title: Ciona_smRNA_larva

status: Public on Mar 27 2010

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

description: small RNA sequenced from larva stage Ciona intestinalis

data_processing: Files converted from Illumina sequences.txt (Qsolexa) format to fastq (Qphred). GSE21078_cionaMirTable.txt.gz contains a table of small RNA frequencies.

source_name: larva stage

growth_protocol: Adult Ciona intestinalis animals were collected from Half Moon Bay, California and maintained in an artificial seawater tank.

extract_protocol: Total RNA was extracted using the mirVana™ miRNA Isolation Kit (Ambion). From ~30 μg of total RNA, only 17-25-nt RNAs were size selected via 15% denaturing PAGE. The 3’ “modban-1” adaptor (IDT) was ligated to this fraction with RNA ligase (Ambion) in the presence of ATP-free reaction buffer, and appropriately ligated RNAs were size selected via 15% denaturing PAGE. The modified RNAs were subsequently ligated to a 5’ linker (Solexa linker) in the presence of RNA ligase and reaction buffer with ATP. The resulting RNA library was reverse transcribed to a cDNA library with SuperScript II (Invitrogen).

treatment_protocol: Fertilization and dechorionation were performed

tag: developmental stage

value: larva stage


title: muscle_pre-training_rep2

status: Public on Apr 09 2010

type: SRA

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: NlaIII digested polyA RNA

library_source: transcriptomic

data_processing: reps 1-3 were processed using the illumina IPAR v1.01 pipeline. Reps 4-7 were processed using Illumina pipeline v1.4. Tag counts correspond to equCab2 ensembl 49 build.

molecule: polyA RNA

organism: Equus caballus

source_name: gluteus medius muscle

extract_protocol: The Illumina cDNA library was prepared according to the Illumina procotol document "Preparing Samples for Digital Gene Expression-Tag profiling with NlaIII" Part # 11251702 Rev. A   (icom.illumina.com).

tag: tissue

value: gluteus medius muscle

tag: training timepoint

value: pre

tag: horse number


title: muscle_pre-training_rep3

description: NlaIII digested polyA RNA


title: SRS009480.1_p300_T30-2.fq

status: Public on Mar 30 2010

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: Chromatin IP against p300

library_source: genomic

data_processing: Alignment (also enrichment): We ran the Illumina GAPipeline, ran GAPSS (www.lgtc.nl/GAPSS to remove first bps, aligned with Rmap to human NCBI build 36, and construct UCSC wiggle  files) and to make wiggle file size manageable and reduce background base pairs with only a single tag aligning were not reported.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human glioblastoma T98G cells

growth_protocol: Human glioblastoma T98G cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), penicillin (100 ug/ml), and streptomycin (100 ug/ml). Then serum starved for 2-3 days (DMEM supplemented with 0.1% FBS).

extract_protocol: Chromatin was prepared  and ChIPs were carried out as previously described, including  fragmentation by sonication (Denissov et al. 2007) (fragment size around 500 bp). For ChIP-seq all samples were prepared with Illumina's DNA sampleprep Kit (FC-102-1001) according to the manufacturer's protocol. Single ends of each sample were then sequenced on a single lane of the Illumina Genome Analyzer for 36 cycles.

treatment_protocol: stimulation with serum (20%) and Tetradecanoyl phorbol acetate (TPA 100 ng/ml; Sigma)

tag: time after stimulation

value: T30 (minutes)

tag: cell line

tag: antibody


title: Ciona_smRNA_gastrula

country: USA

description: small RNA sequenced from gastrula stage Ciona intestinalis

molecule: total RNA

organism: Ciona intestinalis

source_name: gastrula stage

value: gastrula stage


title: muscle_post-training_rep2

description: NlaIII digested polyA RNA

value: post


title: muscle_post-training_rep1

description: NlaIII digested polyA RNA


title: kst_trans transcriptome

status: Public on Mar 25 2010

city: Bremen

first: Marc

last: Strous

address: Celciusstrasse 1

department: Microbial Fitness Group

country: Germany

institute: MPI Bremen

description: library_source: Total community RNA

data_processing:
The software to generate the processed data was MAQ 6.3. The aligner was designed by Sanger (http://maq.sourceforge.net/).

