title: ChIP-Seq analysis of H3K36me3 in human hiPS-18a cells; DNA_Lib 347

description:
sample_term_id: NTR_0001165
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 347
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8717
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9471
****************
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: GSM773027_BI.iPS-18a.H3K36me3.DNA_Lib_347.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 347-DNA_Lib 347-DNA_Lib 347-DNA_Lib 347.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-18a Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the iPS-18a Cell Line, Library DNA_Lib 347, 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.10705
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,852,793
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1886
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.2197
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9789
IROC_PERCENTILE: 65
POISSON_SCORE: 0.3746
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773027_BI.iPS-18a.H3K36me3.DNA_Lib_347.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 347-DNA_Lib 347-DNA_Lib 347-DNA_Lib 347.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18a Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the iPS-18a Cell Line, Library DNA_Lib 347, 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.10969
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 5
BROWSER_TRACK_NAME: iPS18a H3K36me3 47
BROWSER_TRACK_DESCRIPTION: BI iPS-18a Cell Line Histone H3K36me3 Library DNA_Lib 347 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,852,793
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1886
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.2197
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9789
IROC_PERCENTILE: 65
POISSON_SCORE: 0.3746
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: induced pleuripotent 18a stem cell line; DNA_Lib 347

value: induced pluripotent stem cells

value: BioSam 173

value: iPS-18a Cell Line

value: induced pluripotent cells

value: 10% KOSR (Invitrogen)

value: genomic DNA

value: presumed normal

value: BioSAli 176

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard

value: Abcam

value: Histone H3K36me3

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human hippocampus middle cells; DNA_Lib 584

status: Public on Dec 28 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 584
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8711
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM773021_BI.Brain_Hippocampus_Middle.H3K4me1.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 584-DNA_Lib 584-DNA_Lib 584.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Hippocampus Middle, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10725
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,323,574
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2461
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3352
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9583
IROC_PERCENTILE: 37
POISSON_SCORE: 0.4703
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM773021_BI.Brain_Hippocampus_Middle.H3K4me1.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 584-DNA_Lib 584-DNA_Lib 584.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10989
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 5
BROWSER_TRACK_NAME: BHM H3K4me1 49 84
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K4me1 Donor 149 Library DNA_Lib 584 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,323,574
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2461
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3352
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9583
IROC_PERCENTILE: 37
POISSON_SCORE: 0.4703
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

molecule: genomic DNA

organism: Homo sapiens

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 584

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD evident at demise

tag: molecule

tag: disease

value: Hippocampus Middle

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K4me1


title: ChIP-Seq analysis of WCE in human hippocampus middle cells; DNA_Lib 582

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 582
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8709
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
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: GSM773019_BI.Brain_Hippocampus_Middle.Input.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 582-DNA_Lib 582-DNA_Lib 582.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Hippocampus Middle, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10787
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,604,639
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0075
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.0739
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9583
IROC_PERCENTILE: 43
POISSON_SCORE: 0.0933
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM773019_BI.Brain_Hippocampus_Middle.Input.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 582-DNA_Lib 582-DNA_Lib 582.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Hippocampus Middle, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11051
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 5
BROWSER_TRACK_NAME: BHM Input 49 82
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle ChIP-Seq Input Donor 149 Library DNA_Lib 582 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,604,639
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0075
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.0739
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9583
IROC_PERCENTILE: 43
POISSON_SCORE: 0.0933
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 582

value: genomic DNA

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of WCE in human hiPS-18a cells; DNA_Lib 342

description:
sample_term_id: NTR_0001165
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 342
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8714
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9471
****************
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: GSM773024_BI.iPS-18a.Input.DNA_Lib_342.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 342-DNA_Lib 342-DNA_Lib 342-DNA_Lib 342.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-18a Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS-18a Cell Line, Library DNA_Lib 342, 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.10671
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,203,512
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0052
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.0114
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0506
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773024_BI.iPS-18a.Input.DNA_Lib_342.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 342-DNA_Lib 342-DNA_Lib 342-DNA_Lib 342.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18a Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS-18a Cell Line, Library DNA_Lib 342, 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.10935
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 5
BROWSER_TRACK_NAME: iPS18a Input 42
BROWSER_TRACK_DESCRIPTION: BI iPS-18a Cell Line ChIP-Seq Input Library DNA_Lib 342 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,203,512
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0052
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.0114
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0506
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: induced pleuripotent 18a stem cell line; DNA_Lib 342

