title: Whole genome shotgun bisulfite sequencing: H1 cell line diff. into neural progenitor cells; methylC-seq_h1-npc_r1a

description:
Design description: Whole genome shotgun bisulfite sequencing: H1 cell line diff. into neural progenitor cells
Library name: methylC-seq_h1-npc_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6201
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
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: GSM675542_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1-npc_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-npc_r1a.hg19.level.2.release.3
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells, Library methylC-seq_h1-npc_r1a were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6364
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HDNP BS 1a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Library methylC-seq_h1-npc_r1a EA Release 3

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.91
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM675542_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-npc_r1a-methylC-seq_h1-npc_r1b-methylC-seq_h1-npc_r1c-methylC-seq_h1-npc_r2a-methylC-seq_h1-npc_r2b.hg19.level.2.release.3
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6367
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HDNP BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Combined Libraries EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.91
SPECIAL NOTE: generated from combined data in GSM675542, GSM675543, GSM675544, GSM675545, GSM675546 (thus .wig files on these records are identical)

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

source_name: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); methylC-seq_h1-npc_r1a

tag: Sex

value: Replicate 1

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole genome shotgun bisulfite sequencing: H1 cell line diff. into neural progenitor cells; methylC-seq_h1-npc_r2a

status: Public on Feb 16 2011

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
Design description: Whole genome shotgun bisulfite sequencing: H1 cell line diff. into neural progenitor cells
Library name: methylC-seq_h1-npc_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6204
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
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: GSM675545_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1-npc_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-npc_r2a.hg19.level.2.release.3
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells, Library methylC-seq_h1-npc_r2a were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6362
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HDNP BS 2a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Library methylC-seq_h1-npc_r2a EA Release 3

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.95
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM675545_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-npc_r1a-methylC-seq_h1-npc_r1b-methylC-seq_h1-npc_r1c-methylC-seq_h1-npc_r2a-methylC-seq_h1-npc_r2b.hg19.level.2.release.3
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6367
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HDNP BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Combined Libraries EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.91
SPECIAL NOTE: generated from combined data in GSM675542, GSM675543, GSM675544, GSM675545, GSM675546 (thus .wig files on these records are identical)

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

molecule: genomic DNA

organism: Homo sapiens

source_name: H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); methylC-seq_h1-npc_r2a

extract_protocol: Library construction protocol: Five µg of genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 100-150 bp, followed by end repair and addition of a 3' A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 31 µM dNTPs, 1 µl Primer 1, 1 µl Primer 2 (50 µl final). The thermocycling parameters were: 95C 2 min, 98C 30 sec, then 4-8 cycles of 98C 15 sec, 60C 30 sec and 72C 4 min, ending with one 72C 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to three independent libraries from the same biological sample.

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: embryonic stem cell differentiated into neural progenitor cells

value: H1 cells were differentiated by culturing in insulin, SB, Noggin

tag: passage

tag: medium

value: TeSR

value: Male

tag: batch

value: Replicate 2

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg


title: D.yak_E0-4h_KW3-Pcl-D2_INPUT_1

status: Public on Feb 15 2011

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

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

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

organism: Drosophila yakuba

growth_protocol: 1. the iso1 (y; bw cn sp) flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No Treatment

tag: developmental stage


title: RNA_whole_worm_mixed_stages [mskcc]

city: New York

first: Kristin

middle: C

last: Gunsalus

state: NY

department: Biology

institute: NYU Center for Genomics and Systems Biology

description:
streaked_minipools
This run contains 49,152 barcoded amplicons which are the deconvolved minipools from Sample GSM659170.
It also contains an additional 5,952 minipools without barcodes.

library_source: transcriptomic

data_processing: The rawdata .sff file, and the .fna and .qual processed data files, were generated by the 454 GS FLX System Software version 2.3.  The processed data .sam files were generated by mapping the reads to the WS190 genome using the Galaxy server's LASTZ tool (http://main.g2.bx.psu.edu/).  LASTZ is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. This version is geared towards aligning short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence.  Parameters used were: --strand=both, --seed=12of19, --transition=1, --gap_open_penalty=400, -- gap_extend_penalty=30, --output=result.sam, --format=sam

molecule: total RNA

organism: Caenorhabditis elegans

source_name: N2 wildtype

growth_protocol: Mixed stage worms were grown on 10 cm2 NGM plates seeded with OP50.