The command used to generate mapping:
maq map -n 2 -m 0.001 -u unmapped_readsv2  -e 70 output_mappingv2.map total_kust.bfa s_7_sequence.bfq

After that, the command to get human readable format:
maq mapview output_mappingv2.map > output_mapping_s7_sequence

In summary per position coverage was calculated for each contig and average coverage was calculated for each orf

organism: Candidatus Kuenenia stuttgartensis

source_name: suspended cells, 90% are K stuttgartiensis, anammox enrichment culture

growth_protocol: 10L continuous stirred tank reactor with biomass retention via a filter as described by Van der Star et al. (2008) Biotechnol Bioeng. 101(2):286-94.

extract_protocol: RNA extracted with Ribopure Bacteria Kit. First strand cDNA was synthesized with random primers using the RevertAid™ H Minus First Strand cDNA Synthesis Kit, second strand was synthesized with DNA polymerase (Fermentas, Vilnius, Lithuania).

tag: cells

value: suspended cells from Kuenenia stuttgartiensis


title: muscle_post-training_rep3

description: NlaIII digested polyA RNA


title: GxGF-IR/GFP shoot rep2

status: Public on Mar 24 2010

city: Cambridge

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

description: Grafted plants are described using “shoot/root” notation

data_processing: Small RNA adapters were removed using an exact match to the sequence of the appropriate adapter.   Reads were aligned to the Arabidopsis thaliana genome (TAIR v8) using SSAHA v3.1.

organism: Arabidopsis thaliana

source_name: shoot total RNA

growth_protocol: standard growth conditions (10hr light, 20 C)

extract_protocol: Total nucleic acid (TNA) extracts were prepared from pooled shoot and root samples derived from 3-4 individual grafts according to White and Kaper, 1989. To clone small RNAs, sRNAfractions were enriched from 12.5-25 µg of TNA using MirVana columns (Ambion) according to the manufacturer’s instruction. SRNAs were cloned by the Illumina sRNAcloning kit.

tag: ecotype

tag: sample time

value: five weeks after grafting


title: GxA-sde4/Col shoot rep2


title: GxA/Col shoot rep1


title: GxA/Col shoot rep2


title: GxGF-IR/GFP rep2

source_name: root total RNA


title: GxA-sde4/Col shoot rep1


title: GxA/Col-dcl2,3,4 rep2


title: wt/GxGF-IR

organism: Nicotiana benthamiana

value: 4 weeks after grafting


title: GxGF-IR/GFP shoot rep1


title: Col-dcl2,3,4/Col-dcl2,3,4 rep2


title: Col/GxGF-IR rep1


title: GxA-sde4/Col-dcl2,3,4 rep1


title: wt/wt


title: GxA-sde4/Col rep2


title: GxGF-IR/GxGF-IR


title: GFP/GxGF-IR


title: Reference Epigenome: ChIP-Seq Input from IMR90 Cells; renlab.Input.IMR90-08.01

status: Public on Mar 22 2010

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from IMR90 Cells. Sequencing was done on the Illumina GAII platform.
Library name: SK-I3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2128
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2046
****************
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: GSM521933_UCSD.IMR90.Input.SK-I3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-08.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the IMR90 Cell Line, Library SK-I3 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.4437
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: 0.1011
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.1603
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.7703
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3367
POISSON_PERCENTILE: 84

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

ANALYSIS FILE NAME: GSM521933_UCSD.IMR90.Input.SK-I3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-08.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the IMR90 Cell Line, Library SK-I3 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.4484
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: IMR90 Input SKI3
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line ChIP-Seq Input Library SK-I3 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.1011
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.1603
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.7703
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3367
POISSON_PERCENTILE: 84