value: induced pluripotent stem cells

value: BioSam 173

value: iPS-18a Cell Line

tag: lineage

value: induced pluripotent cells

tag: medium

value: 10% KOSR (Invitrogen)

value: presumed normal

tag: passage

tag: line

tag: batch

value: BioSAli 176

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard

value: Branson


title: CK_RNA-Seq

status: Public on Dec 30 2011

city: Beijing

first: Menglong

last: Yuan

address: Zhongguancunnan 12th

country: China

institute: Biotechnology Research Institute,  Chinese Academy of Agricultural Sciences,

library_source: transcriptomic

data_processing: High-throughput cDNA sequencing was performed using the Firecrest, Bustard and GERALD programs. The low quality bases (Q<5) at the ends of the reads were trimmed. The reads that were longer than 20 bps were kept and aligned to the Deinococcus gobiensis genome using Burrows-Wheeler Aligner (BWA) . The reads that were mapped into the rRNA regions were not included in further analysis. A transcript coverage map was calculated based on the alignment of whole transcript reads. For each of the genes, the 5'-end of the translation regions were defined as positions supported by at least 5 reads summarized in both of the samples. To identify the non-coding RNA, the continuous regions (30 bp) with an average sequencing depth of  15 times/bp in the intergenic regions were extracted and compared against GenBank using blastx and blastn. Those regions that lacked similarities to known protein coding genes or were similar to known ncRNAs were classified as possible non-coding RNAs. To compare the different samples, the fragments per kb of CDS per million mapped reads (FPKM) value were used to normalize the data and represent the overall gene expression. The differently expressed genes between the two samples were selected according to their significance in Chi-square tests (p = 0.05, with Bonferroni correction) and at least 2-fold differences.

molecule: total RNA

organism: Deinococcus gobiensis

source_name: Deinococcus gobiensis I-0

growth_protocol: Cells of Deinococcus gobiensis I-0 (= DSM 21396) were grown in TGY broth (1.0 % peptone, 0.5 % yeast extract, 0.1 % glucose) at 30oC and were harvested at the late-log phase (2 x 108  CFUs mL-1)

extract_protocol: Bacterial cells were collected and ground into a fine powder in liquid nitrogen. Total RNA was isolated using Trizol reagent (Invitrogen), subsequently purified using RNeasy MinElute Cleanup Kit (Qiagen) and eluted in RNase-free water. Bacterial ribosomal RNAs were removed via a mixed treatment using the MICROB Express kit (Ambion) and the mRNA-ONLY Prokaryotic mRNA isolation Kit (Epeicentre® Biotech.) according to the manufacturer's instructions. Heating at 94oC fragmented the mRNA. First strand cDNA was synthesized with random hexamer primers, and second strand cDNA was synthesized with DNA polymerase. Double strand cDNA was end-repaired, a single adenosine was added, and the Illumina adapters were ligated. Gel-electrophoresis was used to select DNA fragments between 200-250 bp. Libraries were amplified by PCR using Phusion polymerase.

treatment_protocol: Cells were harvested at the late-log phase (2 x 108 CFUs mL-1) and then washed twice with equal volumes of potassium phosphate buffer (100 mM, pH 7.0). UV light (254 nm, 200 uW cm-2) was used to irradiate a 20 mL suspension for 5 min in a 9 cm plate with stirring. As a control, an additional non-irradiated suspension was incubated for the same duration. After treatment, cells were harvested by centrifugation at 8,000 rpm for 3 min.

tag: strain

tag: treatment

value: control


title: Bayanus Rep 1

status: Public on Dec 31 2011

city: Chestnut Hill

first: Gabor

last: Marth

address: 140 Commonwealth Ave

institute: Boston College

description: ribosome-depleted RNA from S. bayanus

data_processing: S. cerevisiae build  is sacCer2. S. paradoxus, S. mikatae, and S. bayanus annotations are from Kellis et al. (2003). Read counts included in "all aligned reads" include reads that align to multiple positions in the genome.  "Uniquely aligned reads" aligned unambiguously to one position.

