title: MSL3-TAP ChIP-seq

city: Boston

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description: MSL3-TAP ChIP of TrojantElephant mutant larvae

data_processing:
Alignment: reads were aligned against D.melanogaster dm3 assembly using bowtie (using -m 1 option)
Processed data: ChIP and input ratios were calculated using sliding 7Kbp window. The 99% confidence interval (CI) was determined at each window position based based on the counts using Poisson model. The conservative enrichment profile reports lower CI bound if it is above 0 (on log2 scale), and upper CI bound if it is below 0. Positions at which CI included 0 were reported with the enrichment value of 0.

source_name: larvae

growth_protocol: Flies were kept on standard cornmeal-molasses medium at 25 °C. Two yellow+-marked attP landing sites were used, attP18 and attP3, inserted at positions 6648525 bp and 20201600 bp of the X chromosome, respectively (R5.18) (Markstein et al. 2008). Briefly, TrojanHorse/TrojanHorseD/TrojanElephant DNA was injected into y1 w67c23 P{y+ attP=CaryP}; M{Avic\RFPE.3xP3, vas-int.B}ZH-102D embryos. The integrase source was a kind gift of Johannes Bischoff and Konrad Basler. Flies with colored eyes were selected in G1 progeny from a cross with the y w stock and bred to homozygosity. Accuracy and integrity of insertions was verified by PCR. P{mini-white+ MSL3-TAP-pCaSpeR3-1}; msl31 background (Alekseyenko et al. 2006) was introduced by standard genetic crosses. When needed for ChIP purposes, male larvae were obtained by crossing the TrojanHorse (or TrojanElephant); MSL3-TAP; msl31 females with FM7c, P{GAL4-Kr.C}DC1, P{UAS-GFP.S65T}DC5, sn+/Y; MSL3-TAP; msl31 males, and sexed based on their non-GFP phenotype. For embryo sorting, Sxl/PE-GFP transgene integrations on the X (G5B) or the third chromosome (G78A), expressing GFP under the early Sxl promoter specifically in female embryos were recombined into TrojanHorse and TrojanHorseD stocks.

extract_protocol: Preparation of chromatin and libraries from sexed larvae for ChIP-seq was performed as described in Alekseyenko et al., Cell 134(4): 599-609.

value: MSL3-TAP ChIP

tag: developmental stage

value: larvae


title: AdultFemale_H3K9Ac_ChIPSeq_1

status: Public on Aug 13 2009

type: SRA

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

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

department: Institute for Genomics and Systems Biology

country: USA

institute: University of Chicago

description: corresponding input record: GSM400671

library_source: genomic

data_processing: Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300Â bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: AdultFemale

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of Drosophila Adult Female 2-3 days old, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Adult flies are collected 2 to 3 days after the first adult hatched. They are sorted for sex under a dissecting microscope after being put to sleep with CO2. Females and males are placed into different eppendorff tubes on ice and then rinsed with EWB before cross-linking in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation.

treatment_protocol: No Treatment

tag: development point

value: AdultFemale

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

tag: antibody lot number


title: E12-16_H3K9Ac_ChIPSeq_1

description: corresponding input record: GSM432634


title: Section1_base_Mo17

status: Public on Aug 15 2009

city: Ithaca

first: Lalit

last: Ponnala

state: NY

address: 616 Rhodes Hall

institute: Cornell University

description:
mRNA-seq from base
processed data file: Sample1.copynumber.txt
processed data file: Sample1.alignment.txt
The copynumber file shows the number of times each read is detected in our sample. The alignment file shows the alignment for each read in the copynumber file. Please see the README.txt file (linked as supplementary file on Series record) for a description of each file's contents.

library_source: transcriptomic

data_processing: The data in the alignment table was generated by aligning the first 32bp of each raw read to the maize genome (release 4.53a, available at:    http://www.maizesequence.org/index.html). The software tool "Eland" provided by Illumina was used to perform the alignments, with settings -10,5,2, i.e. allowing up to 10 perfect alignments, 5 1-mismatch alignments, and 2 2-mismatch alignments for each read.

