild type ovaries

source_name: mRNA from wild-type y,w female fly ovary


title: E18.5 wild type LIVER   small RNA

city: cold spring harbor

first: sihem

last: cheloufi

address: 1 bungtown road

institute: Cold spring harbor laboratory

data_processing:
The 3' linker (CTGTAGGCACCATCAATCGTATGCCGTCTTCTGCTTG) was clipped from the sequences, which are then collapsed and mapped perfectly to the mouse genome. Annotation tracks (RefSeq genes, miRBase miRNAs and RepeatMasker) were used to assign annotations to mapped sequences.
All of the processed data for both Samples are available in a single 'combined_annotations.txt' file on the Series record.

molecule: total RNA

source_name: fetal liver

extract_protocol: Total RNA was isolated from fetal livers with Trizol, then separated PAGE to obtain a small RNA fraction ranging from 19 to 30 nt. Adapters for Solexa sequencing were ligated, then the ligated product amplified by RT-PCR. The PCR product is gel-purified for sequencing

value: liver

tag: developmental stage

tag: genotype/variation

value: wild type


title: E18.5 Ago2 catalytically   inactive LIVER small RNA


title: 2 months CONTROL2_lane1

value: CONTROL

value: Sprague Dawley


title: 2 weeks SNL2_lane4

value: 2 weeks


title: 2 months CONTROL1_lane1

value: 2 months


title: 2 weeks SNL2_lane3

value: L5 SNL


title: 2 weeks SNL2_lane2


title: Richland (I/I, yellow seed) immature seed coats

status: Public on May 14 2010

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

description: Sample 1 Richland immature seed coats

data_processing: Sequence information was extracted from the image files with the Illumina Firecrest and Bustard applications. Adapter trimming was performed using the first occurrences of substring TCG as the unique identifier for the beginning of the adapter (TCGTATGCCGTCTTCTGCTTG). The sizes of the small RNAs after adapter trimming ranged from 14-33 nt with the majority in the range of 19-24 nucleotides. Adapter trimmed sequences were compared to obtain the number of unique sequences and occurrences of each.  Sequences with less than a minimum count were removed as possible artifacts and to reduce the computational cost for subsequent data processing steps. In the processed files, the minimum count was set to 5 in the Richland yellow seed coat, Williams yellow seed coat, and Williams cotyledon libraries that have total read count of approximately 3 million raw reads and set to 10 for the Williams black seed coat library with 6 million reads.

organism: Glycine max

source_name: immature seed coats

growth_protocol: Plants were grown in the greenhouse and seeds harvested from at least four plants of each isoline. Seed coats and cotyledons were dissected from seeds at varying stages of development based on the fresh weight of the entire seed. Dissected seed coats and cotyledons from seeds of the 50-75 mg weight range were fast frozen in liquid nitrogen. All tissues were stored at -70°C till further use.

extract_protocol: See Tuteja et al., (2009) Plant Cell Plant Cell 21:3063-3077 (PMID: 19820189) for details of small RNA extraction and enrichment.   Gel purification, cloning and sequencing of small RNAs were performed at Illumina Inc. (San Diego, CA) using the SBS (sequencing by synthesis) technology. Briefly, 2.5 – 5 ug of the purified LMW RNA fraction of each of the four samples was provided to Illumina, which after quality checks, was separated on 15% polyacrylamide gels containing 7 M urea in TBE buffer (45 mM Tris-borate, pH 8.0, and 1.0 mM EDTA). A gel slice containing RNAs of 15 to 35 nucleotides was excised and eluted. Gel-purified small RNAs were ligated to the 3’ adapter (TCGTATGCCGTCTTCTGCTTG), and the small RNA libraries sequenced using the Illumina Genome Analyzer. Sequence information was extracted from the image files with the Illumina Firecrest and Bustard applications.

treatment_protocol: optimal greenhouse growth conditions

tag: cultivar

value: Richland

tag: genotype

value: homozygous for dominant I allele at the I locus controlling seed color

tag: tissue and developmental stage

value: immature seed coats dissected from seeds of 50-75 mg fresh weight


title: Williams (i-i/i-i yellow seed) immature cotyledons

description: Sample 3 Williams immature cotyledons

source_name: immature cotyledons

value: Williams

value: homozygous for the dominant i-i allele that specifies yellow seed coat with pigmented hilum

value: immature cotyledons dissected from seeds of 50-75 mg fresh weight


title: Williams (i-i/i-i yellow seed) immature seed coats

description: Sample 2 Williams immature seed coats


title: Williams 55 (i/i, pigmented seed) immature seed coats

description: Sample 4 Williams mutant 55, pigmented seed coats

value: Williams, mutant 55

value: a Williams isogenic line homozygous for the recessive i allele that specifics pigmented seed coats


title: 2 weeks SNL2_lane1


title: 2 weeks SNL1_lane3


title: 2 weeks SNL1_lane2

data_processing:
WIOS (Wildau In-Silico Sequence) Analysis Pipeline  [www.th-wildau.de/bioinformatics/wios] : Read Preprocessing (Quality Check and Read Splitting), Eland Alignment and Read Recombination, Known Gene/Exon/SpliceJunction Expression Estimation, Gene-Level Fold Change Analysis, De-Novo Gene Discovery.