organism: Saccharomyces uvarum CLIB 533

source_name: Bayanus

growth_protocol: Grown in complete media

extract_protocol: WT-Seq was performed according to a protocol/kit now available fromLife Technologies, with minor modifications that are included below. Briefly, 5–10 μg of RNA isolated from mouse cortical cultures was depleted of ribosomal RNAs using two rounds of Eukaryotic RiboMinus treatment (Life Technologies) with overnight ethanol precipitations for sample re-concentration. The removal of ribosomal RNAs was confirmed on a Bioanalyser Nano Chip (Agilent). A total of 500–1,000 ng of riboRNA-depleted total RNA was fragmented for 18 min at 95 °C in NEB buffer 3 followed by 30 minutes PNK treatment in the same buffer. Fragmentation was followed by size selection of ~50 to ~150 bp fragments using the flashPAGE denaturing PAGE-fractionator (Life Technologies) and ethanol precipitation overnight. The resulting RNA was directionally ligated, reverse-transcribed and RNaseH treated. After trial PCR to assess library quality and quantity, 30 μl cDNA was run on a native 6% PAGE gel. The 90–120-bp size window (corresponding to 50–80-bp RNA insert size) was cut from the gel, shredded and inserted directly into a 400 µl PCR reaction using standard WT-Seq kit components and submitted to 11–15 cycles of PCR. The PCR product was phenol-chloroform extracted, ethanol precipitated and re-suspended in 20 μl WT-Seq gel loading buffer. The resulting sample was run on a 6% native PAGE gel, and the 150–175-bp size range (corresponding to 60–85 bp) was cut from the gel, shredded, and extracted overnight in WT-Seq PAGE elution buffer. The resulting library was filtered through 0.45 μm spin filters (Life Technologies) to remove gel pieces and ethanol precipitated.


title: UV_RNA-Seq

description: Suspension of cells were exposed to UV (254 nm, 200 Î¼W cm-2) in potassium phosphate buffer

treatment_protocol: Cells were harvested at the late-log phase (2 x 108  CFUs mL-1) and then washed twice with equal volumes of potassium phosphate buffer (100 mM, pH 7.0). UV light (254 nm, 200 uW cm-2) was used to irradiate a 20 mL suspension for 5 min in a 9 cm plate with stirring. As a control, an additional non-irradiated suspension was incubated for the same duration. After treatment, cells were harvested by centrifugation at 8,000 rpm for 3 min.

value: UV


title: ChIP-Seq analysis of H3K9ac in human HUES64 derived CD184+ cells; DNA_Lib 238

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 238
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8693
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9460
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM773003_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9ac.DNA_Lib_238.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 238-DNA_Lib 238-DNA_Lib 238-DNA_Lib 238-DNA_Lib 238.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 238, 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.10825
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,879,749
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1142
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1597
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9982
IROC_PERCENTILE: 95
POISSON_SCORE: 0.1982
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM773003_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9ac.DNA_Lib_238.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 238-DNA_Lib 238-DNA_Lib 238-DNA_Lib 238-DNA_Lib 238.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 238, 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.11089
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 5
BROWSER_TRACK_NAME: hDCE H3K9ac 38
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9ac Library DNA_Lib 238 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,879,749
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1142
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1597
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9982
IROC_PERCENTILE: 95
POISSON_SCORE: 0.1982
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 238

value: CD184+ endoderm cultured cells

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

value: genomic DNA

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 137

value: differentiated

value: Male

value: Harvard University

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K36me3 in human mid frontal lobe cells; DNA_Lib 610

