title: Set Q, Micrococcal nuclease digestion

description:
Mnase digestion.
Fragment length statistics - median; mean; standard deviation - 98; 104.2; 51.5
sequenced in Paired-End mode

data_processing: Sequencing reads were aligned to the mm9 mouse genome annotation using ELAND and the Illumina Genome Analizer pipeline. The resulting export.txt files were converted to the BAM format with Samtools/Picard.

source_name: testis

extract_protocol: Lysates from mice testis cells were sonicated, clarified and DNA protein complexes were isolated with anti Dmc1 or anti Rad51 or H3K4Me3 antibodies. DNA purified from proteins and libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample preparing kit part number 1000181. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenowpolymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ 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 18 cycles and library fragments of 150~250 bp were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. To prepare Micrococcal Nuclease-digested fractions of chromatin DNA, homogenized testis cells were treated with MN and pelleted. The supernatant containing the digested fraction was separated and the DNA was purified from proteins. The library was prepared the same way as described above and all were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain

value: 9R/13R cross

tag: mutation

tag: enzyme

value: Micrococcal nuclease

tag: enzyme manufacturer

value: New England Biolabs

tag: enzyme catalog

tag: enzyme lot

tag: fraction

value: Mnase digested fraction


title: HA ER E2F1ÎC_MCF7 stables_ChIP-seq_rep1

status: Public on Apr 04 2011

type: SRA

city: Palo Alto

first: Philip

last: Cayting

state: CA

address: 1501 S California Ave

department: Genetics

country: USA

institute: Stanford University

description: Chromatin IP against HA ER E2F1ÎC mutant

library_source: genomic

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome assembly hg18 (March, 2006) or hg19 (February, 2009) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)

molecule: genomic DNA

organism: Homo sapiens

source_name: breast adenocarcinoma cell line

growth_protocol: All cells were grown according to ENCODE standards (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines)

extract_protocol:
ChIP assay was performed following the ChIP protocol provided at: http://farnham.genomecenter.ucdavis.edu/pdf/FarnhamLabChIP%20Protocol.pdf
Lysates were clarified from sonicated nuclei and protein-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 (3 to 5 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.

tag: cell type

value: MCF7 cell line stably expressing HA ER E2F1ÎC mutant

tag: harvest date

tag: chip antibody

value: mouse anti-HA (Covance, catalog # MMS-101P)


title: Set R, Control for Set Q

city: Bethesda

first: Ivan

last: Gregoretti

state: MD

address: 5 Memorial Dr, Building 5, Room 205.

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

description:
input DNA
Fragment length statistics - median; mean; standard deviation -  96; 109.8; 54.3
Sequenced in Paired-End mode

organism: Mus musculus

growth_protocol: Cells were extracted from testis (or liver) of euthanized mice and immediately subjected to immunoprecipitation.

value: input DNA


title: HA ER E2F1 DNA Binding Domain mutant_MCF7 stables_ChIP-seq_rep1

description: Chromatin IP against HA ER E2F1 DNA binding domain mutant

value: MCF7 cell line stably expressing HA ER E2F1 DNA binding domain mutant


title: HA ER E2F1 wild type_MCF7 stables_ChIP-seq_rep2

description: Chromatin IP against HA ER E2F1 wild type

value: MCF7 cell line stably expressing HA ER E2F1 wild type


title: Set I, Pool of controls for Sets A, B, C, D, E, F, G and H

description: input DNA and non-specific IP. Pool of controls for Sets A, B, C, D, E, F, G and H.

data_processing:
Sequencing reads were aligned to the mm9 mouse genome annotation using ELAND and the Illumina Genome Analizer pipeline. The resulting export.txt files were converted to the BAM format with Samtools/Picard.
Peak finding was performed with MACS 1.3.7 (http://liulab.dfci.harvard.edu/MACS/) with a p-value threshold of 0.0001 and the. The resulting peaks were kept only if the MCAS-estimated FDR was 50% or less. In the case of Dmc1, the peaks were resized to 3.4kb.

source_name: adult testis

extract_protocol: Lysates from mice testis cells were sonicated, clarified and DNA protein complexes were isolated with anti Dmc1 or anti Rad51 or H3K4Me3 antibodies. DNA purified from proteins and libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample preparing kit part number 1000181. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenowpolymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ 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 18 cycles and library fragments of 150~250 bp were 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.

value: 13R/9R and 9R/13R crosses

tag: genotype/variation

value: input DNA and IgG


title: Set JK, DMC1

description: Chromitin IP against DMC1. Pool of Sets J and K.

source_name: pups testis

value: wild type

tag: antibody catalog number

tag: antibody lot

tag: antibody vendor

value: Santa Cruz


title: Set H, DMC1

description: Chromitin IP against DMC1

value: C57BL/6J/129R cross


title: Set B, DMC1

description: Chromitin IP against DMC1

value: 13R/9R cross


title: Mouse_Liver_FOXA2_rep1 (GAI)

status: Public on Apr 06 2011

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description:
Chromatin IP against FOXA2
processed data file:  Mouse_Liver_FOXA2_GLITR_1p5_FDR.bed

data_processing:
Fastq Files: Sequencing output was analyzed using the Illumina Genome Analyzer Pipeline. Sequence tags that aligned uniquely to the reference genome with zero, one, or two mismatches, according to the ELAND alignment algorithm, were used for further analysis.
Bed Files: All ChIP-Seq data sets were analyzed using GLITR with default parameters and a 1.5% FDR cutoff. Pseudo-ChIP data sets that had the same number of tags as each filtered data set were sampled from the input sequence tag data available for MM8 and HG18 at http://web.me.com/kaestnerlab1/GLITR/, and the remaining input sequence tags in these sets were used as background for the GLITR sampling procedure. Data were further filtered to remove peaks that resulted from amplification bias.
processed data file build: mm8, hg18

source_name: Homogenized Mouse Liver

growth_protocol: Adult mice were sacrificed and liver was dissected.