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.Input.IMR90-08.01

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

value: IMR90 cells

tag: molecule

value: genomic DNA

tag: disease

value: ATCC

value: Cell Line

tag: line

tag: lineage

tag: batch

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

tag: Sex

value: Female

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Input from IMR90 Cells; renlab.Input.IMR90-07.01

description:
Design description: ChIP-Seq Input from IMR90 Cells. Sequencing was done on the Illumina GAII platform.
Library name: IMR90-07-I1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2126
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2046
****************
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: GSM521932_UCSD.IMR90.Input.IMR90-07-I1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-07.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the IMR90 Cell Line, Library IMR90-07-I1 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.4430
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: 0.1024
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2408
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.8755
IROC_PERCENTILE: 58
POISSON_SCORE: 0.3717
POISSON_PERCENTILE: 91

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

ANALYSIS FILE NAME: GSM521932_UCSD.IMR90.Input.IMR90-07-I1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-07.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the IMR90 Cell Line, Library IMR90-07-I1 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.4447
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: IMR90 Input 07I1
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line ChIP-Seq Input Library IMR90-07-I1 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.1024
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2408
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.8755
IROC_PERCENTILE: 58
POISSON_SCORE: 0.3717
POISSON_PERCENTILE: 91

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.Input.IMR90-07.01


title: GxA-sde4/Col-dcl2,3,4 rep2


title: Reference Epigenome: ChIP-Seq Input from IMR90 Cells; renlab.Input.IMR90-05.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from IMR90 Cells. Sequencing was done on the Illumina GAII platform.
Library name: IMR90-05-I1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2122
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1961
****************
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: GSM521930_UCSD.IMR90.Input.IMR90-05-I1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-05.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the IMR90 Cell Line, Library IMR90-05-I1 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.4429
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: 0.153
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.2108
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.8619
IROC_PERCENTILE: 56
POISSON_SCORE: 0.3534
POISSON_PERCENTILE: 88

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

ANALYSIS FILE NAME: GSM521930_UCSD.IMR90.Input.IMR90-05-I1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-05.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the IMR90 Cell Line, Library IMR90-05-I1 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.4487
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: IMR90 Input 05I1
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line ChIP-Seq Input Library IMR90-05-I1 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.153
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.2108
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.8619
IROC_PERCENTILE: 56
POISSON_SCORE: 0.3534
POISSON_PERCENTILE: 88

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.Input.IMR90-05.01


title: GxGF-IR/Col rep2


title: GxGF-IR/Col rep1


title: Reference Epigenome: ChIP-Seq Input from IMR90 Cells; renlab.Input.IMR90-04.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from IMR90 Cells. Sequencing was done on the Illumina GAII platform.
Library name: SK-I2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2120
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1957
****************
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: GSM521929_UCSD.IMR90.Input.SK-I2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-04.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the IMR90 Cell Line, Library SK-I2 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.4431
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: 0.1904
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.226
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.898
IROC_PERCENTILE: 63
POISSON_SCORE: 0.3872
POISSON_PERCENTILE: 94

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

ANALYSIS FILE NAME: GSM521929_UCSD.IMR90.Input.SK-I2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-04.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the IMR90 Cell Line, Library SK-I2 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.4479
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: IMR90 Input SKI2
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line ChIP-Seq Input Library SK-I2 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.1904
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.226
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.898
IROC_PERCENTILE: 63
POISSON_SCORE: 0.3872
POISSON_PERCENTILE: 94

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.Input.IMR90-04.01


title: Col-dcl2,3,4/GxGF-IR rep2


title: GxGF-IR/GFP rep1


title: Col-dcl2,3,4/GxGF-IR rep1


title: Reference Epigenome: ChIP-Seq Input from IMR90 Cells; renlab.Input.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from IMR90 Cells. Sequencing was done on the Illumina GAII platform.
Library name: LL-I2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2116
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
****************
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: GSM521927_UCSD.IMR90.Input.LL-I2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the IMR90 Cell Line, Library LL-I2 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.4406
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: 0.1027
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.2434
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.8898
IROC_PERCENTILE: 61
POISSON_SCORE: 0.3494
POISSON_PERCENTILE: 87