extract_protocol:
Total RNA was incubated at 55°C for one hour in presence of Superscript III Reverse Transcriptase (Invitrogen) and a universal VN poly-dT reverse primer, according the manufacture specifications. 3'UTR amplification were performed in 96-well plates format using transcript-specific forward primers and the universal reverse primer in presence of RNA prepared in the first strand reaction, using the following PCR parameters: denaturing 94°C 30 sec, annealing 60°C 30 sec, extension 72°C for 3 minutes. 3'UTRs were recombined into pDONR P2R-P3 entry vector using the BP Clonase II Enzyme Mix kit (Invitrogen) following the manufacturer's specifications and transformed into MultiShot Stripwell TOP 10 plates (Invitrogen). The transformed bacteria were grown overnight at 37°C under kanamycin selection.   The 6,432 minipools were manually streaked into large agar plates and 8 single colonies each minipool (total 51,456 colonies) were manually recovered, propagated and pooled in 8 different sets using the Aquarius automated multi-channel pipetting system (Tecan Trading AG, Switzerland). Each set contains none or one unique 3'UTR isoform.  Plasmid DNA was recovered for each set using the Wizard Plus miniprep Kit (Promega) and used as template for PCR amplification reaction with the following barcoded primers (the barcode is in lowercase):
Forward primers:  GW_A catgGTTTCTCGTTCAACTTTCTTGTACAAAGTGGGA  GW_B tagtGTTTCTCGTTCAACTTTCTTGTACAAAGTGGGA  GW_C gatcGTTTCTCGTTCAACTTTCTTGTACAAAGTGGGA  GW_D cactGTTTCTCGTTCAACTTTCTTGTACAAAGTGGGA  GW_E tacgGTTTCTCGTTCAACTTTCTTGTACAAAGTGGGA  GW_F gagcGTTTCTCGTTCAACTTTCTTGTACAAAGTGGGA  GW_G ctgcGTTTCTCGTTCAACTTTCTTGTACAAAGTGGGA  GW_H atcgGTTTCTCGTTCAACTTTCTTGTACAAAGTGGGA  GW_T gtgaGTTTCTCGTTCAACTTTCTTGTACAAAGTGGGA
Reverse primers:  PolyA_A catgTAAAGTTGGATCCTCGAGTTTTTTTTTTTTTTT  PolyA_B actaTAAAGTTGGATCCTCGAGTTTTTTTTTTTTTTT  PolyA_C gatcTAAAGTTGGATCCTCGAGTTTTTTTTTTTTTTT  PolyA_D agtgTAAAGTTGGATCCTCGAGTTTTTTTTTTTTTTT  PolyA_E gctaTAAAGTTGGATCCTCGAGTTTTTTTTTTTTTTT  PolyA_F gctcTAAAGTTGGATCCTCGAGTTTTTTTTTTTTTTT  PolyA_G gcagTAAAGTTGGATCCTCGAGTTTTTTTTTTTTTTT  PolyA_H cgatTAAAGTTGGATCCTCGAGTTTTTTTTTTTTTTT
The PCR amplicons were then pooled, gel purified and prepared for 454 sequencing using manufacture instructions.

treatment_protocol: RNA extraction was performed following the vendor’s protocol with the following modification: 3 times freeze/thaw/vortex and disruption with pellet pestle was included to increase worm lysis efficiency.

tag: genotype/variation

value: N2 wildtype

value: mixed stages


title: D.yak_E0-4h_KW3-Psq-D2_INPUT_1


title: D.yak_E0-4h_KW3-Kr-D2_INPUT_1


title: D.yak_E0-4h_KW3-Psq-D2_ChIPSeq_1 and 2

tag: antibody name

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: D.yak_E0-4h_KW3-Kr-D2_ChIPSeq_1


title: D.yak_WPP_KW3-Trl-D2_ChIPSeq_1 and 2


title: D.yak_E0-4h_KW3-Trl-D2_INPUT_1


title: D.yak_E0-4h_KW3-Trl-D2_ChIPSeq_1 and 2


title: D.sim_E0-4h_H3K27me3_INPUT_1

organism: Drosophila simulans


title: D.yak_WPP_KW3-Trl-D2_INPUT_1


title: D.sim_WPP_H3K27me3_INPUT_1


title: D.sim_E0-4h_H3K27me3_ChIPSeq_1 and 2

value: Upstate-Millipore


title: D.sim_WPP_H3K27me3_ChIPSeq_1 and 2


title: D.yak_E0-4h_KW3-Pcl-D2_ChIPSeq_1 and 2


title: D.sim_E0-4h_KW3-Kr-D2_INPUT_1


title: D.sim_E0-4h_KW3-Pcl-D2_ChIPSeq_1 and 2


title: D.sim_E0-4h_KW3-Pcl-D2_INPUT_1


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in hESC H9 Cells; renlab.H4K8ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: YL241
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5608
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667637_UCSD.H9.H4K8ac.YL241.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K8ac ChIP-Seq on the H9 Cell Line, Library YL241 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.6278
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 3

QUALITY SCORES:
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0319
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1714
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.7323
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2937
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM667637_UCSD.H9.H4K8ac.YL241.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K8ac ChIP-Seq read mappings from the H9 Cell Line, Library YL241 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.6620
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 3
BROWSER_TRACK_NAME: H9 H4K8ac 41
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H4K8ac Library YL241 EA Release 3

QUALITY SCORES:
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0319
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1714
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.7323
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2937
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H4K8ac.hESC.H9.01.01

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

value: H9 Cell Line

value: genomic DNA

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: Between 30 and 50

value: mTeSER

value: Female

value: Histone H4K8ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: D.sim_E0-4h_KW3-Trl-D2_INPUT_1


title: D.sim_WPP_KW3-Pcl-D2_ChIPSeq_1 and 2


title: D.sim_E0-4h_KW3-Kr-D2_ChIPSeq_1 and 2


title: D.sim_E0-4h_KW3-Trl-D2_ChIPSeq_1 and 2


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in hESC H9 Cells; renlab.H3K9me3.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: SK100
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5612
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667631_UCSD.H9.H3K9me3.SK100.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the H9 Cell Line, Library SK100 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.6275
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 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.1683
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.2196
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.873
IROC_PERCENTILE: 58
POISSON_SCORE: 0.4039
POISSON_PERCENTILE: 85