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 610
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8703
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9448
****************
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: GSM773013_BI.Brain_Mid_Frontal_Lobe.H3K36me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 610-DNA_Lib 610-DNA_Lib 610.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Mid Frontal Lobe, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10598
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,090,545
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0733
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1774
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.8973
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3141
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM773013_BI.Brain_Mid_Frontal_Lobe.H3K36me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 610-DNA_Lib 610-DNA_Lib 610.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Mid Frontal Lobe, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10862
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 5
BROWSER_TRACK_NAME: BMFL H3K36me3 49 10
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K36me3 Donor 149 Library DNA_Lib 610 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,090,545
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0733
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1774
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.8973
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3141
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 610

value: Brain, Mid Frontal Lobe

value: Post-Mortem

value: no AD evident at demise

value: Mid Frontal Lobe

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: Histone H3K36me3

value: Branson


title: ChIP-Seq analysis of H3K27ac in human CD25- CD45RA+ naive cells; DNA_Lib 730

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 730
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8694
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9443
****************
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: GSM773004_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K27ac.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 730-DNA_Lib 730-DNA_Lib 730-DNA_Lib 730.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10702
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,051,302
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.5702
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.577
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9953
IROC_PERCENTILE: 68
POISSON_SCORE: 0.6134
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773004_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K27ac.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 730-DNA_Lib 730-DNA_Lib 730-DNA_Lib 730.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10966
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 5
BROWSER_TRACK_NAME: CCCN H3K27ac 62 30
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 730 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,051,302
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.5702
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.577
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9953
IROC_PERCENTILE: 68
POISSON_SCORE: 0.6134
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 730

value: BioSam 133

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: presumed normal

value: genomic DNA

tag: markers

value: CD4+ T cell

value: CD25- CD45RA+ naive

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: Protein A-Sepharose 4B

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K36me3 in human hippocampus middle cells; DNA_Lib 583

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 583
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8708
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
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: GSM773018_BI.Brain_Hippocampus_Middle.H3K36me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 583-DNA_Lib 583-DNA_Lib 583.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Hippocampus Middle, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10601
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,798,145
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1297
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.2421
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9147
IROC_PERCENTILE: 45
POISSON_SCORE: 0.3538
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM773018_BI.Brain_Hippocampus_Middle.H3K36me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 583-DNA_Lib 583-DNA_Lib 583.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10865
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 5
BROWSER_TRACK_NAME: BHM H3K36me3 49 83
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K36me3 Donor 149 Library DNA_Lib 583 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,798,145
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1297
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.2421
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9147
IROC_PERCENTILE: 45
POISSON_SCORE: 0.3538
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 583

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD evident at demise

value: Hippocampus Middle

value: Male

value: Primary Tissue

value: Brain

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam


title: kumo mutant

city: Singapore

first: Toshie

last: Kai

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
The adapter sequences were removed from the reads and the resulting clipped small RNA sequences were mapped to the Release 5 genome. We ignored the sequences matching to the Uextra region of drosophila genome. Only reads matching to the fly genome without any mismatches were accounted.  small RNA counts were normalized to small non-coding RNAs. For the piRNA analysis, small RNAs, which exceeded 22 nt in length and did not match any other defined class of small RNAs such as  miRNA, rRNA, snRNA etc, were taken in consideration.
Genome Build:
kumo-mutant-genome-mappers.txt: Dmel rel 5

organism: Drosophila melanogaster

source_name: Ovarian tissue

growth_protocol: 25 degree Centigrade

extract_protocol: Trizol Phenol/chloroform extraction. Small RNA were isolated by size fractionation and were ligated to adapter 5'TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG 3'. Reverse transcription and PCR was followed as per manufacturer's instructions. Purified amplicons were sequenced on Illumina Genome Analyzer II.

tag: tissue

value: Ovaries


title: ChIP-Seq analysis of H3K27ac in human angular gyrus cells; DNA_Lib 634

description:
sample_term_id: UBERON_0002686
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 634
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8706
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9456
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM773016_BI.Brain_Angular_Gyrus.H3K27ac.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 634-DNA_Lib 634-DNA_Lib 634.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on Brain Angular Gyrus, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10624
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,783,805
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.1411
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.2157
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9491
IROC_PERCENTILE: 24
POISSON_SCORE: 0.3726
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773016_BI.Brain_Angular_Gyrus.H3K27ac.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 634-DNA_Lib 634-DNA_Lib 634.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from Brain Angular Gyrus, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10888
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 5
BROWSER_TRACK_NAME: BAG H3K27ac 49 34
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus Histone H3K27ac Donor 149 Library DNA_Lib 634 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,783,805
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.1411
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.2157
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9491
IROC_PERCENTILE: 24
POISSON_SCORE: 0.3726
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 634