extract_protocol: Libraries for each ChIP experiment were prepared as per Illumina's instructions (http://www.illumina.com). Briefly, DNA fragments were blunted, phosphorylated, and ligated to Illumina library adapters. For input DNA preparation, 10 ng of starting material was used. Size selection was performed using gel electrophoresis by excising DNA fragments at 200 ± 25 base pairs. Following gel purification, PCR amplification was performed [30 s at 98°C; (10 s at 98°C, 30 s at 65°C, 30 s at 72°C) × 18 cycles; 5 min at 72°C]. Amplified material was evaluated on a Agilent 2100 bioanalyzer using the DNA 1000 Kit to ensure proper size selection, and was subsequently diluted to a concentration of 10 nM.

treatment_protocol: Mouse and human livers were minced finely in cold PBS and cross-linked in 1% formaldehyde for 10 min while rotating. Cross-linking was quenched by adding glycine to a final concentration of 0.125 M for 5 min while rotating. The tissue was rinsed in cold PBS and homogenized with a Dounce homogenizer in cold cell lysis buffer (10 mM Tris–Cl, pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) and protease inhibitors. Cells were incubated at 48C for 5 min to release nuclei. Nuclei were centrifuged at 13000 g for 5 min to form a pellet. The pellet was resuspended in nuclear lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris–Cl, pH 8.1) and protease inhibitors and sonicated using the Diagenode Bioruptor for 10 min on high, using 30 s intervals. Debris were removed by centrifugation at 13000 g for 10 min, and the supernatant was collected and snap frozen in liquid nitrogen. A 10 ml aliquot was reversed by the addition of NaCl to a final concentration of 192 mM, overnight incubation at 658C, and purification using a PCR urification kit (Qiagen). The chromatin concentration was determined using a NanoDrop 3.1.0 nucleic acid assay (Agilent Technologies). Ten micrograms of chromatin per sample was precleared by adding 90 ml of protein G-agarose in 1 ml of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 167 mM NaCl, 16.7 mM Tris–Cl, pH 8.1) and rotating the sample for 1 h at 48C. Protein G-agarose was sedimented by centrifugation at 3000 g for 30 s. Two micrograms of rabbit anti-Foxa2 serum (provided by J.A. Whitsett), was added to the supernatant and incubated overnight at 48C. Protein G-agarose was blocked overnight at 48C with 1mg/ml bovine serum albumin and 0.1mg/ml herring sperm DNA in ChIP dilution buffer, added to the chromatin, and rotated for 1 h at 48C. Following three consecutive washes of 5 min each with TSE I (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris–Cl, pH 8.1, 150mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris–Cl, pH 8.1, 500mM NaCl) and ChIP buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris–Cl, pH 8.1), chromatin was eluted by adding 100 ml of freshly made ChIP elution buffer (1% SDS, 0.1 M NHCO3) to the pellet and rotating the sample for 10 min. Elution was repeated with an additional 100 ml of ChIP elution buffer, and the eluates were combined. Cross-linking was reversed by the addition of NaCl to a final concentration of 192mM and overnight incubation at 658C.

value: Liver tissue

tag: antibody provider

value: Dr. Jeffrey Whitsett

tag: antibody reference

value: Gene Expr Patterns. 2004 Dec;5(2):193-208. Immunohistochemical localization of Foxa1 and Foxa2 in mouse embryos and adult tissues. Besnard V, Wert SE, Hull WM, Whitsett JA.


title: Set J, DMC1

description: Chromatin IP against DMC1

value: 9R/13R cross


title: Set ABCD, DMC1

description: Chromitin IP against DMC1. Pool of Sets A, B, C, D.


title: Set N, Control for Set M

description: input DNA


title: HA ER E2F1 wild type_MCF7 stables_ChIP-seq_rep1


title: Set M, H3K4me3, adult testis

description: Chromatin IP against H3K4me3

value: Millipore


title: Input_MCF7 stables_ChIP-seq_rep1a

description: genomic DNA used as input for Chromatin IP


title: Set E, DMC1

description: Chromitin IP against DMC1


title: Set K, DMC1

description: Chromatin IP against DMC1


title: Set L, Control for Sets J and K

description: input DNA


title: breast tumor 1

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

country: Germany

institute: University of Cologne

description: genomic DNA hydrosheared in 9.9 kb fragments (std dev: 2,271 bp below median; 1,183 above median), 2x25bp paired-end (mate pair) sequences

data_processing: For the project, sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems). If sequence tags had multiple mapping locations and one of them was located in the expected distance and orientation to its mate, this location was chosen by a process termed ‘rescue’. Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described by Hillmer et al.: Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. The Readme file includes additional information about the supplementary cluster and gff files.