processed data file build: RGSC3.4.50

processed data file types:
*18-cut_right.eland [exon alignment, right fragment]
*32-cut_left.eland [exon alignment, left fragment]
*1_25-cut_left.eland [splice junction alignment, first half, left fragment]
*1_25-cut_right.eland [splice junction alignment, first half, right fragment]
*2_25-cut_left.eland [splice junction alignment, second half, left fragment]
*2_25-cut_right.eland [splice junction alignment, second half, right fragment]


title: 2 weeks SNL1_lane1


title: 2 weeks CONTROL2_lane1


title: 2 weeks CONTROL1_lane3


title: 2 weeks CONTROL2_lane3


title: 2 weeks SNL1_lane4


title: p53-/- HCT116 40 Hrs

status: Public on May 01 2010

city: Worcester

first: Michael

middle: R.

last: Green

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

description: p53-/- human colorectal HCT116 cell lines was stably transduced with a short hairpin RNA (shRNA) library encoded by lentiviruses

data_processing: Illumina Genome analyzer pipeline, text file poste filtering, alignment and clustering

source_name: Lentiviruses integrated in genomic DNA

growth_protocol:
The Open Biosystems pGIPZ lentiviral  shRNA library was obtained through the University of Massachusetts Medical School shRNA library core facility.  Twelve lentiviral pools, each comprising ~5000 shRNA clones, were generated with titers of ~2.106 pfu/ml. These lentiviral stocks were produced following co-transfection with the packaging mix into the 293T packaging cell line.

HCT116 WT and and HCT116 P53-/- were plated at 1 Million cells per 100mm plate and transduced the next day with one pool/plate of ShRNA lentivirus library at a MOI of 1. Forty hours after transfection 75% of the cells were fluorescent and each plate was split in two. Half of the cells were transferred in 150mm plates for further growth while the remaining part was pooled and the genomic DNA was extracted, and the purified DNA provided the early reference point for HCT116 WT and HCT116 P53-/- transduced populations.  The remaining cells were passaged by four-fold dilutions in the 150mm plates for 10 days at which point the cells were pooled and the genomic DNA was extracted for the two cell lines. This provided the end point for HCT116 WT and HCT116 P53-/- transduced populations.

extract_protocol:
Genomic DNA was extracted by sequential proteinase K treatment, phenol/chloroform extraction and spooling after addition of 2 volumes of ethanol.

To analyze the frequency of individual lentiviruses in the four populations, 72ug of genomic DNA was used as substrate (split in 24 tubes) and amplified for 15 cycles with GIPZF (GAGTTTGTTTGAATGAGGCTTCAGTAC) and GIPZHR (CGCGTCCTAGGTAATACGAC) primers. The PCR product was gel purifed and 50 ng was used as substrate for a second 15 cycles PCR with Forward Acu1 primer (AMN5¹-CAACAGAAGGCTCCTGAAGGTATATTGCTGTTGA) and Reverse Acu 1 primer (AMN5¹-AAATTTAAACTGAAGTACATCTGTGGCTTCACTA); One ug of the PCR product was digested to completion with Acu 1 (New England Biolabs) according to the manufacturer instructions. The digested product was ligated to the following pre-annealed adapters: L1ShSolexA/5bio/-ACACTCTTTCCCTACACGACGCTCTTCCGATCTCA L1ShSolexB/5Phos/-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT/3AmM and L2ShSolexB/5Phos/-AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG/3BIO/L2ShSolexA/5AmMC6/-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCTAC.  The product of the 3 way ligation was run on a 3% TAE agarose gel, visualized with ethidium bromide, purified and used as a substrate for a 15 cycle PCR reaction using Illumina primers 1.1 and 2.1 as recommended by the manufacturer.

tag: cell line

value: P53 deficient human colorectal HCT116


title: p53-/- HCT116 10 days

institute: University of Massachusetts Medical School


title: p53+/+ HCT116 40 Hrs

description: p53+/+ human colorectal HCT116 cell lines was stably transduced with a short hairpin RNA (shRNA) library encoded by lentiviruses

value: P53 wild type human colorectal HCT116


title: 2 weeks CONTROL1_lane2


title: Wild type soybean seed

city: St. Louis

first: Eliot

middle: Mark

last: Herman

state: MO

address: 975 N. Warson Rd

department: Plant Genetics  Research

institute: USDA/ARS

data_processing: Sequence reads were obtained and mapped to the Soybean gene index GMGI version 14 (http://compbio.dfci.harvard.edu/cgi-bin/tgi/gimain.pl?gudb=soybean) with the BOWTIE aligner ver 0.9.9.3 (Langmead et al 2009) with default parameters.

source_name: Seed

growth_protocol: Greenhouse grown plants

extract_protocol: Libraries were prepared according to Illumina's instructions, Following second strand synthesis, end repair, and A-tailing, adapters complementary to sequencing primers were ligated to cDNA fragments (mRNA-Seq Sample Prep Kit, Illumina, San Diego, CA, USA).