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

ANALYSIS FILE NAME: GSM667631_UCSD.H9.H3K9me3.SK100.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H9 Cell Line, Library SK100 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.6617
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 3
BROWSER_TRACK_NAME: H9 H3K9me3 00
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K9me3 Library SK100 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.1683
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.2196
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.873
IROC_PERCENTILE: 58
POISSON_SCORE: 0.4039
POISSON_PERCENTILE: 85

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K9me3.hESC.H9.01.01

value: Cell Line

value: Histone H3K9me3

value: Abcam


title: D.sim_WPP_KW3-Pcl-D2_INPUT_1


title: Reference Epigenome: ChIP-Seq Input from hESC H1 Cells; renlab.Input.hESC.H1.08.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from hESC H1 Cells. Sequencing was done on the Illumina GAIIx platform.
Library name: YL328
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5977
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5976
****************
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: GSM667641_UCSD.H1.Input.YL328.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC.H1.08.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library YL328 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.6289
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 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 30
FINDPEAKS_SCORE: 0.0733
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.2124
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.7472
IROC_PERCENTILE: 41
POISSON_SCORE: 0.2707
POISSON_PERCENTILE: 97

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

ANALYSIS FILE NAME: GSM667641_UCSD.H1.Input.YL328.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC.H1.08.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library YL328 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.6631
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 3
BROWSER_TRACK_NAME: H1 Input 28
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line ChIP-Seq Input Library YL328 EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 30
FINDPEAKS_SCORE: 0.0733
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.2124
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.7472
IROC_PERCENTILE: 41
POISSON_SCORE: 0.2707
POISSON_PERCENTILE: 97

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.Input.hESC.H1.08.01

value: H1 Cell Line

value: Male

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me2 in hESC H9 Cells; renlab.H3K79me2.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me2 in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: SK190
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5991
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667630_UCSD.H9.H3K79me2.SK190.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me2 ChIP-Seq on the H9 Cell Line, Library SK190 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.6299
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 3

QUALITY SCORES:
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.1654
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2115
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9826
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3066
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM667630_UCSD.H9.H3K79me2.SK190.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me2 ChIP-Seq read mappings from the H9 Cell Line, Library SK190 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.6641
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 3
BROWSER_TRACK_NAME: H9 H3K79me2 90
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K79me2 Library SK190 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.1654
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2115
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9826
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3066
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K79me2.hESC.H9.01.01

value: H9 Cell Line

value: genomic DNA

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: Histone H3K79me2


title: RNA_C3

first: Carolyn

middle: Elizabeth

last: Cain

address: 920 E. 58th Street - CLSC 301

department: Human Genetics

institute: The University of Chicago

description: polyA RNA

data_processing:
Alignment: Raw data was analyzed by Illumina pipeline 1.4.0. Reads were mapped to each appropriate genome (hg18, panTro2, rheMac2) with MAQ version 0.6.8. Reads were filtered to remove those with a MAQ quality score less than 10.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) with default parameters, except for a p-value cutoff of 0.0005.
Counts of reads mapped to exons: The RNA-seq reads from each individual were mapped to a set of previously annotated 150,107 orthologous exons from 20,689 genes in human, chimpanzee, and rhesus macaque (Bleckhman et al. 2010). The output file for each individual has one line for each exon to which at least one read mapped, and two columns. The first column includes the Ensembl Gene ID, exon number, and chromosomal position of the exon, separated by dots. The second column shows the number of reads mapped to that exon for that individual.

organism: Pan troglodytes

source_name: LCL

growth_protocol: Regardless of species, cells were maintained at identical conditions of 37° with 5% CO2 in RPMI media with 15% FBS, supplemented with 2mM L-glutamate, 100 I.U./mL penicillin and 100ug/mL streptomycin. Cells were split when confluent (~900k cells/mL split to ~300k cells/mL) every 2-3 days.

extract_protocol:
RNA Extraction: RNA was extracted using a QIAGEN RNeasy Mini Kit.
Sequencing libraries were prepared as described previously (Marioni et al. 2008). Briefly, DNA (or cDNA) was end-repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. A single 'A' base was added with Klenow fragment (3’ to 5’ exo-) and dATP. Illumina adapters were ligated with DNA ligase, a gel extraction was performed to size select for fragments ~200bp, and the samples were PCR amplified for 15 cycles. After purification, libraries were sequenced on an Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: ChIP: Briefly, cells were fixed with 1.5% formaldehyde, lysed with a 1% SDS lysis buffer, and chromatin was sonicated to ~200-300bp with a Diagenode Bioruptorsonicated. Each immunoprecipitation used chromatin from 10 million cells, incubated with 4ug of H3K4me3 antibody (ab8580, lot 500368, Abcam) at 4 degrees C overnight. The antibody and bound chromatin was collected with protein G beads, which were washed several times before eluting the chromatin with a 1% SDS, 0.1M NaHCO3 elution buffer. Protein was decrosslinked NaCl, and RNA and protein were degraded with RNase A and proteinase K, respectively. DNA was cleaned with a QIAGEN QIAquick PCR Purification Kit. For more detailed protocol, see Cain et al. 2010.