source_name: Primary breast tumor

growth_protocol: standard growth conditions for cell lines

extract_protocol: Genomic DNA was hydrosheared, EcoP15I recognition sites were methylated and EcoP15I CAP adaptors were ligated to the ends of DNA fragments. The methylated DNA constructs were separated on agarose gel and 10 Kb sized fragments were selected for ligation resulting in circularized products where 5’ and 3’ ends of 10 Kb fragments were connected by an internal biotinylated adaptor with two flanking non-methylated EcoP15I CAP adaptors. Constructs were digested by methylation sensitive EcoP15I to release 5’ and 3’ paired-end tag (PET) constructs. Sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by the Applied Biosystems SOLiD system.

tag: tumor type

value: basal-like subgroup based on micro array expression data

tag: tissue

value: mammary gland; breast


title: Set A, DMC1

description: Chromitin IP against DMC1

tag: strain


title: Set G, RAD51

description: Chromitin IP against RAD51


title: Set F, RAD51

description: Chromitin IP against RAD51.


title: Set D, DMC1

description: Chromitin IP against DMC1


title: Set C, DMC1

description: Chromitin IP against DMC1


title: MEF_GROseq_Rep1

status: Public on Apr 01 2011

first: Josh

last: Waterfall

address: 37 Convent Dr Room 6138

institute: NIH

description:
Global Run On RNA
library strategy: GRO-seq
library source: run on RNA

library_source: transcriptomic

data_processing:
All fastq files have sanger-fastq format q values.
Reads were aligned to the mm9 genome assembly with eland.  Reads in areas similar to rRNA sequence (as defined by RepeatMasker) were then removed.

molecule: total RNA

source_name: mouse embryonic fibroblasts

growth_protocol: V6.5 ESCs were grown on irradiated feeders in media that consisted of 15% FBS (Hyclone), DMEM, L-glutamine, non-essential amino acids, penicillin/streptomycin, Sodium Pyruvate (all from Invitrogen), 2-mercaptoethanol (Sigma), and LIF (Chemicon). MEFs were cultured in the same media except that 10% of FBS (Invitrogen) were used and LIF were not included. ESCs were routinely checked to confirm they remained undifferentiated by alkaline phosphatase assay and by SSEA1 immunostaining.

extract_protocol: Cells were lysed directly by adding 10 ml of lysis buffer (0.5% NP-40, 5 mM DTT, 1 mM PMSF, 10 mM Tris-Cl, pH7.4, 300 mM sucrose, 3 mM CaCl2, 2 mM MgAc2, EDTA-free protease cocktail inhibitors (Roche)) on ice for 5 min. Lysed cells were collected with scraper and spun down at 900 g for 5 min.  Cell pellets in 2 ml lysis buffer were dounced 50 times with dounce homogenizer. Nuclei were collected by spinning down at 1,200 g for 5 min. Nuclei were stored in storage buffer (50 mM Tris-Cl, pH8.3, 40% glycerol, 0.1 mM EDTA, 5 mM MgAc2, 5 mM DTT, 1 mM PMSF, and EDTA-free protease cocktail inhibitors) and flash frozen in liquid nitrogen. Trypan blue staining was used to the count the number of nuclei from each preparation.  the GRO-seq assay entails a short nuclear run-on using five million nuclei with 0.5 mM concentrations of Br-UTP and other NTP substrates (0.165 µM [32P]-CTP were added as a tracer) in the presence of 1% sarkosyl detergent, 5 mM MgCl2, RNase inhibitor, 1 mM DTT, 10 mM Tris-Cl, pH 8 to generate run-on transcripts about ~100 base length.  After DNase I and proteinase K treatment, bulk-RNA was purified.  Bulk RNA was then base hydrolyzed to about ~100 nucleotide-length with 0.2 M sodium hydroxide. Unincorporated nucleotides were removed using Biorad p30 spin column. Br-UTP-incorporated run-on transcripts were selectively enriched using anti-Br-dUTP antibody that also has high affinity to Br-UTP (Santa Cruz Technology, Inc.) three times: after hydrolysis, after 5’ adaptor ligation, and after 3’ adaptor ligation. Both ends of the RNA were repaired (using tobacco acid pyrophosphatase and T4 polynucleotide kinase) and ligated to adapters.  These RNA libraries were reverse transcribed and PCR amplified non-selectively. The number of nuclei used in the reaction, run-on reaction time, base hydrolysis time, and amount of nucleotides were each titrated to ensure maximal incorporation of nucleotides with an average size of roughly 100 bases.

value: MEFs isolated from male E13.5 embryo

tag: passages

tag: antibody for run-on transcript enrichment

value: anti-Br-dUTP antibody

value: Santa Cruz Technology, Inc.

tag: antibody catalog #


title: MEF_GROseq_Rep2


title: MESC_GROseq_Rep3

source_name: embryonic stem cells

value: V6.5 ESCs


title: MESC_GROseq_Rep2


title: MESC_GROseq_Rep1


title: IMR90 MNase-seq

city: Los Angeles

first: Benjamin

last: Berman

department: USC Epigenome Center

institute: University of Southern California

description: MNase digested mononucleosomes from IMR90 cell line, single end sequence tags

data_processing: Illumina Real Time Analyis (RTA 1.6) was used for base-calling. Maq 0.7.1 (Li et. al. 2008) was used for genome alignment to NCBI36/hg18 with default command line parameters.