tag: age

value: midmaturation

tag: tissue

value: seed

tag: sample type


title: 2 weeks CONTROL2_lane2

tag: time

tag: protocol

value: CONTROL

tag: strain


title: p53+/+ HCT116 10 days


title: SP- soybean seed

value: SP-


title: 2 weeks CONTROL1_lane1

value: 2 weeks

value: Sprague Dawley


title: MLF_RNASeq

first: Mitchell

last: Guttman

address: 7 Cambridge Center

description: RNASeq of polyA+ RNA from ATCC Lung fibroblasts

data_processing: Reads were aligned against build mm9 using TopHat v1.0.13.

source_name: Mouse Lung Fibroblasts

growth_protocol: Mouse embryonic stem cells (V6.5) were co-cultured with irradiated MEFs (GlobalStem; GSC-6002C) on 0.2% gelatin coated plates in a culture media consisting of Knockout DMEM (Invitrogen; 10829018) containing 10% FBS (GlobalStem; GSM-6002), 1% pen-strep 1% Non-essential amino acids, 1% L-glutamine, 4ul Beta-mercaptoethanol, and .01% LIF (Millipore; ESG1106). mES cells were passaged once on gelatin without MEFs before RNA extraction. V6.5 ES cells were differentiated into neural progenitor cells (NPCs) through embryoid body formation for 4 days and selection in ITSFn media for 5–7 days, and maintained in FGF2 and EGF2 (R&D Systems) as described27. The cells uniformly express nestin and Sox2 and can differentiate into neurons, astrocytes and oligodendrocytes. Mouse lung fibroblasts (ATCC), were grown in DMEM with 10% fetal bovine serum and penicillin/streptomycin at 37°, 5% CO2.

extract_protocol:
RNA was extracted using the protocol outlined in the RNeasy kit (Qiagen).  Extracts were treated with DNase (Ambion 2238).  Polyadenylated RNAs was selected using Ambion’s MicroPoly(A)Purist kit (AM1919M) and RNA integrity confirmed using Bioanalyzer (Agilent). A ‘regular’ RNA sequencing library (non strand specific) was created as previously described, with the following modifications.
250 ng of polyA+ RNA was fragmented by heating at 98°C for 33 minutes in 0.2 mM sodium citrate, pH 6.4 (Ambion).  Fragmented RNA was mixed with 3 μg random hexamers, incubated at 70°C for 10 minutes, and placed on ice briefly before starting cDNA synthesis.  First strand cDNA synthesis was performed using Superscript III (Invitrogen) for 1 hour at 55°C, and second strand using E. coli DNA polymerase and E. coli DNA ligase at 16°C for 2 hours.  cDNA was eluted using Qiagen MiniElute kit with 30ul EB buffer.  DNA ends were repaired using dNTPs and T4 polymerase, (NEB) followed by purification using the MiniElute kit.  Adenine was added to the 3’ end of the DNA fragments to allow adaptor ligation using dATP and Kelnow exonuclease (NEB; M0212S) and purified using MiniElute.  Adaptors were ligated and incubated for 15 minutes at room temperature.  Phenol/choloform/isoamyl alcohol (Invitrogen 15593-031) extraction followed to remove the DNA ligase.  The pellet was then resuspend in 10ul EB Buffer.
The sample was run on a 3% Agarose gel (Nusieve 3:1 Agarose) and a 160 - 380 base pair fragment was cut out and extracted.  PCR was performed with Phusion High-Fidelity DNA Polymerase with GC buffer (New England Biolabs) and 2M Betaine (Sigma).  [PCR conditions: 30 sec at 98°C, (10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C -16 cycles) 5 min at 72°C, forever at 4°C], and products were run on a poly-acrylamide gel for 60 minutes at 120 volts. The PCR products were cleaned up with Agencourt AMPure XP magnetic beads (A63880) to completely remove primers and product was submitted for Illumina sequencing.

value: lung

tag: cell type

value: fibroblasts


title: ESC_RNASeq

description: RNASeq of polyA+ RNA from V6.5 embryonic stem cells

source_name: Embyonic stem cells

value: embryonic stem cells


title: NPC_RNASeq

description: RNASeq of polyA+ RNA from neural progenitor cells, derived from V6.5 embryonic stem cells

source_name: Neural progenitor cells

value: neuronal precursor cells


title: Rsc8_Tap_IP_7-25-09

city: Cold Spring Harbor

first: Jude

last: Kendall

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Reads were mapped to the Saccharomyces cerevisiae genome sequence downloaded from the Saccharomyces Genome Database website (http://www.yeastgenome.org/) on 30 June 2009.  Reads were mapped with the MAQ mapping software from http://maq.sourceforge.net/ using default parameters.  We loaded the data into a database where both sides of the pair were rated 18, mapped to the same chromosome, faced each other and were within 250 bp of each other.  For each good pair the chromosome number and the start and end position on the chromosome was loaded into the database.