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

ANALYSIS FILE NAME: GSM521927_UCSD.IMR90.Input.LL-I2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the IMR90 Cell Line, Library LL-I2 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.4558
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: IMR90 Input LLI2
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line ChIP-Seq Input Library LL-I2 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.1027
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.2434
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.8898
IROC_PERCENTILE: 61
POISSON_SCORE: 0.3494
POISSON_PERCENTILE: 87

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

source_name: IMR90 Cell Line, biological replicate 1 (r1); renlab.Input.IMR90-02.01

value: Branson Tip Sonicator


title: GxGF-IR/Col-dcl2,3,4 rep1


title: GxA/Col rep2


title: Reference Epigenome: ChIP-Seq Input from IMR90 Cells; renlab.Input.IMR90-01.01

description:
Design description: ChIP-Seq Input from IMR90 Cells. Sequencing was done on the Illumina GAII platform.
Library name: LL-I1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2112
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
****************
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: GSM521926_UCSD.IMR90.Input.LL-I1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the IMR90 Cell Line, Library LL-I1 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.4393
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: 0.1297
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.244
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9075
IROC_PERCENTILE: 66
POISSON_SCORE: 0.3871
POISSON_PERCENTILE: 93

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

ANALYSIS FILE NAME: GSM521926_UCSD.IMR90.Input.LL-I1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the IMR90 Cell Line, Library LL-I1 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.4555
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: IMR90 Input LLI1
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line ChIP-Seq Input Library LL-I1 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.1297
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.244
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9075
IROC_PERCENTILE: 66
POISSON_SCORE: 0.3871
POISSON_PERCENTILE: 93

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

source_name: IMR90 Cell Line, biological replicate 1 (r1); renlab.Input.IMR90-01.01


title: GxA/Col rep1


title: GxA-sde4/Col rep1


title: Reference Epigenome: ChIP-Seq Analysis of H4K91ac in IMR90 Cells; renlab.H4K91ac.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K91ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK49
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2009
****************
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: GSM521925_UCSD.IMR90.H4K91ac.SK49.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K91ac ChIP-Seq on the IMR90 Cell Line, Library SK49 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.5140
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_H4K91ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.6105
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5743
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9973
IROC_PERCENTILE: 100
POISSON_SCORE: 0.692
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521925_UCSD.IMR90.H4K91ac.SK49.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K91ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK49 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.4464
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: IMR90 H4K91ac 49
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H4K91ac Library SK49 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.6105
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5743
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9973
IROC_PERCENTILE: 100
POISSON_SCORE: 0.692
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H4K91ac.IMR90-02.01

value: Histone H4K91ac

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: GxA/Col-dcl2,3,4 rep1

value: five weeks after grafting


title: GxGF-IR/Col-dcl2,3,4 rep2


title: Reference Epigenome: ChIP-Seq Analysis of H4K91ac in IMR90 Cells; renlab.H4K91ac.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K91ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL08
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2107
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM521924_UCSD.IMR90.H4K91ac.YL08.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K91ac ChIP-Seq on the IMR90 Cell Line, Library YL08 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.5195
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_H4K91ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.5884
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4622
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.994
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6194
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM521924_UCSD.IMR90.H4K91ac.YL08.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K91ac.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H4K91ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K91ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL08 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.4478
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: IMR90 H4K91ac 08
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H4K91ac Library YL08 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K91ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.5884
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4622
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.994
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6194
POISSON_PERCENTILE: 67

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H4K91ac.IMR90-01.01


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in IMR90 Cells; renlab.H4K8ac.IMR90-04.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL142
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2098
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2046
****************
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: GSM521923_UCSD.IMR90.H4K8ac.YL142.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.IMR90-04.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K8ac ChIP-Seq on the IMR90 Cell Line, Library YL142 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.5187
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_H4K8ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.5908
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.4842
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.993
IROC_PERCENTILE: 50
POISSON_SCORE: 0.6683
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM521923_UCSD.IMR90.H4K8ac.YL142.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.IMR90-04.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K8ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL142 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.4490
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: IMR90 H4K8ac 42
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H4K8ac Library YL142 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.5908
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.4842
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.993
IROC_PERCENTILE: 50
POISSON_SCORE: 0.6683
POISSON_PERCENTILE: 50