growth_protocol: IMR90 cells were cultured according to ATCC’s guidelines, and 1E6 cells were harvested.

extract_protocol: Mononucleosomes of 125-175bp were extracted from agarose gel, yeilding 30ng DNA. 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 18 cycles and library fragments of 150-300 (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 Illumina Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: Mononucleosomes were generated by digesting 1E6 cells with 0.5, 1 and 5 Units of micrococcal nuclease (MNase; Worthington Biochemicals) for 15 minutes at 37 °C in three separate reactions. The three MNase preparations were combined

value: fetal fibroblast

tag: cell line


title: 5.3hpf

status: Public on Mar 31 2011

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description: RNA extracted from post-MBT stage embryo (5.3hpf) was used. PolyA RNA was selected from the total RNA and used sequencing following ABI SOLiD protocol.

data_processing:
ABI pipeline BioScope v1.0.1
Data analysis: The SOLiD-generated RNA-Seq reads was in 50bp length and an initial filtering process was taken to remove any non-desirable contamination sequences, such as rRNA, tRNA, and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation, a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences, created by taking 46bp from the joining ends of adjacent and non-adjacent exons for each gene and putting them together, simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed, the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map, and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read, from which a unique alignment is found based on the score generated for these alignments.
Mapping parameters:  Mapping was done using Applied Biosystems’ SOLiD BioScope alignment for whole transcriptome analysis pipeline.  Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.  A score is computed for each mapping location and any location that scored <22 were filtered.
Generation of gff and bedgraph files: GFF files were produced by parsing the output (BAM format) and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.

organism: Danio rerio

source_name: developing embryos

growth_protocol: Zebrafish embryos (AB background) collected just after fertilization, were reared and harvested at, desired time points.   Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap-frozen in liquid nitrogen and stored in −80°C. Total RNA was extracted from whole embryos using Trizol (Invitrogen) according to manufacturer’s instructions. RNA concentrations were determined using NanoDrop 2000 (Thermo Scientific). Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.

extract_protocol: mRNA-seq was performed by Mission Biotech (Taiwan). SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD™ Sequencing kit (ABI) according to manufacturer’s instructions. About 200-280 µg of total RNAs were used as starting materials, which were subjected to poly(A) selection using Applied Biosystems Poly(A) Purist Kit (AM1916), fragmentation, and library construction using distinct adapters for each library (SOLiD Barcoding). From each library, equal volumes were pooled together and sequenced in SOLiD3 (ABI) platform generating 50bp tags.

treatment_protocol: Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.

tag: background

value: AB; wild type

tag: developmental stage

value: post-MBT stage embryo (5.3hpf)


title: 128/256 cells

description: RNA extracted from mixure of 128/256 cell embryos was used. PolyA RNA was selected from the total RNA and used sequencing following ABI SOLiD protocol.

value: mixure of 128/256 cell embryos


title: 3.5hpf

description: RNA extracted from MBT stage embryo (3.5hpf) was used. PolyA RNA was selected from the total RNA and used sequencing following ABI SOLiD protocol.

value: MBT stage embryo (3.5hpf)


title: 16/32 cells

description: RNA extracted from mixure of 16/32 cell embryos was used. PolyA RNA was selected from the total RNA and used sequencing following ABI SOLiD protocol.

value: mixure of 16/32 cell embryos


title: 1 cell

description: RNA extracted from just fertilized one cell embryos was used. PolyA RNA was selected from the total RNA and used sequencing following ABI SOLiD protocol.

value: just fertilized one cell embryos


title: Maternal

description: RNA extracted from unfertilized eggs was used. PolyA RNA was selected from the total RNA and used sequencing following ABI SOLiD protocol.

source_name: Unfertilized egg

value: unfertilized eggs


title: Bisulfite-Seq analysis of RRBS788 derived from human HUES_45p21   EB_d16 cells; RRBS788

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: UBERON_0014374
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS788
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6114
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6163
****************
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: GSM670084_BI.HUES45_Derived_Embryoid_Body_Cultured_Cells.RRBS.RRBS788-789.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS788-RRBS789.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES45 Derived Embryoid Body Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from HUES45 Derived Embryoid Body Cultured Cells, Libraries RRBS788-789 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6836
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HU45DEB RRBS 88
BROWSER_TRACK_DESCRIPTION: BI HUES45 Derived Embryoid Body Cultured Cells RRBS Library RRBS788-789 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.33

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

source_name: embryoid body culture derived from HUES45 human embrionic stem cells; RRBS788

extract_protocol: Library construction protocol: Smith et al., Methods 48, 226-232

tag: sample alias

tag: sample common name

value: healthy

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: Medium:10% KOSR (Invitrogen); Differentiation Method:NA

value: HUES_45p21   EB_d16

value: unknown

value: Female

value: Primary Cell Culture

value: Donor of HUES45 cells

value: Harvard University

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS749 derived from human HUES13 cells; RRBS749

description:
sample_term_id: NTR_0000844
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS749
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6117
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6176
****************
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: GSM670087_BI.HUES13.RRBS.RRBS749-750.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS749-RRBS750.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES13 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES13 Cell Line, Libraries RRBS749-750 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6838
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES13 RRBS 49
BROWSER_TRACK_DESCRIPTION: BI HUES13 Cell Line RRBS Libraries RRBS749-750 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.23