Paired end sequence statistics are as follows:
mean insert length = 127
stdev insert length = 44

organism: Saccharomyces cerevisiae

source_name: Chromatin immunoprecipitation of Rsc8 on MN treated chromatin

growth_protocol: Cells were grown exponentially for at least 16 h at 30 °C to OD 0.5-0.9 prior to harvesting.  Cells were fixed formaldehyde at a final concentration at 0.5% for 30 minute.  The fixing reaction was stopped by addition of glycine at a final concentration of 0.125 M.  Cells were spun down washed with H2O and then frozen at -20 °C.

extract_protocol: 100 ml yeast cell culture (after being spun down and frozen) was resuspended in 500 µl of FA lysis buffer without EDTA: 50 mM Hepes-KOH (pH 7.5), 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate.  The resuspended cells were sonicated twice for 10 s using a Branson Sonifier 250 equipped with a micro tip with the output set at 4.  Cell debris was then spun down and the chromatin supernatant transferred to a new tube.  A total of 26 µl was then distributed to 8 separate tubes, and 120 µl of FA lysis buffer without EDTA was added.  To each tube, 10 µl of a micrococcal nuclease solution in H2O was added at a range of concentrations from 4 U to 0.00098 U in a 4-fold dilution series; one tubes had no nuclease.  The reaction was started by adding 5.6 µl of 2 mM CaCl2 to each tube.  The reactions were incubated for 1.5 h at 37 °C and stopped by the addition of 8.8 µl of 0.5 M EDTA each.  Ten microliters of a solution containing 200 mM Tris (pH 7.4), 4 M NaCl, and 0.2 µl of Protease K (recombinant, Roche) were added to each tube, followed by incubation at 42 °C for 1 h and at 65 °C for at least 4 h.  This procedure was performed for 4 separate 100 ml yeast cell culture samples from the same 400 ml yeast harvest.  The four separate samples for each of the eight levels of MN digest were pooled together.  The tube that corresponded to the 0.0625 U MN was then used in the immunoprecipitation reaction.  100 µl of IgG Sepherose (GE Healthcare) was added to the chromatin and incubated for 1 hr.  Beads were then washed twice with TSE-150 (1% Triton X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris-HCL pH 8.1, 150 mM NaCl) once with LiCl/Detergent (0.25 M LiCl, 1% NP-40, 1% Sodium Deooxycholate, 1 mM EDTA, 10mM Tris-HCl, pH 8.1) and twice in TE.  DNA was eluted with Elution Buffer (1% SDS and 0.1M NaHCO3) followed by addition of 0.5 µl proteinase K (Roche) NaCl 0.2 M, Tris 4 mM pH 7.5 (final concentration) incubated at 42ºC for one hour and 65ºC overnight.  DNA was then cleaned up using QIAquick 96 well plates as per manufacturers instructions (QIAGEN Inc.).  This purified DNA was then used for Illumina sequencing.

tag: genome/variation

value: MATa his3D1 leu2D0 met15D0 ura3D0 rsc8-TAP::HIS3MX6

tag: growth temperature


title: rsc3_25C_B_7-25-09

data_processing:
Reads were mapped to the Saccharomyces cerevisiae genome sequence downloaded from the Saccharomyces Genome Database website (http://www.yeastgenome.org/) on 30 June 2009.  Reads were mapped with the MAQ mapping software from http://maq.sourceforge.net/ using default parameters.  We loaded the data into a database where both sides of the pair were rated 18, mapped to the same chromosome, faced each other and were within 250 bp of each other.  For each good pair the chromosome number and the start and end position on the chromosome was loaded into the database.

Paired end sequence statistics are as follows:
mean insert length = 96
stdev insert length = 33

source_name: MN digest of rsc3-1 at the permisive tempurature 25C

growth_protocol: Cells were grown exponentially for at least 16 h at 25 °C to OD 0.5-0.9 prior to harvesting.  Cells were fixed formaldehyde at a final concentration at 0.5% for 1 minute.  The fixing reaction was stopped by addition of glycine at a final concentration of 0.125 M.  Cells were spun down washed with H2O and then frozen at -20 °C.

extract_protocol: 100 ml yeast cell culture (after being spun down and frozen) was resuspended in 500 µl of FA lysis buffer without EDTA: 50 mM Hepes-KOH (pH 7.5), 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate.  The resuspended cells were sonicated twice for 10 s using a Branson Sonifier 250 equipped with a micro tip with the output set at 4.  Cell debris was then spun down and the chromatin supernatant transferred to a new tube.  A total of 26 µl was then distributed to 8 separate tubes, and 120 µl of FA lysis buffer without EDTA was added.  To each tube, 10 µl of a micrococcal nuclease solution in H2O was added at a range of concentrations from 4 U to 0.00098 U in a 4-fold dilution series; one tubes had no nuclease.  The reaction was started by adding 5.6 µl of 2 mM CaCl2 to each tube.  The reactions were incubated for 1.5 h at 37 °C and stopped by the addition of 8.8 µl of 0.5 M EDTA each.  Ten microliters of a solution containing 200 mM Tris (pH 7.4), 4 M NaCl, and 0.2 µl of Protease K (recombinant, Roche) were added to each tube, followed by incubation at 42 °C for 1 h and at 65 °C for at least 4 h.  This procedure was performed for 10 separate 100 ml yeast cell culture samples from the same 1 L yeast harvest.  The ten separate samples for each of the eight levels of MN digest were pooled together and the DNA was isolated using QIAquick (QIAGEN).  Each of the eight levels of MN digest was then measured by QPCR at a known hypersensitive site (-491 to -436 in the GAL1 promoter using oligos: CAGTAATACGCTTAACTGCTCAT and TCGGCGGCTTCTAATCCGT).  The level of MN digest that reduced the DNA concentration by greater then 2 fold was then used for Illumina sequencing.  For this case that was 0.0625 U MN.