tag: chip antibody

tag: cell type

value: lymphoblastoid cell line


title: Reference Epigenome: ChIP-Seq Analysis of H3K56ac in hESC H9 Cells; renlab.H3K56ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K56ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: YL238
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5989
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667628_UCSD.H9.H3K56ac.YL238.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K56ac ChIP-Seq on the H9 Cell Line, Library YL238 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.6280
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 3

QUALITY SCORES:
NUMBER_OF_H3K56ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0217
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1193
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.5801
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2086
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM667628_UCSD.H9.H3K56ac.YL238.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K56ac ChIP-Seq read mappings from the H9 Cell Line, Library YL238 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.6622
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 3
BROWSER_TRACK_NAME: H9 H3K56ac 38
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K56ac Library YL238 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K56ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0217
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1193
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.5801
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2086
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K56ac.hESC.H9.01.01

tag: sample alias

value: Between 30 and 50

value: mTeSER

tag: Sex

value: Female

value: Histone H3K56ac

value: Biorupter

value: 500 micrograms


title: RNA_C2

description: polyA RNA


title: Reference Epigenome: ChIP-Seq Analysis of H2BK12ac in hESC H9 Cells; renlab.H2BK12ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK12ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK112
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6007
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6006
****************
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: GSM667611_UCSD.H9.H2BK12ac.AK112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK12ac ChIP-Seq on the H9 Cell Line, Library AK112 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.6297
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 3

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0069
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0757
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1833
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM667611_UCSD.H9.H2BK12ac.AK112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK12ac ChIP-Seq read mappings from the H9 Cell Line, Library AK112 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.6639
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 3
BROWSER_TRACK_NAME: H9 H2BK12ac 12
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H2BK12ac Library AK112 EA Release 3

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0069
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0757
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1833
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H2BK12ac.hESC.H9.02.01

tag: sample common name

tag: molecule

value: Cell Line

value: Histone H2BK12ac

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: RNA_C1

description: polyA RNA


title: Input_C

description: Input DNA


title: Reference Epigenome: ChIP-Seq Analysis of H4K5ac in hESC H9 Cells; renlab.H4K5ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K5ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: YL240
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5604
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667635_UCSD.H9.H4K5ac.YL240.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K5ac.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H4K5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K5ac ChIP-Seq on the H9 Cell Line, Library YL240 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.6264
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 3

QUALITY SCORES:
NUMBER_OF_H4K5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0302
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.15
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6856
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2578
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM667635_UCSD.H9.H4K5ac.YL240.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K5ac.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H4K5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K5ac ChIP-Seq read mappings from the H9 Cell Line, Library YL240 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.6606
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 3
BROWSER_TRACK_NAME: H9 H4K5ac 40
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H4K5ac Library YL240 EA Release 3

QUALITY SCORES:
NUMBER_OF_H4K5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0302
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.15
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6856
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2578
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H4K5ac.hESC.H9.01.01

value: H9 Cell Line

tag: disease

tag: line

value: Histone H4K5ac

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in hESC H9 Cells; renlab.H3K27me3.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: SK99
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5985
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667622_UCSD.H9.H3K27me3.SK99.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the H9 Cell Line, Library SK99 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.6294
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 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 20
FINDPEAKS_SCORE: 0.2484
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.3339
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9276
IROC_PERCENTILE: 80
POISSON_SCORE: 0.3684
POISSON_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM667622_UCSD.H9.H3K27me3.SK99.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H9 Cell Line, Library SK99 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.6636
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 3
BROWSER_TRACK_NAME: H9 H3K27me3 99
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K27me3 Library SK99 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 20
FINDPEAKS_SCORE: 0.2484
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.3339
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9276
IROC_PERCENTILE: 80
POISSON_SCORE: 0.3684
POISSON_PERCENTILE: 60

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K27me3.hESC.H9.01.01

value: genomic DNA

value: James Thompson Laboratory

tag: lineage

value: Embryonic Stem Cell

tag: passage

value: Histone H3K27me3

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K23ac in hESC H9 Cells; renlab.H3K23ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: YL236
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6009
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667619_UCSD.H9.H3K23ac.YL236.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on the H9 Cell Line, Library YL236 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.6283
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 3

QUALITY SCORES:
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0082
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.0938
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.454
IROC_PERCENTILE: 50
POISSON_SCORE: 0.1718
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM667619_UCSD.H9.H3K23ac.YL236.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the H9 Cell Line, Library YL236 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.6625
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 3
BROWSER_TRACK_NAME: H9 H3K23ac 36
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K23ac Library YL236 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0082
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.0938
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.454
IROC_PERCENTILE: 50
POISSON_SCORE: 0.1718
POISSON_PERCENTILE: 25

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K23ac.hESC.H9.01.01

value: Between 30 and 50

tag: medium

value: mTeSER

value: Female

tag: batch

value: Histone H3K23ac


title: H3K4me3_C2

description: Chromatin IP against H3K4me3

value: lymphoblastoid cell line


title: Reference Epigenome: ChIP-Seq Analysis of H2BK5ac in hESC H9 Cells; renlab.H2BK5ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK5ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: YL244
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5606
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667612_UCSD.H9.H2BK5ac.YL244.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK5ac ChIP-Seq on the H9 Cell Line, Library YL244 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.6271
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 3