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

source_name: Harvard University Embryonic Stem Cells; RRBS749

value: HUES13 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: 10% KOSR (Invitrogen)

value: genomic DNA

tag: passage

tag: line

tag: batch

value: Cell Line

value: undifferentiated

tag: Sex

value: Male


title: Bisulfite-Seq analysis of RRBS422 derived from human 18 Fib cells; RRBS422

description:
sample_term_id: CL_0000057
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS422
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6111
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6162
****************
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: GSM670081_BI.Primary_Fibroblast.RRBS.RRBS422-423.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS422-RRBS423.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Primary Fibroblast Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the Primary Fibroblast Cell Line, Libraries RRBS422-423 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6832
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: PF RRBS 22
BROWSER_TRACK_DESCRIPTION: BI Primary Fibroblast Cell Line RRBS Libraries RRBS422-423 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.51

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

source_name: human primary fibroblasts; RRBS422

value: Primary Fibroblast Cell Line

value: mesoderm

value: 19 Fib

value: Female

value: Harvard University

value: 2x5hrs Epitect Kit


title: Bisulfite-Seq analysis of RRBS544 derived from human HUES44 cells; RRBS544

description:
sample_term_id: NTR_0000846
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS544
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6044
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6051
****************
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: GSM670089_BI.HUES44.RRBS.RRBS544-545.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS544-RRBS545.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES44 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES44 Cell Line, Libraries RRBS544-545 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6847
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES44 RRBS 44
BROWSER_TRACK_DESCRIPTION: BI HUES44 Cell Line RRBS Libraries RRBS544-545 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.79

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

source_name: Harvard University Embryonic Stem Cells; RRBS544

value: HUES44 Cell Line

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation


title: Bisulfite-Seq analysis of RRBS546 derived from human HUES45 cells; RRBS546

description:
sample_term_id: NTR_0000847
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS546
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6046
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6052
****************
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: GSM670091_BI.HUES45.RRBS.RRBS546-547.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS546-RRBS547.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES45 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES45 Cell Line, Libraries RRBS546-547 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6831
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES45 RRBS 46
BROWSER_TRACK_DESCRIPTION: BI HUES45 Cell Line RRBS Libraries RRBS546-547 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.92

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

source_name: Harvard University Embryonic Stem Cells; RRBS546

value: HUES45 Cell Line

value: embrionic stem cell

value: 10% KOSR (Invitrogen)

value: genomic DNA

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS784 derived from human HUES_6p30   EB_d16 cells; RRBS784

description:
sample_term_id: UBERON_0014374
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS784
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6175
****************
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: GSM670080_BI.HUES6_Derived_Embryoid_Body_Cultured_Cells.RRBS.RRBS784-785.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS784-RRBS785.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES6 Derived Embryoid Body Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from HUES6 Derived Embryoid Body Cultured Cells, Libraries RRBS784-785 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6835
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HU6DEB RRBS 84
BROWSER_TRACK_DESCRIPTION: BI HUES6 Derived Embryoid Body Cultured Cells RRBS Libraries RRBS784-785 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.51

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

source_name: embryoid body culture derived from HUES6 human embrionic stem cells; RRBS784

value: healthy

value: Medium:10% KOSR (Invitrogen); Differentiation Method:NA

value: HUES_6p30   EB_d16

value: unknown

value: Female

value: Primary Cell Culture

value: Donor of HUES6 cells


title: Bisulfite-Seq analysis of RRBS781 derived from human HUES_1p29   EB_d16 cells; RRBS781

description:
sample_term_id: UBERON_0014374
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS781
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6107
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6160
****************
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: GSM670077_BI.HUES1_Derived_Embryoid_Body_Cultured_Cells.RRBS.RRBS780-781.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS780-RRBS781.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES1 Derived Embryoid Body Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from HUES1 Derived Embryoid Body Cultured Cells, Libraries RRBS780-781 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6830
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HU1DEB RRBS 80
BROWSER_TRACK_DESCRIPTION: BI HUES1 Derived Embryoid Body Cultured Cells RRBS Libraries RRBS780-781 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.47

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

source_name: embryoid body culture derived from HUES1 human embrionic stem cells; RRBS781

value: HUES_1p29   EB_d16

value: Donor of HUES1 cells

value: Harvard University

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT


title: Bisulfite-Seq analysis of RRBS596 derived from human Fib27 cells; RRBS596

description:
sample_term_id: CL_0000057
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS596
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6099
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6166
****************
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: GSM670069_BI.Primary_Fibroblast.RRBS.RRBS595-596.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS595-RRBS596.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Primary Fibroblast Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the Primary Fibroblast Cell Line, Libraries RRBS595-596 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6843
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: PF RRBS 95
BROWSER_TRACK_DESCRIPTION: BI Primary Fibroblast Cell Line RRBS Libraries RRBS595-596 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.64