value: MATa his3D1 leu2D0 met15D0 ura3D0 rsc3-1::KanMX


title: MDEC_DMSO-preexposed_rep1 [ChIP-seq]

status: Public on Apr 29 2010

city: Columbus

first: Pei-Yin

last: Hsu

address: BRT836, 460W 12th Ave

institute: OSU

description:
Sample JW21
Chromatin IP against Pol II
JW21-lane-1
JW21-lane-2

data_processing: After extracting raw data from the Sequencer, the number of reads sequenced within non-overlapping kilobase-sized bins was modeled using a normal approximation to a Poisson distribution with mu equal to the mean number of reads per bin (excluding unsampled bins). Modeling was performed on a per-chromosome basis. Enrichment scores were calculated for each bin as 10p(x<=X), giving a score with a range from zero (no probability of binding) to 10 (100% probability of binding).

source_name: mammosphere-derived epithelial cells from #67 patient

extract_protocol: Lysates were clarified from sonicated nuclei and Pol II-DNA complexes were isolated with antibody.  RNA Polymerase II ChIP Ab is from Santa Cruz (sc-899X). We use 10 ng per IP. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: patient

value: reduction mammoplasty patient #67

value: mammosphere-derived epithelial cells (MDECs)

value: DMSO-preexposed

tag: chip antibody

value: RNA Polymerase II (Santa Cruz, sc-899X, 10 ng per IP)


title: MCF-7_DMSO_4 hr [ChIP-seq]

description:
Sample JW01
Chromatin IP against Pol II
JW01-lane-1
JW01-lane-2

source_name: ATCC MCF-7 cells

value: MCF-7 breast cancer cell line

value: DMSO stimulation


title: MCF-7_E2_4 hr [ChIP-seq]

description:
Sample JW02
Chromatin IP against Pol II
JW02-lane-1

value: E2 stimulation


title: MDEC_E2-preexposed_rep1 [ChIP-seq]

description:
Sample JW20
Chromatin IP against Pol II
JW20-lane-1
JW20-lane-2


title: MDEC_E2-preexposed_rep2 [ChIP-seq]

description:
Sample JW23
Chromatin IP against Pol II
JW23-lane-1
JW23-lane-2

source_name: mammosphere-derived epithelial cells from #68 patient

value: reduction mammoplasty patient #68


title: MDEC_DMSO-preexposed_rep2 [ChIP-seq]

description:
Sample JW22
Chromatin IP against Pol II
JW22-lane-1
JW22-lane-2


title: G428T

status: Public on Apr 28 2010

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description:
5' monophosphate dependent small RNA cloning
ggg

data_processing: frequencies of  known and novel miRNAs expressed in human cervical cancer tissues and matched normal tissues calculated (see Series record)

source_name: cervical cancer

growth_protocol: not applicable

extract_protocol: Small RNA isolation was performed using mirVana miRNA isolation kit (Applied Biosystems/Ambion, Austin, TX). Purified small RNAs were ligated to the 3’-adaptor [“Linker-1”, IDT Inc., Coralville, IA] and 5’ adaptor [5’-ACGCTCTTCCGATCTv-3’ (uppercase, DNA; v=barcodes with triple RNA molecules: aaa, ggg, ccc or uuu; IDT Inc., Coralville, IA)] oligonucleotides. Products from the second ligation were gel-purified and reverse transcribed using the RT primer [5'-ATTGATGGTGCCTACAG-3’]. cDNA was amplified with 16-20 PCR cycles, using a forward primer 5'- GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3' and a reverse primer 5’-CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC TAT TGA TGG TGC CTA CAG-3', to produce sequencing libraries that were subjected to Solexa/Illumina sequencing platform.

treatment_protocol: not applicable

tag: diagnosis

value: squamous cell carcinoma

value: tumor


title: G612T

description:
5' monophosphate dependent small RNA cloning
uuu


title: G428N

description:
5' monophosphate dependent small RNA cloning
aaa

source_name: normal cervix

value: normal

value: normal cervix


title: ChIP-Seq analysis of H3K36me3 in human hiPS-20b cells; 61GKJAAXX100226-8-S

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20763
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2528
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2304
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537704_BI.iPS-20b.H3K36me3.Solexa-20763.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the iPS-20b Cell Line, Library Solexa-20763 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.4730
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2346
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.2405
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9757
IROC_PERCENTILE: 61
POISSON_SCORE: 0.4806
POISSON_PERCENTILE: 41

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

ANALYSIS FILE NAME: GSM537704_BI.iPS-20b.H3K36me3.Solexa-20763.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the iPS-20b Cell Line, Library Solexa-20763 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.5004
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS20b H3K36me3 63
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K36me3 Library Solexa-20763 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2346
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.2405
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9757
IROC_PERCENTILE: 61
POISSON_SCORE: 0.4806
POISSON_PERCENTILE: 41