molecule: polyA RNA

organism: Zea mays

source_name: Maize leaf

growth_protocol: Plants were grown for 9 days under a 80:20 mix of metal halide: capsylite halogen lamps at a fluence of 500 umol/m2/sec, 12L:12D, 31ºL, 22ºD, 50% rel. humidiy.

extract_protocol: Total RNA from 1 cm segments of leaf tip and base tissues from the third leaf of 9 day old (DAP) Mo17 seedlings was extracted using Trizol reagent (Invitrogen, TRIZOL® Reagent, Cat. No.  15596-018). Then, 100 ng mRNA was isolated from each total RNA samples using Dynabeads mRNA purification kit (Invitrogen Cat. No.  610-02). cDNA synthesis was primed with random hexamers and libraries constructed according to manufacturer's recommendations (Illumina mRNA-seq Sample Prep Kit part# 1004898 Rev.A).

tag: inbred line

tag: tissue

value: leaf base


title: Dm_emb_16-18h_Total_Ap

city: Woodbury

first: Chris

last: Zaleski

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Labs

description:
library_strategy: Poly-A+ RNA Seq
library_source: RNAs >200 n'tds
library_selection: Stranded, single-ended, 5' bias
>200 ntds

data_processing: Illumina fastq processed into SAM format, see http://samtools.sourceforge.net/ for details.

source_name: embryo

growth_protocol: Fly populations consisted of the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. These flies were maintained at 24˚ C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. These animals were grown in 250ml (pint) bottle that contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). Seven days after being introduced into the bottles, adult stages over five days old were transferred to fresh bottles stuffed with a Kimwipe® to support flies from sticking in the food. Flies were aged the indicated amount of time at 24C, separated by sex (when indicated) on a CO2 pad and transferred to a tube on crushed dry ice. All frozen biological samples were stored at -80C until the RNA could be isolated. A yield of approximately 2 micrograms total RNA per milligram of tissue was typical from young adult males while young females yielded about 3 micrograms total RNA per milligram. Thirty day old males produced about 1 microgram total RNA per milligram and 30 day old females yielded about 1.5 micrograms total RNA per milligram.

extract_protocol: Dm_emb_16-18h_PolyA+_extraction_protocol.txt linked on series record

value: 16-18 hr embryos

tag: biorep


title: E0-4_H3K9Me3_ChIPSeq_1

description: corresponding input record: GSM400657

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-4 hours egg laying, new plates are added after a 2hours pre-egglaying at 10 am and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected at 1.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 2 pm in 1.8% formaldehyde at room temperature for 15 min.


title: 143B

status: Public on Aug 25 2009

city: Cambridge

first: Christine

last: Mayr

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

data_processing: Reads containing linker matches were mapped (after removing linkers) to predicted pre-miRNAs (MirBase version 12.0)

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: RNA was harvested from exponentially growing cells

extract_protocol: Total RNA extracted using standard Trizol extraction. Total RNA fractionated on 15% polyacrylamide gel and 3' and 5' adaptors sequentially ligated requiring a 3' hydroxyl group and 5' phosphate

tag: cell line


title: E4-8_H3K9Me3_ChIPSeq_1

description: corresponding input record: GSM400675

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 4-8 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 4.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 5 pm in 1.8% formaldehyde at room temperature for 15 min.


title: SW480


title: E20-24_H3K9Me3_ChIPSeq_1

description: corresponding input record: GSM400673

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 20-24 hours egg laying, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: L1_H3K9Me3_ChIPSeq_1

description: corresponding input record: GSM400663

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of first instar larvae, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. 3. L1 larvae are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: E8-12_H3K9Me3_ChIPSeq_1

description: corresponding input record: GSM432636

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 8-12 hours egg laying, new plates are added after a 2hours pre-egglaying at 8 pm and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 7.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 8 am in 1.8% formaldehyde at room temperature for 15 min.