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

source_name: human primary fibroblasts; RRBS596

value: Primary Fibroblast Cell Line

value: mesoderm

value: 10% KOSR (Invitrogen)

value: genomic DNA

value: Cell Line

value: undifferentiated

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection


title: Bisulfite-Seq analysis of RRBS833 derived from human hESC 11c p23 cells; RRBS833

description:
sample_term_id: NTR_0001161
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS833
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6103
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6173
****************
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: GSM670073_BI.iPS-11c.RRBS.RRBS832-833.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS832-RRBS833.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-11c Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-11c Cell Line, Libraries RRBS832-833 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6833
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: iPS11c RRBS 32
BROWSER_TRACK_DESCRIPTION: BI iPS-11c Cell Line RRBS Libraries RRBS832-833 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.0

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

source_name: induced pluripotent 11c stem cell line; RRBS833

value: iPS-11c Cell Line

value: induced pluripotent cells

value: hESC 11c p23

value: Male

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS783 derived from human HUES_3p22   EB_d16 cells; RRBS783

description:
sample_term_id: UBERON_0014374
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS783
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6169
****************
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: GSM670075_BI.HUES3_Derived_Embryoid_Body_Cultured_Cells.RRBS.RRBS782-783.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS782-RRBS783.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES3 Derived Embryoid Body Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from HUES3 Derived Embryoid Body Cultured Cells, Libraries RRBS782-783 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6840
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HU3DEB RRBS 82
BROWSER_TRACK_DESCRIPTION: BI HUES3 Derived Embryoid Body Cultured Cells RRBS Libraries RRBS782-783 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.39

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

source_name: embryoid body culture derived from HUES3 human embrionic stem cells; RRBS783

value: healthy

value: Medium:10% KOSR (Invitrogen); Differentiation Method:NA

value: HUES_3p22   EB_d16

value: unknown

value: Primary Cell Culture

value: Donor of HUES3 cells

value: Harvard University

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT


title: Bisulfite-Seq analysis of RRBS594 derived from human hiPS-27b cells; RRBS594

description:
sample_term_id: NTR_0001169
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS594
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6100
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6171
****************
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: GSM670070_BI.iPS-27b.RRBS.RRBS593-594.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS593-RRBS594.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-27b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-27b Cell Line, Libraries RRBS593-594 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6845
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: iPS27b RRBS 93
BROWSER_TRACK_DESCRIPTION: BI iPS-27b Cell Line RRBS Libraries RRBS593-594 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.07

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

source_name: induced pluripotent 27b stem cell line; RRBS594

value: iPS-27b Cell Line

value: 10% KOSR (Invitrogen)

value: genomic DNA

value: Cell Line

value: undifferentiated

value: Female

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection


title: Bisulfite-Seq analysis of RRBS756 derived from human hiPS27 cells; RRBS756

description:
sample_term_id: NTR_0001170
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS756
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6094
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6174
****************
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: GSM670064_BI.iPS-27e.RRBS.RRBS755-756.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS755-RRBS756.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-27e Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-27e Cell Line, Libraries RRBS755-756 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6844
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: iPS27e RRBS 55
BROWSER_TRACK_DESCRIPTION: BI iPS-27e Cell Line RRBS Libraries RRBS755-756 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.02

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

source_name: induced pluripotent 27e stem cell line; RRBS756

value: iPS-27e Cell Line

value: induced pluripotent cells

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS754 derived from human hiPS-17b cells; RRBS754

description:
sample_term_id: NTR_0001164
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS754
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6092
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3957
****************
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: GSM670062_BI.iPS-17b.RRBS.RRBS753-754.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS753-RRBS754.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-17b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-17b Cell Line, Libraries RRBS753-754 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6849
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: iPS17b RRBS 53
BROWSER_TRACK_DESCRIPTION: BI iPS-17b Cell Line RRBS Libraries RRBS753-754 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.93

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

source_name: induced pleuripotent 17b stem cell line; RRBS754

value: iPS-17b Cell Line

value: KSR

value: Harvard University

value: 2x5hrs Epitect Kit

value: 20 ng


title: Bisulfite-Seq analysis of RRBS796 derived from human hiPS_20b p49 KOSR iPS cells; RRBS796

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS796
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6085
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6167
****************
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: GSM670055_BI.iPS-20b.RRBS.RRBS796-797.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS796-RRBS797.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-20b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-20b Cell Line, Libraries RRBS796-797 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6850
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: iPS20b RRBS 96
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line RRBS Libraries RRBS796-797 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.12

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

source_name: IPS cell line 20b; RRBS796

value: induced pluripotent stem cells 20b

value: hiPS_20b p49 KOSR iPS

value: iPS-20b Cell Line

value: 10% KOSR (Invitrogen)

value: genomic DNA

value: Male

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT


title: Bisulfite-Seq analysis of RRBS752 derived from human hiPS-17b cells; RRBS752

description:
sample_term_id: NTR_0001164
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS752
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6097
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3957
****************
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: GSM670067_BI.iPS-17b.RRBS.RRBS751-752.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS751-RRBS752.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-17b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-17b Cell Line, Libraries RRBS751-752 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6848
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: iPS17b RRBS 51
BROWSER_TRACK_DESCRIPTION: BI iPS-17b Cell Line RRBS Libraries RRBS751-752 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.24