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

source_name: IPS cell line 20b; 61GKJAAXX100226-8-S

value: induced pluripotent stem cells 20b

tag: molecule

value: genomic DNA

tag: disease

value: Harvard University

value: Cell Line

tag: line

tag: lineage

value: induced pluripotent cells

value: undifferentiated

tag: passage

tag: medium

value: KSR

tag: Sex

value: Male

tag: batch

value: Histone H3K36me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Abcam


title: ChIP-Seq analysis of WCE in human hiPS-20b cells; 30EDWAAXX090225-2-S

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-10232
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2525
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2298
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537701_BI.iPS-20b.Input.Solexa-10232.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDWAAXX090225-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-20b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS-20b Cell Line, Library Solexa-10232 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.4747
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0122
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.071
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.1176
IROC_PERCENTILE: 19
POISSON_SCORE: 0.1286
POISSON_PERCENTILE: 6

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

ANALYSIS FILE NAME: GSM537701_BI.iPS-20b.Input.Solexa-10232.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDWAAXX090225-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS-20b Cell Line, Library Solexa-10232 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.5021
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS20b Input 32
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line ChIP-Seq Input Library Solexa-10232 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0122
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.071
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.1176
IROC_PERCENTILE: 19
POISSON_SCORE: 0.1286
POISSON_PERCENTILE: 6

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

source_name: IPS cell line 20b; 30EDWAAXX090225-2-S

value: ChIP-Seq Input

value: Input

value: standard


title: ChIP-Seq analysis of H3K27me3 in human hiPS-20b cells; 42LRVAAXX091010-2-S

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-15159
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2524
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2298
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537700_BI.iPS-20b.H3K27me3.Solexa-15159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LRVAAXX091010-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the iPS-20b Cell Line, Library Solexa-15159 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.4660
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1297
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2299
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.8636
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3789
POISSON_PERCENTILE: 21

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

ANALYSIS FILE NAME: GSM537700_BI.iPS-20b.H3K27me3.Solexa-15159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LRVAAXX091010-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the iPS-20b Cell Line, Library Solexa-15159 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.4934
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS20b H3K27me3 59
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K27me3 Library Solexa-15159 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1297
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2299
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.8636
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3789
POISSON_PERCENTILE: 21

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

source_name: IPS cell line 20b; 42LRVAAXX091010-2-S

value: induced pluripotent stem cells 20b

value: genomic DNA

value: Histone H3K27me3

value: Millipore


title: ChIP-Seq analysis of H3K4me3 in human CD15 cells; 42NF9AAXX091210-3-S

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: Solexa-16495
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2526
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
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537702_BI.CD15_Primary_Cells.H3K4me3.23.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42NF9AAXX091210-3-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD15 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.4687
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.7919
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.7312
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.7987
POISSON_PERCENTILE: 97

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

ANALYSIS FILE NAME: GSM537702_BI.CD15_Primary_Cells.H3K4me3.23.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42NF9AAXX091210-3-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD15 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.4961
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD15 H3K4me3 23.0
BROWSER_TRACK_DESCRIPTION: BI CD15 Primary Cells Histone H3K4me3 Donor 23.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.7919
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.7312
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.7987
POISSON_PERCENTILE: 97

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

source_name: flow sorted CD15+ cells from cord blood; 42NF9AAXX091210-3-S

value: FHCRC

value: Primary Cell

value: CD15 Primary Cells

tag: markers

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K27me3 in human CD15 cells; 42NF9AAXX091210-5-S

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: Solexa-16496
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2527
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
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537703_BI.CD15_Primary_Cells.H3K27me3.23.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42NF9AAXX091210-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD15 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 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.4681
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.3321
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.3763
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9779
IROC_PERCENTILE: 88
POISSON_SCORE: 0.5813
POISSON_PERCENTILE: 90

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

ANALYSIS FILE NAME: GSM537703_BI.CD15_Primary_Cells.H3K27me3.23.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42NF9AAXX091210-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD15 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 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.4955
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD15 H3K27me3 23.0
BROWSER_TRACK_DESCRIPTION: BI CD15 Primary Cells Histone H3K27me3 Donor 23.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.3321
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.3763
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9779
IROC_PERCENTILE: 88
POISSON_SCORE: 0.5813
POISSON_PERCENTILE: 90

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

source_name: flow sorted CD15+ cells from cord blood; 42NF9AAXX091210-5-S

value: Male

value: SDS lysis

value: Upstate


title: G603N

description:
5' monophosphate dependent small RNA cloning
ccc

value: normal

tag: tissue

value: normal cervix


title: ChIP-Seq analysis of WCE in human hiPS-15b cells; 42LWTAAXX091016-2-S

description:
sample_term_id: NTR_0001162
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-15157
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2520
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2297
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537696_BI.iPS-15b.Input.Solexa-15157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LWTAAXX091016-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-15b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS-15b Cell Line, Library Solexa-15157 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.4625
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0067
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: NA
IROC_SCORE: 0.5452
IROC_PERCENTILE: 35
POISSON_SCORE: 0.5706
POISSON_PERCENTILE: 99