title: L2_H3K9Me3_ChIPSeq_1

description: corresponding input record: GSM400669

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of second instar larvae (L2), new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Plates are then kept at 25C for another 24 hours.3. L2 larvae are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: E0-4_H3K27Me3_ChIPSeq_1

description: corresponding input record: GSM400657

value: Upstate


title: E4-8_H3K27Me3_ChIPSeq_1

description: corresponding input record: GSM400675


title: E8-12_H3K27Me3_ChIPSeq_1

description: corresponding input record: GSM432636


title: E12-16_H3K27Me3_ChIPSeq_1

description: corresponding input record: GSM432634


title: Pupae_H3K9Me3_ChIPSeq_1

description: corresponding input record: GSM400665

source_name: Pupae

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of pupae at 1-2 days APF (after puparium formation), new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Pupae are collected 2 days after the first pupa formed on the wall of the bottle. They are collected with a brush humidified with EWB and placed into an eppendorf tube. They are rinsed extensively with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.

value: Pupae


title: L1_H3K27Me3_ChIPSeq_1

description: corresponding input record: GSM400663


title: L2_H3K27Me3_ChIPSeq_1

description: corresponding input record: GSM400669


title: E16-20_H3K27Me3_ChIPSeq_1

description: corresponding input record: GSM400659

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 16-20 hours egg laying, new plates are added after a 2hours pre-egglaying at 1 pm and flies are allowed to lay eggs for 4 hours.3. Embryos are collected at 8.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: E16-20_H3K9Me3_ChIPSeq_1

description: corresponding input record: GSM400659


title: E12-16_H3K9Me3_ChIPSeq_1

description: corresponding input record: GSM432634


title: E20-24_H3K27Me3_ChIPSeq_1

description: corresponding input record: GSM400673


title: L3_H3K27Me3_ChIPSeq_1

description: corresponding input record: GSM400661

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of third instar larvae (L3), new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Plates are then kept at 25C for another 48 hours. 3. L3 larvae are collected at 8.45 am using a filter mesh and a brush. L3 larvae are the larvae not going through the first mesh. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: AdultMale_H3K27Me3_ChIPSeq_1

description: corresponding input record: GSM400667

source_name: AdultMale

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of Drosophila Adult Male 2-3 days old, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Adult flies are collected 2 to 3 days after the first adult hatched. They are sorted for sex under a dissecting microscope after being put to sleep with CO2. Females and males are placed into different eppendorff tubes on ice and then rinsed with EWB before cross-linking in 1.8% formaldehyde at room temperature for 15 min.

value: AdultMale


title: HS_CD4_Act_18h_ H4K20me1

status: Public on Aug 10 2009

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Rockville Pike

institute: NHLBI, NIH

description: Chromatin IP against H4K20me1

data_processing: Sequenced 25-bp reads were mapped to the human genome (hg18) using the Solexa Analysis Pipeline, and only those reads that mapped to unique genomic locations with at most 2 mismatches were retained.

source_name: CD4+ T cells

growth_protocol: Human enriched lympocyte fraction was obtained by apheresis. CD4 cells were purified negative purification with kits from Invitrogen or Myltenyi according to manufacturer's protocol.

extract_protocol: After ChIP the libraries were prepared by standard Illumina protocol

treatment_protocol: For activation, anti-CD3/28 beads (Invitrogen) were added to the CD 4 cells for 18h, according to manufacturers protocol. Approximately 86-94% of cells were CD25 positive after the treatment.

tag: antigen


title: U2OS


title: HS_CD4_Act_18h_ Pol II

description: Chromatin IP against Pol II

value: Pol II


title: MCF7_smallRNAseq

status: Public on Sep 07 2009

city: Lund

first: Helena

last: Persson

address: Scheelevagen 2

department: Dept of Clinical Sciences, Oncology

country: Sweden

institute: Lund University

data_processing: Reads were filtered using Illumina Pipeline 1.0 default purity filter (chastity >= 0.6). The 3' adaptor, TCGTATGCCGTCTTCTGCTTG, was removed from the raw reads using ungapped alignment taking base quality into account. The number of reads was then counted for each unique sequence.

source_name: MCF7 cell line

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 10% FBS, 10 µg/ml insulin, 1x non-essential amino acids and 1 mM sodium pyruvate.