QUALITY SCORES:
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0211
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1227
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6287
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2312
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM667612_UCSD.H9.H2BK5ac.YL244.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK5ac ChIP-Seq read mappings from the H9 Cell Line, Library YL244 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.6613
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 3
BROWSER_TRACK_NAME: H9 H2BK5ac 44
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H2BK5ac Library YL244 EA Release 3

QUALITY SCORES:
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0211
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1227
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6287
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2312
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H2BK5ac.hESC.H9.01.01

value: Cell Line

value: Histone H2BK5ac

value: Biorupter

value: 500 micrograms


title: H3K4me3_C1

description: Chromatin IP against H3K4me3


title: RNA_R3

description: polyA RNA

organism: Macaca mulatta


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in hESC H9 Cells; renlab.H2AK5ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2AK5ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: SK193
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5480
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667608_UCSD.H9.H2AK5ac.SK193.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2AK5ac ChIP-Seq on the H9 Cell Line, Library SK193 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.6260
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 3

QUALITY SCORES:
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0951
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.4792
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1874
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM667608_UCSD.H9.H2AK5ac.SK193.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2AK5ac ChIP-Seq read mappings from the H9 Cell Line, Library SK193 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.6602
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 3
BROWSER_TRACK_NAME: H9 H2AK5ac 93
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H2AK5ac Library SK193 EA Release 3

QUALITY SCORES:
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0951
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.4792
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1874
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H2AK5ac.hESC.H9.01.01

value: H9 Cell Line

value: Histone H2AK5ac

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: D.pse_E0-4h_KW3-Trl-D2_INPUT_1

organism: Drosophila pseudoobscura

tag: developmental stage


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in hESC H9 Cells; renlab.H3K9me3.hESC.H9.02.01

description:
Design description: ChIP-Seq Analysis of H3K9me3 in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: SK200
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5610
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667632_UCSD.H9.H3K9me3.SK200.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the H9 Cell Line, Library SK200 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.6279
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 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.192
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2266
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.917
IROC_PERCENTILE: 85
POISSON_SCORE: 0.3564
POISSON_PERCENTILE: 69

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

ANALYSIS FILE NAME: GSM667632_UCSD.H9.H3K9me3.SK200.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H9 Cell Line, Library SK200 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.6621
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 3
BROWSER_TRACK_NAME: H9 H3K9me3 01
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K9me3 Library SK200 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.192
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2266
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.917
IROC_PERCENTILE: 85
POISSON_SCORE: 0.3564
POISSON_PERCENTILE: 69

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K9me3.hESC.H9.02.01

value: genomic DNA

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: Histone H3K9me3


title: RNA_R1

description: polyA RNA


title: H3K4me3_C3

description: Chromatin IP against H3K4me3


title: RNA_R2

description: polyA RNA


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in hESC H9 Cells; renlab.H3K4me1.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: YL123
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5987
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM667626_UCSD.H9.H3K4me1.YL123.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the H9 Cell Line, Library YL123 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.6269
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 28
FINDPEAKS_SCORE: 0.2741
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3782
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9583
IROC_PERCENTILE: 32
POISSON_SCORE: 0.4835
POISSON_PERCENTILE: 39

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

ANALYSIS FILE NAME: GSM667626_UCSD.H9.H3K4me1.YL123.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H9 Cell Line, Library YL123 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.6611
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 3
BROWSER_TRACK_NAME: H9 H3K4me1 23
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K4me1 Library YL123 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 28
FINDPEAKS_SCORE: 0.2741
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3782
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9583
IROC_PERCENTILE: 32
POISSON_SCORE: 0.4835
POISSON_PERCENTILE: 39

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K4me1.hESC.H9.01.01

value: Between 30 and 50

value: mTeSER

value: Histone H3K4me1


title: RNA_H1

description: polyA RNA

value: lymphoblastoid cell line


title: Input_R

description: Input DNA


title: D.pse_E0-4h_KW3-Trl-D2_ChIPSeq_1 and 2

tag: antibody name

value: White Lab


title: RNA_H3

description: polyA RNA


title: Input_H

description: Input DNA


title: D.pse_E0-4h_KW3-Psq-D2_INPUT_1


title: D.pse_WPP_H3K27me3_INPUT_1


title: H3K4me3_R3

description: Chromatin IP against H3K4me3


title: D.pse_WPP_H3K27me3_ChIPSeq_1 and 2

tag: manufacturer

value: Upstate-Millipore


title: wheat leaf_S_0H

city: BEIJING

first: mingming

last: xin

address: YUAN MING YUAN WEST ROAD 2, HAIDIAN DISTRICT

department: plant genetics and breeding

country: China

institute: China Agricultrual University

data_processing:
Automated base calling of the raw sequence and vector removal were performed with PHRED and CROSS MATCH programs. Trimmed 3′ and 5′ adapters sequences, removed RNAs less than 17 nt and polyA , only sequences longer than 17 nt with a unique ID were used for further analysis.
Processed data represents clean tags, 18-30 nt, tab delimited, sequence | count | length.

organism: Triticum aestivum

source_name: wheat young leaf

growth_protocol: Hexaploid wheat (Triticum aestivum L.) line ‘8866’ (S)(susceptible to wheat powdery mildew), ‘Pm30’ (Resistant to wheat powdery mildew),‘CS’ (sensitive to heat stress) and ‘TAM’ (tolerant to heat stress) were grown in a growth chamber at a relative humidity of 75% and 26/20℃ day and night temperature with light intensity of 3000 lx. 2 week-old plants were used for all experiments.