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

source_name: induced pleuripotent 17b stem cell line; RRBS752

value: Cell Line

value: undifferentiated

value: Female

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection


title: Bisulfite-Seq analysis of RRBS530 derived from human Fib15 cells; RRBS530

description:
sample_term_id: CL_0000057
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS530
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6090
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6164
****************
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: GSM670060_BI.Primary_Fibroblast.RRBS.RRBS530-531.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS530-RRBS531.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Primary Fibroblast Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the Primary Fibroblast Cell Line, Libraries RRBS530-531 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6837
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: PF RRBS 30
BROWSER_TRACK_DESCRIPTION: BI Primary Fibroblast Cell Line RRBS Libraries RRBS530-531 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.16

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

source_name: human primary fibroblasts; RRBS530

value: Primary Fibroblast Cell Line

value: mesoderm

value: Harvard University

value: 2x5hrs Epitect Kit

value: 20 ng

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS794 derived from human H9p65  EB_d16 cells; RRBS794

description:
sample_term_id: UBERON_0014374
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS794
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6083
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6165
****************
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: GSM670053_BI.H9_Derived_Embryoid_Body_Cultured_Cells.RRBS.RRBS794-795.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS794-RRBS795.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H9 Derived Embryoid Body Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from H9 Derived Embryoid Body Cultured Cells, Libraries RRBS794-795 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6828
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9DEB RRBS 94
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Embryoid Body Cultured Cells RRBS Libraries RRBS794-795 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.14

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

source_name: embryoid body culture derived from H9 human embrionic stem cells; RRBS794

value: H9 Derived Embryoid Body Cultured Cells

value: healthy

value: genomic DNA

value: Medium:10% KOSR (Invitrogen); Differentiation Method:NA

value: unknown

value: Primary Cell Culture

value: Donor of H9 cells


title: Bisulfite-Seq analysis of RRBS792 derived from human H1p38  EB_d16 cells; RRBS792

description:
sample_term_id: UBERON_0014374
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS792
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6081
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6177
****************
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: GSM670051_BI.H1_Derived_Embryoid_Body_Cultured_Cells.RRBS.RRBS792-793.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS792-RRBS793.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Embryoid Body Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from H1 Derived Embryoid Body Cultured Cells, Libraries RRBS792-793 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6829
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H1DEB RRBS 92
BROWSER_TRACK_DESCRIPTION: BI H1 Derived Embryoid Body Cultured Cells RRBS Libraries RRBS792-793 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.83

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

source_name: embryoid body culture derived from H1 human embrionic stem cells; RRBS792

value: H1 Derived Embryoid Body Cultured Cells

value: Male

value: Donor of H1 cells

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)


title: Bisulfite-Seq analysis of RRBS798 derived from human hiPS_20b p49 TeSR iPS cells; RRBS798

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS798
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6087
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6168
****************
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: GSM670057_BI.iPS-20b.RRBS.RRBS798-799.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS798-RRBS799.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-20b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-20b Cell Line, Libraries RRBS798-799 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6851
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: iPS20b RRBS 98
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line RRBS Libraries RRBS798-799 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.47

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

source_name: IPS cell line 20b; RRBS798

value: induced pluripotent stem cells 20b

value: hiPS_20b p49 TeSR iPS

value: iPS-20b Cell Line

value: induced pluripotent cells

value: TeSR

value: Cell Line

value: undifferentiated

value: Harvard University

value: 2x5hrs Epitect Kit

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection


title: Bisulfite-Seq analysis of RRBS941 derived from human HUES66 cells; RRBS941

description:
sample_term_id: NTR_0000855
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS941
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6079
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.4038
****************
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: GSM670049_BI.HUES66.RRBS.RRBS941.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS941.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of HUES66 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the HUES66 Cell Line, Library RRBS941 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6842
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES66 RRBS 41
BROWSER_TRACK_DESCRIPTION: BI HUES66 Cell Line RRBS Library RRBS941 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.35

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

source_name: Harvard University Embryonic Stem Cells; RRBS941

value: HUES66 Cell Line

value: embrionic stem cell

value: KSR

value: genomic DNA

value: Female

value: 20 ng

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS578 derived from human Fib17 cells; RRBS578

description:
sample_term_id: CL_0000057
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS578
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6080
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6172
****************
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: GSM670050_BI.Primary_Fibroblast.RRBS.RRBS578-579.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS578-RRBS579.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Primary Fibroblast Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the Primary Fibroblast Cell Line, Libraries RRBS578-579 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6853
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: PF RRBS 78
BROWSER_TRACK_DESCRIPTION: BI Primary Fibroblast Cell Line RRBS Libraries RRBS578-579 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.83

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

source_name: human primary fibroblasts; RRBS578

value: Primary Fibroblast Cell Line

value: mesoderm

value: 10% KOSR (Invitrogen)

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)


title: Bisulfite-Seq analysis of RRBS576 derived from human Fib11 cells; RRBS576

description:
sample_term_id: CL_0000057
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS576
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6077
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6170
****************
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: GSM670047_BI.Primary_Fibroblast.RRBS.RRBS576-577.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS576-RRBS577.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Primary Fibroblast Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the Primary Fibroblast Cell Line, Libraries RRBS576-577 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6852
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: PF RRBS 76
BROWSER_TRACK_DESCRIPTION: BI Primary Fibroblast Cell Line RRBS Libraries RRBS576-577 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.39