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

ANALYSIS FILE NAME: GSM537696_BI.iPS-15b.Input.Solexa-15157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LWTAAXX091016-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-15b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS-15b Cell Line, Library Solexa-15157 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.4899
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS15b Input 57
BROWSER_TRACK_DESCRIPTION: BI iPS-15b Cell Line ChIP-Seq Input Library Solexa-15157 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0067
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: NA
IROC_SCORE: 0.5452
IROC_PERCENTILE: 35
POISSON_SCORE: 0.5706
POISSON_PERCENTILE: 99

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

source_name: IPS cell line 15b; 42LWTAAXX091016-2-S

value: Harvard University

value: Cell Line

value: induced pluripotent cells

value: undifferentiated

value: KSR

tag: sex

value: Female

value: Bioruptor


title: G001N


title: G603T

value: squamous cell carcinoma

value: tumor


title: G531N


title: G612N


title: G243T


title: G243N


title: G001T


title: G531T


title: G013N


title: G013T


title: ChIP-Seq analysis of H3K4me3 in human hiPS-11a cells; 30H2EAAXX090521-7-S

description:
sample_term_id: NTR_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-11733
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2518
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2560
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537694_BI.iPS-11a.H3K4me3.Solexa-11733.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H2EAAXX090521-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-11a Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the iPS-11a Cell Line, Library Solexa-11733 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.4643
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3281
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3159
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3582
POISSON_PERCENTILE: 21

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

ANALYSIS FILE NAME: GSM537694_BI.iPS-11a.H3K4me3.Solexa-11733.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H2EAAXX090521-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-11a Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the iPS-11a Cell Line, Library Solexa-11733 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.4917
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS11a H3K4me3 33
BROWSER_TRACK_DESCRIPTION: BI iPS-11a Cell Line Histone H3K4me3 Library Solexa-11733 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3281
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3159
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3582
POISSON_PERCENTILE: 21

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

source_name: IPS cell line 11a; 30H2EAAXX090521-7-S

value: genomic DNA

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Millipore


title: ChIP-Seq analysis of WCE in human hiPS-11a cells; 30H2EAAXX090521-8-S

description:
sample_term_id: NTR_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-11734
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2517
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2560
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537693_BI.iPS-11a.Input.Solexa-11734.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H2EAAXX090521-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-11a Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS-11a Cell Line, Library Solexa-11734 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.4693
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0092
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.0606
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9934
IROC_PERCENTILE: 94
POISSON_SCORE: 0.1553
POISSON_PERCENTILE: 7

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

ANALYSIS FILE NAME: GSM537693_BI.iPS-11a.Input.Solexa-11734.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H2EAAXX090521-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-11a Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS-11a Cell Line, Library Solexa-11734 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.4967
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS11a Input 34
BROWSER_TRACK_DESCRIPTION: BI iPS-11a Cell Line ChIP-Seq Input Library Solexa-11734 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0092
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.0606
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9934
IROC_PERCENTILE: 94
POISSON_SCORE: 0.1553
POISSON_PERCENTILE: 7

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

source_name: IPS cell line 11a; 30H2EAAXX090521-8-S

value: Male

value: ChIP-Seq Input

value: SDS lysis

value: Input

value: standard


title: ChIP-Seq analysis of H3K9ac in human hiPS-15b cells; 61BWEAAXX100226-7-S

description:
sample_term_id: NTR_0001162
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20747
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2516
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2300
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537692_BI.iPS-15b.H3K9ac.Solexa-20747.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-15b Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the iPS-15b Cell Line, Library Solexa-20747 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.4753
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0774
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.1426
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9433
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3531
POISSON_PERCENTILE: 43

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

ANALYSIS FILE NAME: GSM537692_BI.iPS-15b.H3K9ac.Solexa-20747.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-15b Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the iPS-15b Cell Line, Library Solexa-20747 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.5027
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS15b H3K9ac 47
BROWSER_TRACK_DESCRIPTION: BI iPS-15b Cell Line Histone H3K9ac Library Solexa-20747 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0774
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.1426
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9433
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3531
POISSON_PERCENTILE: 43

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

source_name: IPS cell line 15b; 61BWEAAXX100226-7-S

value: Harvard University

value: Cell Line

value: induced pluripotent cells

value: Histone H3K9ac

value: Abcam


title: ChIP-Seq analysis of H3K9me3 in human hiPS-15b cells; 61BWEAAXX100226-6-S

description:
sample_term_id: NTR_0001162
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20732
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2515
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2300
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537691_BI.iPS-15b.H3K9me3.Solexa-20732.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-15b Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the iPS-15b Cell Line, Library Solexa-20732 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.4629
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1573
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.2184
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.884
IROC_PERCENTILE: 71
POISSON_SCORE: 0.4762
POISSON_PERCENTILE: 83

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

ANALYSIS FILE NAME: GSM537691_BI.iPS-15b.H3K9me3.Solexa-20732.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-15b Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the iPS-15b Cell Line, Library Solexa-20732 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.4903
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS15b H3K9me3 32
BROWSER_TRACK_DESCRIPTION: BI iPS-15b Cell Line Histone H3K9me3 Library Solexa-20732 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1573
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.2184
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.884
IROC_PERCENTILE: 71
POISSON_SCORE: 0.4762
POISSON_PERCENTILE: 83