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H4K8ac.IMR90-04.01

value: Histone H4K8ac

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in IMR90 Cells; renlab.H4K8ac.IMR90-03.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK45
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2096
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2009
****************
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: GSM521922_UCSD.IMR90.H4K8ac.SK45.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.IMR90-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K8ac ChIP-Seq on the IMR90 Cell Line, Library SK45 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.5168
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_H4K8ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6289
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5364
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9963
IROC_PERCENTILE: 75
POISSON_SCORE: 0.6891
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM521922_UCSD.IMR90.H4K8ac.SK45.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.IMR90-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K8ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK45 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.4488
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: IMR90 H4K8ac 45
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H4K8ac Library SK45 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6289
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5364
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9963
IROC_PERCENTILE: 75
POISSON_SCORE: 0.6891
POISSON_PERCENTILE: 75

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H4K8ac.IMR90-03.01

value: genomic DNA

value: ATCC


title: Col/Col rep2


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in IMR90 Cells; renlab.H4K8ac.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL57
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2094
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1961
****************
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: GSM521921_UCSD.IMR90.H4K8ac.YL57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K8ac ChIP-Seq on the IMR90 Cell Line, Library YL57 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.5184
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_H4K8ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.5113
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.4645
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9912
IROC_PERCENTILE: 25
POISSON_SCORE: 0.6086
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM521921_UCSD.IMR90.H4K8ac.YL57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K8ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL57 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.4471
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: IMR90 H4K8ac 57
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H4K8ac Library YL57 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.5113
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.4645
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9912
IROC_PERCENTILE: 25
POISSON_SCORE: 0.6086
POISSON_PERCENTILE: 25

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H4K8ac.IMR90-02.01

value: Cell Line

value: Fetal lung fibroblast

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in IMR90 Cells; renlab.H4K8ac.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL17
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2090
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM521919_UCSD.IMR90.H4K8ac.YL17.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.IMR90-01.01-renlab.H4K8ac.IMR90-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K8ac ChIP-Seq on the IMR90 Cell Line, Library YL17 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.5192
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_H4K8ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.7401
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5345
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9975
IROC_PERCENTILE: 100
POISSON_SCORE: 0.716
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521919_UCSD.IMR90.H4K8ac.YL17.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.IMR90-01.01-renlab.H4K8ac.IMR90-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K8ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL17 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.4538
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: IMR90 H4K8ac 17
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H4K8ac Library YL17 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.7401
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5345
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9975
IROC_PERCENTILE: 100
POISSON_SCORE: 0.716
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H4K8ac.IMR90-01.01

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

value: Female


title: Reference Epigenome: ChIP-Seq Analysis of H4K5ac in IMR90 Cells; renlab.H4K5ac.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K5ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK08
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1997
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1957
****************
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: GSM521918_UCSD.IMR90.H4K5ac.SK08.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K5ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H4K5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K5ac ChIP-Seq on the IMR90 Cell Line, Library SK08 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.5183
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_H4K5ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.7726
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5026
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9965
IROC_PERCENTILE: 75
POISSON_SCORE: 0.723
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521918_UCSD.IMR90.H4K5ac.SK08.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K5ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H4K5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K5ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK08 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.4554
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: IMR90 H4K5ac 08
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H4K5ac Library SK08 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K5ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.7726
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5026
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9965
IROC_PERCENTILE: 75
POISSON_SCORE: 0.723
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H4K5ac.IMR90-02.01

value: Histone H4K5ac

value: Biorupter


title: GxGF-IR/Col shoot rep2


title: Reference Epigenome: ChIP-Seq Input from IMR90 Cells; renlab.Input.IMR90-03.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from IMR90 Cells. Sequencing was done on the Illumina GAII platform.
Library name: SK-I1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2118
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2019
****************
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: GSM521928_UCSD.IMR90.Input.SK-I1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the IMR90 Cell Line, Library SK-I1 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.4424
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: 0.1275
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.2235
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.8861
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3621
POISSON_PERCENTILE: 90