value: Brain, Angular Gyrus

value: genomic DNA

value: Angular gyrus

value: Rush University Medical Center

value: 81.0 Years

value: Branson


title: kumo heterozygous

data_processing:
The adapter sequences were removed from the reads and the resulting clipped small RNA sequences were mapped to the Release 5 genome. We ignored the sequences matching to the Uextra region of drosophila genome. Only reads matching to the fly genome without any mismatches were accounted.  small RNA counts were normalized to small non-coding RNAs. For the piRNA analysis, small RNAs, which exceeded 22 nt in length and did not match any other defined class of small RNAs such as  miRNA, rRNA, snRNA etc, were taken in consideration.
Genome Build:
kumo-heterozygous-genome-mappers.txt: Dmel rel 5


title: ChIP-Seq analysis of H3K27me3 in human HUES64 derived CD184+ cells; DNA_Lib 239

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 239
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8692
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9460
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM773002_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27me3.DNA_Lib_239.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 239-DNA_Lib 239-DNA_Lib 239-DNA_Lib 239-DNA_Lib 239.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 239, 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.10817
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,625,756
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1855
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.2397
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9874
IROC_PERCENTILE: 86
POISSON_SCORE: 0.343
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM773002_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27me3.DNA_Lib_239.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 239-DNA_Lib 239-DNA_Lib 239-DNA_Lib 239-DNA_Lib 239.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 239, 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.11081
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 5
BROWSER_TRACK_NAME: hDCE H3K27me3 39
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K27me3 Library DNA_Lib 239 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,625,756
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1855
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.2397
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9874
IROC_PERCENTILE: 86
POISSON_SCORE: 0.343
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 239

value: CD184+ endoderm cultured cells

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

value: presumed normal

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 137

value: Cell Line

value: differentiated

value: Harvard University

value: Protein A-Sepharose 4B

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K9me3 in human hippocampus middle cells; DNA_Lib 581

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 581
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8707
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
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: GSM773017_BI.Brain_Hippocampus_Middle.H3K9me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 581-DNA_Lib 581-DNA_Lib 581.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Hippocampus Middle, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10801
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,793,616
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0232
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.0937
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.674
IROC_PERCENTILE: 14
POISSON_SCORE: 0.2315
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM773017_BI.Brain_Hippocampus_Middle.H3K9me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 581-DNA_Lib 581-DNA_Lib 581.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11065
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 5
BROWSER_TRACK_NAME: BHM H3K9me3 49 81
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K9me3 Donor 149 Library DNA_Lib 581 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,793,616
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0232
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.0937
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.674
IROC_PERCENTILE: 14
POISSON_SCORE: 0.2315
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 581

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD evident at demise

value: genomic DNA

value: Hippocampus Middle

value: Male

value: Primary Tissue

value: Brain

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me3 in human inferior temporal lobe cells; DNA_Lib 627

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 627
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8686
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9458
****************
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: GSM772996_BI.Brain_Inferior_Temporal_Lobe.H3K4me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 627-DNA_Lib 627-DNA_Lib 627.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Inferior Temporal Lobe, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10657
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,951,540
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3087
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3465
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9996
IROC_PERCENTILE: 65
POISSON_SCORE: 0.3777
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772996_BI.Brain_Inferior_Temporal_Lobe.H3K4me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 627-DNA_Lib 627-DNA_Lib 627.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10921
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 5
BROWSER_TRACK_NAME: BITL H3K4me3 49 27
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K4me3 Donor 149 Library DNA_Lib 627 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,951,540
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3087
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3465
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9996
IROC_PERCENTILE: 65
POISSON_SCORE: 0.3777
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 627