extract_protocol: Total RNA was extracted using TRIzol and fractionated on a 15% acrylamide, 8M urea gel. Small RNAs 18-35 nt were isolated and ligated sequentially to 5' and 3' adapters as supplied in the sample preparation kit (Illumina). Reverse transcription and PCR amplification were performed according to the manufacturer's instructions.

tag: atcc number


title: MB-MDA231


title: HS_CD4_Act_18h_ H3K79me2

description: Chromatin IP against H3K79me2


title: HS_CD4_Act_18h_ H3K36me3

description: Chromatin IP against H3K36me3


title: input

status: Public on Aug 20 2009

description: chromatin input of TrojantElephant mutant larvae

growth_protocol: Flies were kept on standard cornmeal-molasses medium at 25 °C. Two yellow+-marked attP landing sites were used, attP18 and attP3, inserted at positions 6648525 bp and 20201600 bp of the X chromosome, respectively (R5.18) (Markstein et al. 2008). Briefly, TrojanHorse/TrojanHorseD/TrojanElephant DNA was injected into y1 w67c23 P{y+ attP=CaryP}; M{Avic\RFPE.3xP3, vas-int.B}ZH-102D embryos. The integrase source was a kind gift of Johannes Bischoff and Konrad Basler. Flies with colored eyes were selected in G1 progeny from a cross with the y w stock and bred to homozygosity. Accuracy and integrity of insertions was verified by PCR. P{mini-white+ MSL3-TAP-pCaSpeR3-1}; msl31 background (Alekseyenko et al. 2006) was introduced by standard genetic crosses. When needed for ChIP purposes, male larvae were obtained by crossing the TrojanHorse (or TrojanElephant); MSL3-TAP; msl31 females with FM7c, P{GAL4-Kr.C}DC1, P{UAS-GFP.S65T}DC5, sn+/Y; MSL3-TAP; msl31 males, and sexed based on their non-GFP phenotype. For embryo sorting, Sxl/PE-GFP transgene integrations on the X (G5B) or the third chromosome (G78A), expressing GFP under the early Sxl promoter specifically in female embryos were recombined into TrojanHorse and TrojanHorseD stocks.

value: input


title: HS_CD4_Act_18h_ H2A.Z

description: Chromatin IP against H2A.Z


title: HS_CD4_Act_18h_ H3K4me1

description: Chromatin IP against H3K4me1


title: HS_CD4_Act_18h_ H3K4me3

description: Chromatin IP against H3K4me3


title: HS_CD4_Act_18h_ H3K9me1

description: Chromatin IP against H3K9me1


title: HS_CD4_Act_18h_ H3K27me3

description: Chromatin IP against H3K27me3


title: HS_CD4_Act_18h_ H3K27me1

description: Chromatin IP against H3K27me1


title: ChIP-Seq analysis of H3K36me3 in human H1 cells, 30HCBAAXX090610-7-S

status: Public on Aug 05 2009

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: Solexa-12524
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.964
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.965

****************
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: GSM433176_BI.H3K36me3.bam
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1504
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM433176_BI.H3K36me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K36me3 in the H1 cell line 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.1505
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM433176_BI.H1.H3K36me3.Solexa-12524.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30HCBAAXX090610-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the H1 Cell Line, Library Solexa-12524 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.4677
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: 0.0671
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.1645
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.8243
IROC_PERCENTILE: 13
POISSON_SCORE: 0.2662
POISSON_PERCENTILE: 6

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

ANALYSIS FILE NAME: GSM433176_BI.H1.H3K36me3.Solexa-12524.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30HCBAAXX090610-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-12524 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.4951
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 H3K36me3 24
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K36me3 Library Solexa-12524 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0671
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.1645
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.8243
IROC_PERCENTILE: 13
POISSON_SCORE: 0.2662
POISSON_PERCENTILE: 6