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

ANALYSIS FILE NAME: GSM521928_UCSD.IMR90.Input.SK-I1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the IMR90 Cell Line, Library SK-I1 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.4474
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: IMR90 Input SKI1
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line ChIP-Seq Input Library SK-I1 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.1275
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.2235
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.8861
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3621
POISSON_PERCENTILE: 90

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.Input.IMR90-03.01

value: IMR90 cells

value: ChIP-Seq Input

value: Input

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H4K20me1 in IMR90 Cells; renlab.H4K20me1.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K20me1 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL59
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1961
****************
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: GSM521917_UCSD.IMR90.H4K20me1.YL59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K20me1.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H4K20me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K20me1 ChIP-Seq on the IMR90 Cell Line, Library YL59 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.5134
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_H4K20me1_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.2812
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.346
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9629
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4918
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM521917_UCSD.IMR90.H4K20me1.YL59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K20me1.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H4K20me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K20me1 ChIP-Seq read mappings from the IMR90 Cell Line, Library YL59 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.4518
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: IMR90 H4K20me1 59
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H4K20me1 Library YL59 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K20me1_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.2812
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.346
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9629
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4918
POISSON_PERCENTILE: 67

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H4K20me1.IMR90-02.01

value: Histone H4K20me1

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in IMR90 Cells; renlab.H3K9me3.IMR90-03.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL104
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2010
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2009
****************
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: GSM521914_UCSD.IMR90.H3K9me3.YL104.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.IMR90-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the IMR90 Cell Line, Library YL104 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.4414
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: 0.2299
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.3143
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.913
IROC_PERCENTILE: 76
POISSON_SCORE: 0.4653
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM521914_UCSD.IMR90.H3K9me3.YL104.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.IMR90-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library YL104 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.4468
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: IMR90 H3K9me3 04
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K9me3 Library YL104 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.2299
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.3143
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.913
IROC_PERCENTILE: 76
POISSON_SCORE: 0.4653
POISSON_PERCENTILE: 75

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K9me3.IMR90-03.01

value: genomic DNA

value: Histone H3K9me3


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in IMR90 Cells; renlab.H3K9ac.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK46
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1995
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1961
****************
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: GSM521912_UCSD.IMR90.H3K9ac.SK46.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the IMR90 Cell Line, Library SK46 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.4402
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: 0.6697
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.6246
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.9961
IROC_PERCENTILE: 80
POISSON_SCORE: 0.7107
POISSON_PERCENTILE: 91

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

ANALYSIS FILE NAME: GSM521912_UCSD.IMR90.H3K9ac.SK46.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK46 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.4510
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: IMR90 H3K9ac 46
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K9ac Library SK46 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.6697
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.6246
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.9961
IROC_PERCENTILE: 80
POISSON_SCORE: 0.7107
POISSON_PERCENTILE: 91

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K9ac.IMR90-02.01

value: ATCC

value: Cell Line

value: Histone H3K9ac

value: Bioruptor

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H4K20me1 in IMR90 Cells; renlab.H4K20me1.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K20me1 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL21
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2100
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM521915_UCSD.IMR90.H4K20me1.YL21.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K20me1.IMR90-01.01-renlab.H4K20me1.IMR90-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H4K20me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K20me1 ChIP-Seq on the IMR90 Cell Line, Library YL21 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.5147
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_H4K20me1_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.5074
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2312
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9774
IROC_PERCENTILE: 100
POISSON_SCORE: 0.523
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521915_UCSD.IMR90.H4K20me1.YL21.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K20me1.IMR90-01.01-renlab.H4K20me1.IMR90-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H4K20me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K20me1 ChIP-Seq read mappings from the IMR90 Cell Line, Library YL21 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.4496
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: IMR90 H4K20me1 21
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H4K20me1 Library YL21 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K20me1_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.5074
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2312
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9774
IROC_PERCENTILE: 100
POISSON_SCORE: 0.523
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H4K20me1.IMR90-01.01