value: Brain, Inferior Temporal Lobe

value: Inferior Temporal Lobe

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: Histone H3K4me3

value: Branson


title: ChIP-Seq analysis of H3K27ac in human hiPS-18a cells; DNA_Lib 349

description:
sample_term_id: NTR_0001165
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 349
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8723
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9471
****************
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: GSM773033_BI.iPS-18a.H3K27ac.DNA_Lib_349.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 349-DNA_Lib 349-DNA_Lib 349-DNA_Lib 349.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-18a Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on the iPS-18a Cell Line, Library DNA_Lib 349, 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.10735
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,977,766
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.0365
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.0872
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9669
IROC_PERCENTILE: 32
POISSON_SCORE: 0.1509
POISSON_PERCENTILE: 3
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773033_BI.iPS-18a.H3K27ac.DNA_Lib_349.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 349-DNA_Lib 349-DNA_Lib 349-DNA_Lib 349.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18a Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the iPS-18a Cell Line, Library DNA_Lib 349, 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.10999
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 5
BROWSER_TRACK_NAME: iPS18a H3K27ac 49
BROWSER_TRACK_DESCRIPTION: BI iPS-18a Cell Line Histone H3K27ac Library DNA_Lib 349 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,977,766
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.0365
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.0872
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9669
IROC_PERCENTILE: 32
POISSON_SCORE: 0.1509
POISSON_PERCENTILE: 3
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: induced pleuripotent 18a stem cell line; DNA_Lib 349

value: induced pluripotent stem cells

value: BioSam 173

value: iPS-18a Cell Line

value: induced pluripotent cells

value: 10% KOSR (Invitrogen)

value: genomic DNA

value: presumed normal

value: BioSAli 176

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K27ac in human inferior temporal lobe cells; DNA_Lib 626

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 626
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8685
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9458
****************
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: GSM772995_BI.Brain_Inferior_Temporal_Lobe.H3K27ac.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 626-DNA_Lib 626-DNA_Lib 626.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on Brain Inferior Temporal Lobe, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10749
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,823,926
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.1807
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.258
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.959
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4254
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772995_BI.Brain_Inferior_Temporal_Lobe.H3K27ac.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 626-DNA_Lib 626-DNA_Lib 626.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11013
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 5
BROWSER_TRACK_NAME: BITL H3K27ac 49 26
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K27ac Donor 149 Library DNA_Lib 626 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,823,926
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.1807
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.258
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.959
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4254
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 626

value: Brain, Inferior Temporal Lobe

value: Post-Mortem

value: no AD evident at demise

value: Inferior Temporal Lobe

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam


title: ChIP-Seq analysis of H3K9me3 in human hiPS-18a cells; DNA_Lib 343

description:
sample_term_id: NTR_0001165
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 343
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8713
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9471
****************
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: GSM773023_BI.iPS-18a.H3K9me3.DNA_Lib_343.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 343-DNA_Lib 343-DNA_Lib 343-DNA_Lib 343.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-18a Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the iPS-18a Cell Line, Library DNA_Lib 343, 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.10681
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,843,140
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1009
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.1324
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.8845
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3467
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773023_BI.iPS-18a.H3K9me3.DNA_Lib_343.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 343-DNA_Lib 343-DNA_Lib 343-DNA_Lib 343.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18a Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the iPS-18a Cell Line, Library DNA_Lib 343, 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.10945
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 5
BROWSER_TRACK_NAME: iPS18a H3K9me3 43
BROWSER_TRACK_DESCRIPTION: BI iPS-18a Cell Line Histone H3K9me3 Library DNA_Lib 343 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,843,140
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1009
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.1324
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.8845
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3467
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: induced pleuripotent 18a stem cell line; DNA_Lib 343

value: induced pluripotent stem cells

value: BioSam 173

value: iPS-18a Cell Line

value: induced pluripotent cells

value: 10% KOSR (Invitrogen)

value: genomic DNA

value: presumed normal

value: BioSAli 176

value: Cell Line

value: undifferentiated

value: Unknown

value: Protein A-Sepharose 4B

value: Histone H3K9me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human inferior temporal lobe cells; DNA_Lib 625