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

source_name: H1 cells; 30HCBAAXX090610-7-S

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

value: genomic DNA

tag: disease

value: Cellular Dynamics

value: Cell Line

tag: line

tag: lineage

value: undifferentiated

tag: passage

tag: medium

value: TESR

tag: sex

value: Unknown

tag: batch

value: Histone H3K36me3

value: SDS lysis

value: Bioruptor

value: standard


title: ChIP-Seq analysis of H3K4me1 in human H1 cells, 314G6AAXX090406-7-S

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: Solexa-10529
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.935
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.980

****************
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: GSM433177_BI.H3K4me1.bam
ANALYSIS TITLE: Mapping of H1 H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me1 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1506
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM433177_BI.H3K4me1.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me1 in the H1 cell line 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.1507
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM433177_BI.H1.H3K4me1.Solexa-10529.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314G6AAXX090406-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the H1 Cell Line, Library Solexa-10529 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.4774
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: 0.1546
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.2785
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.917
IROC_PERCENTILE: 12
POISSON_SCORE: 0.4407
POISSON_PERCENTILE: 12

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

ANALYSIS FILE NAME: GSM433177_BI.H1.H3K4me1.Solexa-10529.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314G6AAXX090406-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-10529 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.5048
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 H3K4me1 29
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K4me1 Library Solexa-10529 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.1546
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.2785
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.917
IROC_PERCENTILE: 12
POISSON_SCORE: 0.4407
POISSON_PERCENTILE: 12

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

value: Histone H3K4me1

value: Abcam


title: ChIP-Seq analysis of H3K9me3 in human H1 cells, 30HCBAAXX090610-8-S

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: Solexa-12525
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.962
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.960

****************
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: GSM433174_BI.H3K9me3.bam
ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1510
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM433174_BI.H3K9me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K9me3 in the H1 cell line 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.1511
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM433174_BI.H1.H3K9me3.Solexa-12525.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30HCBAAXX090610-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the H1 Cell Line, Library Solexa-12525 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.4809
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: 0.0611
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.1525
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.7368
IROC_PERCENTILE: 25
POISSON_SCORE: 0.2666
POISSON_PERCENTILE: 7

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

ANALYSIS FILE NAME: GSM433174_BI.H1.H3K9me3.Solexa-12525.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30HCBAAXX090610-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-12525 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.5083
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 H3K9me3 25
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K9me3 Library Solexa-12525 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0611
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.1525
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.7368
IROC_PERCENTILE: 25
POISSON_SCORE: 0.2666
POISSON_PERCENTILE: 7

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

source_name: H1 cells; 30HCBAAXX090610-8-S

value: Histone H3K9me3


title: H520


title: A549


title: Illumina sequencing of small RNAs from two-to-four cell C. elegans embryos

status: Public on Sep 06 2009

city: Berlin

first: Jonas

last: Maaskola

address: Robert-Roessle Str. 10

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max-Delbrueck Centrum Berlin-Buch

description: Two-to-four cell stage embryos obtained by eFACS.

data_processing: Removal of 3' adapter sequences by searching for best matches of adapter prefixes up to edit distance 4.

organism: Caenorhabditis elegans

source_name: Two to four cell embryo

growth_protocol: Strains were maintained using standard methods (Brenner, 1974) on OP50 seeded NGM plates or in liquid culture.

extract_protocol: Library preparation as well as cluster generation and deep sequencing was performed according to the 5’ ligation dependent (5’monophosphate dependent) manufacturer’s protocol (Digital Gene Expression for small RNA, Illumina). Rougly 60,000 embryos (~10µg total RNA) were used for small RNA library preparation. Small RNAs were size selected between 18 and 40 nt according to the ssDNA marker in the small RNA sequencing kit (Illumina).

treatment_protocol: Methanol fixed prior to eFACS

tag: developmental stage

value: Two to four cell embryo

tag: strain

tag: meoh-fixed

tag: sorted

tag: resorted


title: NIH3T3

organism: Mus musculus


title: Illumina sequencing of small RNAs from one cell stage C. elegans embryos

description: One cell stage embryos obtained by eFACS.

source_name: One cell embryo

value: One cell embryo


title: Illumina sequencing of small RNAs from older, fixed C. elegans embryos

description: Older embryos (fixed).