extract_protocol: Total RNA was isolated from the frozen leaves by using Trizol agent (TaKaRa, Inc., Dalian, China) according to the manufacturer’s instructions. Cloning of the small RNAs was performed as described by Sunkar and Zhu. Briefly, low molecular weight RNA was enriched by 0.5 M NaCl and 10% PEG8000 precipitation. About 100 μg low molecular weight RNA was separated on a denaturing 15% polyacrylamide gel. Labeled RNA oligonucleotides with 18 and 26 nt were used as size standards. The nucleotides from 18 to 26 nt were excised, and RNA was eluted overnight with 0.4M NaCl at 4˚C. The RNA was dephosphorylated by alkaline phosphatase (New England Biolabs Inc, Beijing China) and recovered by ethanol precipitated. The small RNAs were then ligated sequentially to RNA/DNA chimeric oligonucleotide adapters, and then reverse transcription was preformed, followed by PCR amplification. The resulting PCR products were sequenced using Solexa technology.

treatment_protocol: For powdery mildew infection, one isolate of Erysiphe graminis f. sp. tritici (Egt) (Isolate E09) was maintained on the wheat cultivar Fidel by weekly transfer to new plants. Inoculations were performed at a density of 100-150 conidia/mm2 by brushing plants. Leaves were collected at 12 hours after infection. For heat stress,the seedlings were subjected to 40°C (heat stress) for 1  hour and returned to normal conditions for 2 hours.

value: 8866 (susceptible to wheat powdery mildew,also designed as ‘S’)

tag: age

value: two week old

tag: tissue

value: leaf

tag: infection

value: control

tag: time

value: 0 hours


title: D.pse_E0-4h_KW3-Psq-D2_ChIPSeq_1 and 2

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

tag: lot/batch#

tag: catalog


title: RNA_H2

description: polyA RNA

tag: chip antibody

tag: cell type


title: H3K4me3_H3

description: Chromatin IP against H3K4me3


title: H3K4me3_R2

description: Chromatin IP against H3K4me3


title: Gingeras_K562_cytosol_longPolyA_1

status: Public on Feb 14 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisRnaSeq

molecule: polyA RNA

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/K562_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisRnaSeq

tag: cell

tag: cell organism

value: Human

tag: cell description

value: leukemia

tag: cell karyotype

value: cancer

tag: cell lineage

value: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

tag: cell sex

value: F

tag: localization

value: cytosol

tag: rnaextract

value: longPolyA

tag: replicate


title: H3K4me3_R1

description: Chromatin IP against H3K4me3


title: wheat_leaf_R_12H

tag: line

value: pm30 (resistant to wheat powdery mildew， also designed as ‘R’)

tag: age

value: powdery mildew

value: 12 hours


title: H3K4me3_H2

description: Chromatin IP against H3K4me3

value: lymphoblastoid cell line


title: D.pse_E0-4h_H3K27me3_INPUT_1

tag: developmental stage


title: Gingeras_K562_cytosol_longPolyA_2 (superseded by GSE94234)

description:
****************************
GSM672835 record metadata submitted on Feb 10 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE94234
****************************


title: Miguel_CMC__rep29

status: Public on Feb 12 2011

city: Shenzhen

first: Yao

last: Qiong

state: Guangdong

address: Beishan Industrial Zone,Yantian District

institute: BGI-SZ

description:
sample for paired-end library with insert size of 200 bp
library selection: different insertion size

data_processing: Filter adaptors, detect possible contamination of samples, count data output(including read length, total read counts, data production), and on this basis, accomplish standardized analysis and personalized information analysis.  (1) Reads alignment with reference genome     Align all reads against ref.c2t and ref.g2a with SOAPaligner after converting C to T  on forward strand, G to A on backward strand. Each reads mapping to an unique location with minimum mismatches and clear information of positive and negative chain will be defined as uniquely matching reads and used to determine the methylated C.  (2) Combine original sequences and the soap results , according to the reads ID in soap results, find the corresponding sequences which have not converted C to T or G to A in raw data ,and then use the corresponding sequences to substitute the sequences in soap results.  (3) Align the sequences against the reference, record the information of base sites, and according to these sites information , select the reads with better aligning results: align the human.fa sequence with soap results according to certain patterns, and use symbols to record the results , on the basis of the results, extract local fragment of reads with best aligning results, getting align matching results.  (4) According to the align matching results, select the best results among repeat present sequences , the selection criteria being to select reads with larger sum of aligning length, and judge a chain is Watson chain or Click chain.  (5) Perform a detail statistic on mappable reads and remove redundancy.  (6) Methylation level of whole genome and/or different regions are deduced from the original sequence.