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 625
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8684
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9458
****************
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: GSM772994_BI.Brain_Inferior_Temporal_Lobe.H3K9me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 625-DNA_Lib 625-DNA_Lib 625.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Inferior Temporal Lobe, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10603
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,336,640
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0344
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.1167
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.723
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2673
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772994_BI.Brain_Inferior_Temporal_Lobe.H3K9me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 625-DNA_Lib 625-DNA_Lib 625.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10867
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 5
BROWSER_TRACK_NAME: BITL H3K9me3 49 25
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K9me3 Donor 149 Library DNA_Lib 625 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,336,640
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0344
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.1167
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.723
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2673
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 625

value: Brain, Inferior Temporal Lobe

value: Post-Mortem

value: no AD evident at demise

value: Inferior Temporal Lobe

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug


title: ChIP-Seq analysis of H3K4me3 in human hippocampus middle cells; DNA_Lib 586

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 586
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8712
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
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: GSM773022_BI.Brain_Hippocampus_Middle.H3K4me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 586-DNA_Lib 586-DNA_Lib 586.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Hippocampus Middle, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10849
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,960,935
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2519
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.2914
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.3306
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM773022_BI.Brain_Hippocampus_Middle.H3K4me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 586-DNA_Lib 586-DNA_Lib 586.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11113
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 5
BROWSER_TRACK_NAME: BHM H3K4me3 49 86
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K4me3 Donor 149 Library DNA_Lib 586 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,960,935
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2519
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.2914
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.3306
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 586

value: Brain, Hippocampus Middle

value: genomic DNA

value: Hippocampus Middle

value: 10 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of WCE in human CD25- CD45RO+ mem cells; DNA_Lib 722

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 722
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8689
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9449
****************
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: GSM772999_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.Input.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 722-DNA_Lib 722-DNA_Lib 722-DNA_Lib 722.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10675
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,391,347
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0086
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.0882
HOTSPOT_PERCENTILE: 97
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1344
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772999_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.Input.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 722-DNA_Lib 722-DNA_Lib 722-DNA_Lib 722.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10939
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 5
BROWSER_TRACK_NAME: CCCM Input 62 22
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells ChIP-Seq Input Donor 62 Library DNA_Lib 722 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,391,347
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0086
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.0882
HOTSPOT_PERCENTILE: 97
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1344
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 722

value: BioSam 132

value: CD4+ CD25- CD45RO+ Memory Primary Cells

value: presumed normal

value: CD4+ T cell

value: CD25- CD45RO+ mem

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: standard

value: ChIP-Seq Input

value: Input

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human inferior temporal lobe cells; DNA_Lib 623

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 623
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8682
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9458
****************
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: GSM772992_BI.Brain_Inferior_Temporal_Lobe.H3K4me1.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 623-DNA_Lib 623-DNA_Lib 623.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Inferior Temporal Lobe, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10807
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,962,495
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.187
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.282
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.949
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4586
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772992_BI.Brain_Inferior_Temporal_Lobe.H3K4me1.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 623-DNA_Lib 623-DNA_Lib 623.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11071
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 5
BROWSER_TRACK_NAME: BITL H3K4me1 49 23
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K4me1 Donor 149 Library DNA_Lib 623 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,962,495
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.187
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.282
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.949
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4586
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 623

value: Brain, Inferior Temporal Lobe

value: Post-Mortem

value: no AD evident at demise

value: genomic DNA

value: Inferior Temporal Lobe

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: Abcam

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K36me3 in human inferior temporal lobe cells; DNA_Lib 628

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 628
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8672
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9458
****************
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: GSM772982_BI.Brain_Inferior_Temporal_Lobe.H3K36me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 628-DNA_Lib 628-DNA_Lib 628.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Inferior Temporal Lobe, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10687
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,020,839
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1249
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.2136
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9343
IROC_PERCENTILE: 51
POISSON_SCORE: 0.3693
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772982_BI.Brain_Inferior_Temporal_Lobe.H3K36me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 628-DNA_Lib 628-DNA_Lib 628.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10951
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 5
BROWSER_TRACK_NAME: BITL H3K36me3 49 28
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K36me3 Donor 149 Library DNA_Lib 628 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,020,839
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1249
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.2136
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9343
IROC_PERCENTILE: 51
POISSON_SCORE: 0.3693
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 628

value: 10 ul bed volume

value: Histone H3K36me3

value: Branson