source_name: Older embryos (fixed)

treatment_protocol: Older embyos were obtained by eFACS of the TX189 strain and sorting the GFP negative population.

value: embryo


title: ChIP-Seq Analysis of H3K27me3 in hESC H1 Cells, 30CMAAAXX081006-2-S

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: Solexa-8039
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.935
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.936

****************
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: GSM433167_BI.H3K27me3.bam
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1502
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM433167_BI.H3K27me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K27me3 in the H1 cell line 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.1503
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM433167_BI.H1.H3K27me3.Solexa-8039.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CMAAAXX081006-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the H1 Cell Line, Library Solexa-8039 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.4819
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: 0.2329
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2783
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9954
IROC_PERCENTILE: 96
POISSON_SCORE: 0.3694
POISSON_PERCENTILE: 15

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

ANALYSIS FILE NAME: GSM433167_BI.H1.H3K27me3.Solexa-8039.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CMAAAXX081006-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-8039 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.5093
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 H3K27me3 39
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K27me3 Library Solexa-8039 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2329
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2783
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9954
IROC_PERCENTILE: 96
POISSON_SCORE: 0.3694
POISSON_PERCENTILE: 15

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

source_name: hESC H1 Cells; 30CMAAAXX081006-2-S

value: Histone H3K27me3

value: Upstate


title: ChIP-Seq Analysis of H3K4me3 in hESC H1 Cells, 30CMAAAXX081006-5-S

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: Solexa-8038
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.939
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.940

****************
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: GSM433170_BI.H3K4me3.bam
ANALYSIS TITLE: Mapping of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1545
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM433170_BI.H3K4me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me3 in the H1 cell line 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.1546
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM433170_BI.H1.H3K4me3.Solexa-8038.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CMAAAXX081006-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the H1 Cell Line, Library Solexa-8038 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.4587
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: 0.4291
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.4388
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4967
POISSON_PERCENTILE: 56

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

ANALYSIS FILE NAME: GSM433170_BI.H1.H3K4me3.Solexa-8038.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CMAAAXX081006-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-8038 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.4861
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 H3K4me3 38
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K4me3 Library Solexa-8038 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.4291
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.4388
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4967
POISSON_PERCENTILE: 56

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

source_name: hESC H1 Cells; 30CMAAAXX081006-5-S

value: genomic DNA

value: Cellular Dynamics

value: Histone H3K4me3


status: Public on Aug 03 2009

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: H3K4me3 ChIP-Seq analysis of H1 embryonic stem cell line (HS1345) using Illumina Genome Analyzer II
library name: HS1345
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 7.06 ug
SIZE_FRACTION: N/A
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751
CHIP_ANTIBODY_LOT: 2
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM432392_UCSF-UBC.H3K4me3.2.bam
ANALYSIS TITLE: Mapping of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1550
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM432392_UCSF-UBC.H3K4me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me3 in the H1 cell line 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.1552
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
SPECIAL NOTE: generated from combined H3K4me3 data in GSM410808 and GSM432392 (thus .wig files on these records are identical)

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

ANALYSIS FILE NAME: GSM432392_UCSF-UBC.H1.H3K4me3.H1EScd2-me3K4-C.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1345-1_305H8AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the H1 Cell Line, Library H1EScd2-me3K4-C 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.4308
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: 0.738
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.7097
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.7578
POISSON_PERCENTILE: 95

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

ANALYSIS FILE NAME: GSM432392_UCSF-UBC.H1.H3K4me3.H1EScd2-me3K4-C.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1345-1_305H8AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Cell Line, Library H1EScd2-me3K4-C 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.4357
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 H3K4me3 C
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line Histone H3K4me3 Library H1EScd2-me3K4-C EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.738
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.7097
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.7578
POISSON_PERCENTILE: 95