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

source_name: human primary fibroblasts; RRBS576

value: Cell Line

value: undifferentiated

value: Male

value: Harvard University

value: 2x5hrs Epitect Kit

value: DNA Methylation


title: Bisulfite-Seq analysis of RRBS510 derived from human Fib 20 cells; RRBS510

description:
sample_term_id: CL_0000057
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS510
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6076
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6161
****************
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: GSM670046_BI.Primary_Fibroblast.RRBS.RRBS510-511.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS510-RRBS511.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Primary Fibroblast Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the Primary Fibroblast Cell Line, Libraries RRBS510-511 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6839
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: PF RRBS 10
BROWSER_TRACK_DESCRIPTION: BI Primary Fibroblast Cell Line RRBS Libraries RRBS510-511 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.38

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

source_name: human primary fibroblasts; RRBS510

value: genomic DNA

value: Fib 20

value: Smith et al., Methods 48, 226-232

value: Gel size selection


title: ChIP-Seq analysis of WCE; substantia nigra cells; Lib:XZ:20100921:07--ChIP:XZ:20100914:07:substantia nigra:WCE

description:
sample_term_id: UBERON_0002038
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:07--ChIP:XZ:20100914:07:substantia nigra:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5783
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5938
****************
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: GSM670042_BI.Brain_Substantia_Nigra.Input.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:07--ChIP:XZ:20100914:07:substantia nigra:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Substantia Nigra ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Substantia Nigra, Donor 112 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.6512
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: 61
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0045
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0249
POISSON_PERCENTILE: 13

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

ANALYSIS FILE NAME: GSM670042_BI.Brain_Substantia_Nigra.Input.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:07--ChIP:XZ:20100914:07:substantia nigra:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Substantia Nigra, Donor 112 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.6722
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: BSN Input 12
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra ChIP-Seq Input Donor 112 Library Lib:XZ:20100921:07--ChIP:XZ:20100914:07:substantia nigra:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0045
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0249
POISSON_PERCENTILE: 13

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:07--ChIP:XZ:20100914:07:substantia nigra:WCE

extract_protocol: Library construction protocol: Single read - Illumina

value: Brain, Substantia Nigra

value: post-mortem

value: Substantia Nigra

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in HUES48 cells; Lib:MC:20101025:09--ChIP:MC:20101020:09:ES cell HUES_48:H3K36Me3

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20101025:09--ChIP:MC:20101020:09:ES cell HUES_48:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5780
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5930
****************
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: GSM670039_BI.HUES48.H3K36me3.Lib_MC_20101025_09--ChIP_MC_20101020_09_ES_cell_HUES_48_H3K36Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:09--ChIP:MC:20101020:09:ES cell HUES_48:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES48 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the HUES48 Cell Line, Library Lib:MC:20101025:09--ChIP:MC:20101020:09:ES cell HUES_48:H3K36Me3 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.6532
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_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3382
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3122
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9913
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4971
POISSON_PERCENTILE: 54

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

ANALYSIS FILE NAME: GSM670039_BI.HUES48.H3K36me3.Lib_MC_20101025_09--ChIP_MC_20101020_09_ES_cell_HUES_48_H3K36Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:09--ChIP:MC:20101020:09:ES cell HUES_48:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the HUES48 Cell Line, Library Lib:MC:20101025:09--ChIP:MC:20101020:09:ES cell HUES_48:H3K36Me3 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.6742
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: HUES48 H3K36me3 e3
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K36me3 Library Lib:MC:20101025:09--ChIP:MC:20101020:09:ES cell HUES_48:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3382
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3122
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9913
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4971
POISSON_PERCENTILE: 54

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

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:09--ChIP:MC:20101020:09:ES cell HUES_48:H3K36Me3

value: HUES48 stem cells

value: HUES48 Cell Line

value: embrionic stem cell

value: KSR

value: ES cell HUES_48-1

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K4me3; substantia nigra cells; Lib:XZ:20100921:02--ChIP:XZ:20100914:02:substantia nigra:H3K4Me3

description:
sample_term_id: UBERON_0002038
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:02--ChIP:XZ:20100914:02:substantia nigra:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5779
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5938
****************
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: GSM670038_BI.Brain_Substantia_Nigra.H3K4me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:02--ChIP:XZ:20100914:02:substantia nigra:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Substantia Nigra Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Substantia Nigra, Donor 112 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.6465
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_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.1289
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1703
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9984
IROC_PERCENTILE: 52
POISSON_SCORE: 0.2145
POISSON_PERCENTILE: 8

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

ANALYSIS FILE NAME: GSM670038_BI.Brain_Substantia_Nigra.H3K4me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:02--ChIP:XZ:20100914:02:substantia nigra:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Substantia Nigra, Donor 112 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.6675
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: BSN H3K4me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra Histone H3K4me3 Donor 112 Library Lib:XZ:20100921:02--ChIP:XZ:20100914:02:substantia nigra:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.1289
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1703
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9984
IROC_PERCENTILE: 52
POISSON_SCORE: 0.2145
POISSON_PERCENTILE: 8

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:02--ChIP:XZ:20100914:02:substantia nigra:H3K4Me3

value: Brain, Substantia Nigra

value: post-mortem

value: genomic DNA

value: Substantia Nigra

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: SDS lysis

value: Millipore

value: Histone H3K4me3