source_name: iPSC clone (CMC28)

extract_protocol: a)  Mix up all genome DNA and randomly shear into fragments of 100~500bp.  b)  Repair the terminal of DNA fragments, 3'-dA and attach with methylation sequencing adaptors.  c)  Subject whole genome DNA to bisulfite processing.  d)  Subject to gel electrophoresis of 2% TAE, extract fragments of 320~380bp with IAquich Gel Extraction recycling, desalination and PCR amplification.  e)  Construct libraries with appropriate fragments for sequencing usin standard Illumina Genome Analyzer II protocol

value: iPSC clone


title: Miguel_CMC__rep32


title: Miguel_CMC__rep23

description:
sample for paired-end library with insert size of 150 bp
library selection: different insertion size


title: Miguel_CMC__rep28


title: H3K4me3_H1

description: Chromatin IP against H3K4me3


title: Miguel_CMC__rep22


title: Miguel_CMC__rep30

description:
sample for paired-end library with insert size of 250 bp
library selection: different insertion size


title: Miguel_CMC__rep20


title: Miguel_CMC__rep24


title: D.pse_E0-4h_H3K27me3_ChIPSeq_1 and 2

tag: antibody name

tag: manufacturer

value: Upstate-Millipore


title: Miguel_CMC__rep21


title: Miguel_CMC__rep31


title: Miguel_CMC__rep25


title: Miguel_CMC__rep19


title: Miguel_CMC__rep18


title: Miguel_CMC__rep27


title: Gingeras_H1-hESC_cell_longPolyA_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/H1_ES_protocol.pdf

value: Human Embryonic Stem Cells

value: normal

value: embryonic stem cells

value: M

value: cell


title: Miguel_CMC__rep16


title: wheat_leaf_R_0H

value: two week old

tag: tissue

value: leaf

tag: infection

value: control

tag: time

value: 0 hours


title: Miguel_CMC__rep14

tag: cell type


title: Miguel_CMC__rep13


title: Miguel_CMC__rep11


title: Miguel_CMC__rep15


title: Miguel_CMC__rep12


title: Miguel_CMC__rep10


title: Miguel_CMC__rep9


title: Miguel_CMC__rep17


title: Miguel_CMC__rep8


title: Miguel_CMC__rep2


title: Miguel_CMC__rep4


title: Miguel_CMC__rep3


title: aly_floral-16-mRNA2

status: Public on Feb 11 2011

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

country: Germany

institute: Max Planck Institute for Developmental Biology

data_processing: bed: We mapped mRNA-seq data to the A. lyrata genome using SHORE (http://shore.sourceforge.net)

organism: Arabidopsis lyrata

source_name: floral tissue

growth_protocol: 16°C, 16 hour light period

extract_protocol: RNA was extracted from floral tissue (stages 1-14) using the Trizol(Invitrogen) RNA extraction protocol. rRNAs were depleted from 10 μg of RNA using the Ribominus kit (Invitrogen). Tobacco acid pyrophosphatase (Epicentre Biotechnologies) was used to remove the 5’ CAP, followed by metal ion fragmentation for 10 minutes at 70oC (RNA fragmentation kit, Ambion). The RNA was dephosphorylated using CIP, then size selected for fragments of 100-150 nt by PAGE. RNA was extracted from the gel by semi-dry electrotransfer to DE81 chromatography paper (Whatman), followed by salt elution. The Illumina 3’ and 5’ sRNA adapters were sequentially ligated with size selection and re-phosphorylation by PNK between ligations. Following a further cycle of PAGE size selection, the RNA was reverse transcribed with Fermentas Revertaid and PCR amplified for 15 cycles with Phusion DNA polymerase (Finnzymes) before sequencing (Illumina sequencing-by-synthesis).

tag: strain

value: floral

value: stages 1-14


title: Miguel_CMC__rep7


title: Miguel_CMC__rep6


title: aly_floral-16-mRNA1


title: Miguel_CMC__rep1


title: aly_floral-16-mRNA4


title: colfloral-16-rep2

description: small RNA

data_processing: Sequencing adapters were removed and sequences without adapter were discarded. The txt files list unique sequences together with their counts.

organism: Arabidopsis thaliana

extract_protocol: Libraries were constructed as per (Mosher RA et al., 2009), except small RNA were isolated by PAGE, and RNA amplicons were reverse transcribed using the Fermentas Revertaid kit (Fermentas Life Sciences) and then amplified by PCR using the Phusion DNA polymerase (Finnzymes).

value: stage 1-14


title: c24floral-23-rep2

description: small RNA

growth_protocol: 23°C, 16 hour light period


title: c24floral-23-rep1

description: small RNA


title: colfloral-23-rep1

description: small RNA


title: Miguel_CMC__rep5


title: aly_floral-16-mRNA3


title: colfloral-16-rep1

description: small RNA


title: Pro-B cell Rad21

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

description:
Chromatin IP against Rad21
Sample ID: 8419
average insert size: 159 nt

data_processing:
Illumina GA pipeline v1.4
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm8, ncbi36) using bowtie 0.12.2 ( -v 2 --best --strata --tryhard  -m 1  --solexa1.3-quals   --chunkmbs 256)
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) program (http://liulab.dfci.harvard.edu/MACS/) version 1.6.3.1 using default parameters

organism: Mus musculus

source_name: Rad21 ChIP DNA from Pro-B cells

growth_protocol: Cells were cultured for 5 days.