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

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

tag: submitted sample id

value: cell line

tag: Sex

value: male

tag: body site

value: Embryo ICM

tag: histological type

value: Embryonic stem cell

tag: is tumor

value: No


description:
design description: H3K36me3 ChIP-Seq analysis of H1 embryonic stem cell line (HS1032) using Illumina Genome Analyzer II
library name: HS1032
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 32.7 ug
SIZE_FRACTION: 30-280 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 395432
****************
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: GSM428296_UCSF-UBC.H3K36me3.1.bam
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1526
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428296_UCSF-UBC.H3K36me3.2.bam
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1527
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428296_UCSF-UBC.H3K36me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K36me3 in the H1 cell line 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.1528
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM428296_UCSF-UBC.H1.H3K36me3.H1EScd1-me3K36-A.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1032-1_30WLMAAXX-HS1032-1_305H8AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the H1 Cell Line, Library H1EScd1-me3K36-A 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.4336
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: 0.2095
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.245
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9602
IROC_PERCENTILE: 46
POISSON_SCORE: 0.4109
POISSON_PERCENTILE: 22

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

ANALYSIS FILE NAME: GSM428296_UCSF-UBC.H1.H3K36me3.H1EScd1-me3K36-A.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1032-1_30WLMAAXX-HS1032-1_305H8AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H1 Cell Line, Library H1EScd1-me3K36-A 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.4385
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 H3K36me3 A
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line Histone H3K36me3 Library H1EScd1-me3K36-A EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2095
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.245
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9602
IROC_PERCENTILE: 46
POISSON_SCORE: 0.4109
POISSON_PERCENTILE: 22

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


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in hESC H1 (CDI-01) Cells; renlab.H3K9ac.CDI-01.02

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL240
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.890
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1241

****************
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: GSM434785_UCSD.H3K9ac.bam
ANALYSIS TITLE: Mapping of H1 H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9ac in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1518
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM434785_UCSD.H3K9ac.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K9ac in the H1 cell line 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.1519
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM434785_UCSD.H1.H3K9ac.LL240.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.CDI-01.02.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 LL240 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.4433
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: 0.1195
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.2413
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.8367
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3773
POISSON_PERCENTILE: 57

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

ANALYSIS FILE NAME: GSM434785_UCSD.H1.H3K9ac.LL240.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.CDI-01.02.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 LL240 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.4502
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 40
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K9ac Library LL240 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1195
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.2413
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.8367
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3773
POISSON_PERCENTILE: 57

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

source_name: CDI-01; renlab.H3K9ac.CDI-01.02

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

tag: molecule

tag: disease

value: Cellular Dynamics International

value: Cell Line

value: Embryonic Stem Cell

value: Between 30 and 50

value: mTeSER

value: Male

value: Histone H3K9ac

value: Branson Tip Sonicator

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


description:
design description: H3K4me1 ChIP-Seq analysis of H1 embryonic stem cell line (HS1413) using Illumina Genome Analyzer IIx
library name: HS1413
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 35.3 ug
SIZE_FRACTION: 90-350 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab8895
CHIP_ANTIBODY_LOT: 535659
****************
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: GSM434762_UCSF-UBC.H3K4me1.bam
ANALYSIS TITLE: Mapping of H1 H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me1 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1530
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM434762_UCSF-UBC.H3K4me1.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me1 in the H1 cell line 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.1531
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM434762_UCSF-UBC.H1.H3K4me1.H1EScd1-me1K4-D.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1413-1_42ENEAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the H1 Cell Line, Library H1EScd1-me1K4-D 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.4335
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: 0.2914
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.3605
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9632
IROC_PERCENTILE: 31
POISSON_SCORE: 0.562
POISSON_PERCENTILE: 51

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

ANALYSIS FILE NAME: GSM434762_UCSF-UBC.H1.H3K4me1.H1EScd1-me1K4-D.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1413-1_42ENEAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H1 Cell Line, Library H1EScd1-me1K4-D 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.4384
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 H3K4me1 D
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line Histone H3K4me1 Library H1EScd1-me1K4-D EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.2914
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.3605
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9632
IROC_PERCENTILE: 31
POISSON_SCORE: 0.562
POISSON_PERCENTILE: 51

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

tag: line


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in hESC H1 (CDI-01) Cells; renlab.H3K27me3.CDI-01.02