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

source_name: IPS cell line 15b; 61BWEAAXX100226-6-S

value: undifferentiated

value: KSR

value: Female

value: Histone H3K9me3

value: Bioruptor


title: sRNA from grape stem and leaves

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

country: United Kingdom

institute: University of East Anglia

description: Total endogenous small RNAs from the leaves of Vitis vinifera cv. Pinot noir, clone ENTAV115

data_processing: Removed adaptors. Sequences without adaptor matches were discarded.

organism: Vitis vinifera

source_name: Vitis vinifera cv. Pinot noir, clone ENTAV115, leaves and stem

growth_protocol: Samples were collected from plants grown in collection field during the vegetative start.

extract_protocol: Size fractionated small RNA from total RNA extracts was ligated to adaptors, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina sequencing

value: RNA extracted from stem and leaves


title: G026N

value: normal

value: normal cervix


title: ChIP-Seq analysis of H3K36me3 in human hiPS-15b cells; 61BWEAAXX100226-5-S

description:
sample_term_id: NTR_0001162
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20749
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2514
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2300
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537690_BI.iPS-15b.H3K36me3.Solexa-20749.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-15b Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the iPS-15b Cell Line, Library Solexa-20749 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.4716
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1624
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.2221
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9532
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3973
POISSON_PERCENTILE: 19

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

ANALYSIS FILE NAME: GSM537690_BI.iPS-15b.H3K36me3.Solexa-20749.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-15b Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the iPS-15b Cell Line, Library Solexa-20749 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.4990
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS15b H3K36me3 49
BROWSER_TRACK_DESCRIPTION: BI iPS-15b Cell Line Histone H3K36me3 Library Solexa-20749 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1624
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.2221
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9532
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3973
POISSON_PERCENTILE: 19

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

source_name: IPS cell line 15b; 61BWEAAXX100226-5-S

value: genomic DNA

value: Histone H3K36me3

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume


title: G220T

value: adenocarcinoma

value: tumor


title: G220N


title: ChIP-Seq analysis of H3K9me3 in human hiPS-20b cells; 61BWEAAXX100226-1-S

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20765
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2512
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2304
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537688_BI.iPS-20b.H3K9me3.Solexa-20765.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the iPS-20b Cell Line, Library Solexa-20765 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.4690
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1632
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.1839
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.869
IROC_PERCENTILE: 68
POISSON_SCORE: 0.3777
POISSON_PERCENTILE: 47

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

ANALYSIS FILE NAME: GSM537688_BI.iPS-20b.H3K9me3.Solexa-20765.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the iPS-20b Cell Line, Library Solexa-20765 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.4964
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS20b H3K9me3 65
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K9me3 Library Solexa-20765 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1632
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.1839
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.869
IROC_PERCENTILE: 68
POISSON_SCORE: 0.3777
POISSON_PERCENTILE: 47

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

source_name: IPS cell line 20b; 61BWEAAXX100226-1-S

value: induced pluripotent stem cells 20b

value: Harvard University

value: Cell Line

value: induced pluripotent cells

value: Male

value: SDS lysis


title: ChIP-Seq analysis of H3K9ac in human H1 cells; 42LR0AAXX091002-5-S

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-14962
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2500
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2509
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537685_BI.H1.H3K9ac.Solexa-14962.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LR0AAXX091002-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the H1 Cell Line, Library Solexa-14962 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.4751
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1231
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1796
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9986
IROC_PERCENTILE: 94
POISSON_SCORE: 0.3107
POISSON_PERCENTILE: 20

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

ANALYSIS FILE NAME: GSM537685_BI.H1.H3K9ac.Solexa-14962.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LR0AAXX091002-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-14962 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.5025
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K9ac 62
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K9ac Library Solexa-14962 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1231
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1796
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9986
IROC_PERCENTILE: 94
POISSON_SCORE: 0.3107
POISSON_PERCENTILE: 20

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

source_name: H1 stem cells from Cellular Dynamics; 42LR0AAXX091002-5-S

value: Cellular Dynamics

value: undifferentiated

value: TESR

value: Histone H3K9ac

value: Bioruptor

value: Abcam


title: ChIP-Seq analysis of H3K4me3 in human hiPS-15b cells; 61BWEAAXX100226-8-S

description:
sample_term_id: NTR_0001162
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20743
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2511
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2300
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537687_BI.iPS-15b.H3K4me3.Solexa-20743.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-15b Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the iPS-15b Cell Line, Library Solexa-20743 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.4748
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3868
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.3714
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.469
POISSON_PERCENTILE: 52

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

ANALYSIS FILE NAME: GSM537687_BI.iPS-15b.H3K4me3.Solexa-20743.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-15b Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the iPS-15b Cell Line, Library Solexa-20743 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.5022
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS15b H3K4me3 43
BROWSER_TRACK_DESCRIPTION: BI iPS-15b Cell Line Histone H3K4me3 Library Solexa-20743 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3868
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.3714
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.469
POISSON_PERCENTILE: 52

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

source_name: IPS cell line 15b; 61BWEAAXX100226-8-S

value: genomic DNA

value: KSR

value: Female

value: Histone H3K4me3

value: 10 million cells

value: Millipore