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

treatment_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer(500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

value: Pro-B cell

tag: genotype

tag: antibody

tag: antibody vendor

value: Abcam

tag: antibody lot#

tag: antibody catalog#


title: DP T cell wt CTCF

description:
Chromatin IP against CTCF
Sample ID: 8307
average insert size: 348 nt

source_name: Ctcf ChIP DNA from DP T wt cells

value: DP T cell

value: wt

value: CTCF

value: Milipore


title: Mature B cell CTCF

description:
Chromatin IP against CTCF
Sample ID: 8310
average insert size: 307 nt

source_name: Ctcf ChIP DNA from Mature B cells

value: Mature B cell


title: Pro-B cell Rag2-/- CTCF

description:
Chromatin IP against CTCF
Sample ID: 8308
average insert size: 332 nt

source_name: Ctcf ChIP DNA from Pro-B cell Rag2-/- cells


title: t14hrs

city: Edinburgh

first: James

last: Prendergast

address: Crewe Road

country: United Kingdom

institute: MRC Human Genetics Unit

data_processing: Reads were mapped to the L. pneumophila Phil-1 genome (NC_002942.5) using the Bowtie short read aligner (PMID: 19261174) with the “--best” flag

organism: Legionella pneumophila

source_name: Whole cell

growth_protocol: Legionella pneumophila Phil-1 WT and the constitutively GFP-expressing bacterial strain Legionella pneumophila Phil-1 pMip.gfp ( both kindly provided by Antje Flieger, Wernigerode, Germany) were cultured on buffered charcoal-yeast extract agar (BCYE, Sigma-Aldrich, Gillingham, UK) for 3 days at 37°C (15) or grown in buffered yeast extract (BYE) broth at 37°C with shaking at 250 rpm. Bacterial growth was monitored at an optical density of 600 nm (OD600) after inoculation to an OD600 of 0.1. Acanthamoeba castellanii Neff (ATCC 30010) was cultured in PYG medium (Formedium, Norfolk, UK) at 30°C. The infection assays were performed according to Moffat and Tompkins. In brief A. castellanii cells were washed in A. c. buffer and adjusted to 106 cells per mL. 10 mL amoebal suspension was transferred to a 75 cm2 tissue culture flask and incubated at 37°C for 1 h. Stationary phase L. pneumophila Phil-1 grown on BCYE agar, diluted in A.c. buffer, were mixed with A. castellanii at a MOI of 100, defining the start point of the time-course experiment. Subsequent to invasion for 1 h at 37°C A. castellanii cells were washed three times to remove external bacteria. The infection was monitored by fluorescence microscopy and viable cell counts of L. pneumophila on BCYE agar.

extract_protocol: Strand specific RNAseq libraries were prepared for the Illumina GAIIx (Illumina Inc, San Diego, Ca, USA) using a variation on a previously published protocol (Croucher et al., Nucleic Acids Res 2009, 37:e148). Briefly the rRNA depleted RNA from each time-point was fragmented using divalent cations. First strand cDNA synthesis was carried out in a reaction containing Super Script II reverse transcriptase, random hexamer primers and dNTPs.  First strand reaction components were removed with Illustra MicroSpin G-50 columns (GE Healthcare Biosciences, Pittsburg, PA, USA).  dUTP containing second strand cDNA was generated with DNA Polymerase  and RNaseH in a reaction mix containing dATP, dCTP, dGTP and dUTP but no dTTP.  Products were further processed, end repaired, addition of a single A to the 3´-end and ligation of indexed adapters. 6 nt barcoded Illumina compatible adapters were utilized in place of the commercially supplied adapters (Craig et al., Nat Methods 2008, 5:887-893 2008).  Libraries were sized selected (cut at 200+50 nt) on 2.5% TAE agarose gels. Finally prior to library amplification the dUTP containing second strand was removed via digestion with Uracil DNA Glycoylase (1 unit)  (Bioline, London, UK).  Clustering and sequencing of the material was carried out as per manufacturers instructions – v2 Single Read Cluster Kits and v3 SBS kits (Illumina Inc, San Diego, Ca, USA) were utilized for all sequencing.

treatment_protocol: ribosomal RNA depleted total RNA

value: Acanthamoeba castellanii


title: t11hrs


title: t10hrs

value: none, BYE broth


title: t12hrs


title: t7hrs


title: WTTh17STAT3 (ChIP-Seq)

status: Public on Feb 09 2011

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

description: Chromatin IP against STAT3

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Cisgenome was used for peak-calling.
CisGenome ( Nature Biotechnology, 26: 1293-1300)

source_name: primary CD4+ T cells from spleen and lymph nodes

growth_protocol: Naïve CD4+CD44-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells were cultured for 72h with platebound anti-CD3, anti-CD28 (10 mg/ml each), IL-6 (20 ng/ml), TGF-beta (2 ng/ml), anti-IL-4 (10 mg/ml) and anti-IL-2 (100IU/ml) for 3 days.

extract_protocol: Cell lysates were made by sonication and protein-DNA complexes were isolated with anti-STAT5 (STAT5a (PA-ST5A: R&D) and STAT5b (PA-ST5B: R&D) antibodies, 2 ul each per IP) and anti-STAT3 (14-6727: eBioScience, 5 ug per IP.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: After 3 day culture in vitro, cells were restimulated for either IL-6 (40 ng/ml) or IL-2  (200 IU/ml) before chemically cross linked by 1% formaldehyde.

tag: genotype/variation

value: wild type

value: in vitro polarized T helper17 cells

tag: passages

value: FACS sorted naive CD4+T cells cultured in vitro for 3 days under Th17 condition and restimulated with IL-6 for 30 minutes

tag: chip antibody

value: 5 ug of STAT3 (14-6727:eBioScience) per IP