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL241
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.890
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1194

****************
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: GSM434776_UCSD.H3K27me3.bam
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1512
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM434776_UCSD.H3K27me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K27me3 in the H1 cell line 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.1513
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM434776_UCSD.H1.H3K27me3.LL241.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.CDI-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the H1 Cell Line, Library LL241 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.4411
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: 0.2804
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.3607
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9179
IROC_PERCENTILE: 52
POISSON_SCORE: 0.5061
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM434776_UCSD.H1.H3K27me3.LL241.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.CDI-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 Cell Line, Library LL241 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.4532
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 H3K27me3 41
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K27me3 Library LL241 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2804
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.3607
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9179
IROC_PERCENTILE: 52
POISSON_SCORE: 0.5061
POISSON_PERCENTILE: 67

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

source_name: CDI-01; renlab.H3K27me3.CDI-01.02

value: genomic DNA

tag: lineage

tag: passage

value: Histone H3K27me3

value: Upstate


description:
design description: ChIP-Seq input analysis of H1 embryonic stem cell line (HS1028) using Illumina Genome Analyzer II
library name: HS1028
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 44 ug
SIZE_FRACTION: 30-280 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM428289_UCSF-UBC.input.2.bam
ANALYSIS TITLE: Mapping of H1 Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced as ChIP-Seq Input from the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1745
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428289_UCSF-UBC.input.3.bam
ANALYSIS TITLE: Mapping of H1 Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced as ChIP-Seq Input from the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1746
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428289_UCSF-UBC.input.1.bam
ANALYSIS TITLE: Mapping of H1 Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced as ChIP-Seq Input from the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1744
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM428289_UCSF-UBC.input.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for Input in the H1 cell line 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.1748
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM428289_UCSF-UBC.H1.Input.TOTAL-H1EScd1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1028-1_3061PAAXX-HS1028-1_30WLMAAXX-HS1028-1_305Y8AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library TOTAL-H1EScd1 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.4311
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: 0.0059
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.033
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.947
IROC_PERCENTILE: 71
POISSON_SCORE: 0.186
POISSON_PERCENTILE: 19

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

ANALYSIS FILE NAME: GSM428289_UCSF-UBC.H1.Input.TOTAL-H1EScd1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1028-1_3061PAAXX-HS1028-1_30WLMAAXX-HS1028-1_305Y8AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library TOTAL-H1EScd1 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.4360
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 Input d1
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line ChIP-Seq Input Library TOTAL-H1EScd1 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0059
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.033
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.947
IROC_PERCENTILE: 71
POISSON_SCORE: 0.186
POISSON_PERCENTILE: 19

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

value: cell line

value: male

value: Embryo ICM


description:
design description: H3K4me3 ChIP-Seq analysis of H1 embryonic stem cell line (HS0996) using Illumina Genome Analyzer II
library name: HS0996
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 44 ug
SIZE_FRACTION: 60-280 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751
CHIP_ANTIBODY_LOT: 1
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM410808_UCSF-UBC.H3K4me3.1.bam
ANALYSIS TITLE: Mapping of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1549
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM410808_UCSF-UBC.H3K4me3.wig
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me3 in the H1 cell line 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.1551
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
SPECIAL NOTE: generated from combined H3K4me3 data in GSM410808 and GSM432392 (thus .wig files on these records are identical)

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

ANALYSIS FILE NAME: GSM410808_UCSF-UBC.H1.H3K4me3.H1EScd1-me3K4-A.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS0996.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the H1 Cell Line, Library H1EScd1-me3K4-A 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.4302
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: 0.6091
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.5868
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6268
POISSON_PERCENTILE: 79

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

ANALYSIS FILE NAME: GSM410808_UCSF-UBC.H1.H3K4me3.H1EScd1-me3K4-A.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS0996.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Cell Line, Library H1EScd1-me3K4-A 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.4351
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 H3K4me3 A
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line Histone H3K4me3 Library H1EScd1-me3K4-A EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.6091
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.5868
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6268
POISSON_PERCENTILE: 79

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

value: Embryonic stem cell

value: No