value: Fetal lung fibroblast

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

value: Female


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me2 in IMR90 Cells; renlab.H3K79me2.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me2 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK43
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2088
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2009
****************
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: GSM521911_UCSD.IMR90.H3K79me2.SK43.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me2 ChIP-Seq on the IMR90 Cell Line, Library SK43 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.5186
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_H3K79me2_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6184
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.4768
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9964
IROC_PERCENTILE: 100
POISSON_SCORE: 0.682
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521911_UCSD.IMR90.H3K79me2.SK43.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me2 ChIP-Seq read mappings from the IMR90 Cell Line, Library SK43 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.4466
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: IMR90 H3K79me2 43
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K79me2 Library SK43 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6184
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.4768
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9964
IROC_PERCENTILE: 100
POISSON_SCORE: 0.682
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K79me2.IMR90-02.01

value: Histone H3K79me2

value: Biorupter


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in IMR90 Cells; renlab.H3K79me1.IMR90-04.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL145
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2081
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2046
****************
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: GSM521908_UCSD.IMR90.H3K79me1.YL145.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.IMR90-04.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on the IMR90 Cell Line, Library YL145 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.5152
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_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.5501
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.3555
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9774
IROC_PERCENTILE: 57
POISSON_SCORE: 0.644
POISSON_PERCENTILE: 57

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

ANALYSIS FILE NAME: GSM521908_UCSD.IMR90.H3K79me1.YL145.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.IMR90-04.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the IMR90 Cell Line, Library YL145 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.4450
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: IMR90 H3K79me1 45
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K79me1 Library YL145 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.5501
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.3555
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9774
IROC_PERCENTILE: 57
POISSON_SCORE: 0.644
POISSON_PERCENTILE: 57

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K79me1.IMR90-04.01

value: Histone H3K79me1

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in IMR90 Cells; renlab.H3K9me3.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK06
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2006
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1957
****************
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: GSM521913_UCSD.IMR90.H3K9me3.SK06.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the IMR90 Cell Line, Library SK06 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.4391
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: 0.3807
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.1913
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.8428
IROC_PERCENTILE: 56
POISSON_SCORE: 0.4709
POISSON_PERCENTILE: 80

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

ANALYSIS FILE NAME: GSM521913_UCSD.IMR90.H3K9me3.SK06.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library SK06 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.4443
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: IMR90 H3K9me3 06
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K9me3 Library SK06 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.3807
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.1913
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.8428
IROC_PERCENTILE: 56
POISSON_SCORE: 0.4709
POISSON_PERCENTILE: 80

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K9me3.IMR90-02.01

value: IMR90 cells

value: magnetic anti-rabbit


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me2 in IMR90 Cells; renlab.H3K79me2.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me2 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: LL238
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2083
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM521909_UCSD.IMR90.H3K79me2.LL238.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.IMR90-01.01-renlab.H3K79me2.IMR90-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me2 ChIP-Seq on the IMR90 Cell Line, Library LL238 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.5182
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_H3K79me2_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6884
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4094
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.995
IROC_PERCENTILE: 75
POISSON_SCORE: 0.6489
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM521909_UCSD.IMR90.H3K79me2.LL238.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.IMR90-01.01-renlab.H3K79me2.IMR90-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me2 ChIP-Seq read mappings from the IMR90 Cell Line, Library LL238 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.4461
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: IMR90 H3K79me2 38
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K79me2 Library LL238 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6884
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4094
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.995
IROC_PERCENTILE: 75
POISSON_SCORE: 0.6489
POISSON_PERCENTILE: 75

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K79me2.IMR90-01.01

value: 5 micrograms

value: Abcam


title: GxGF-IR/Col shoot rep1

description: Grafted plants are described using “shoot/root” notation

data_processing: Small RNA adapters were removed using an exact match to the sequence of the appropriate adapter.   Reads were aligned to the Arabidopsis thaliana genome (TAIR v8) using SSAHA v3.1.

source_name: shoot total RNA

value: five weeks after grafting


title: Col/GxGF-IR rep2

source_name: root total RNA