title: Sleeping Beauty induced lymphoma (Shear-splink sample32)

description:
Barcode sequence: GTCGAGAGAG
Shear-splink sample32
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample30)

status: Public on Aug 12 2011

type: SRA

city: Amsterdam

first: Jos

last: Jonkers

email: j.jonkers@nki.nl, m.koudijs@nki.nl

address: Plesmanlaan 121

department: Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
Barcode sequence: GTAGTGATCG
Shear-splink sample30
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

library_source: genomic

data_processing: Sequence reads are mapped to NCBI m37 using BLAT, sorted on barcode and processed using custom made algortihms as described in the associated manuscript. All scripts available on request. The export.txt files contain a summary of all unique integration sites. Per integration site 1 read ID is shown together with the cumulative number of sequence reads (depth), without specifying the individual read IDs per integrations site.

molecule: genomic DNA

organism: Mus musculus

source_name: Lymphosarcoma SPLEEN

extract_protocol: Isolation of gDNA and ligation-mediated amplification of regions flanking retroviral insertions after endonucelase digestion or acoustic shearing of gDNA. Subsequently, barcoded  PCR products were pooled and sequenced on a 454 GS_FLX system according to the manufacturers protocol.

tag: strain

value: mixed C57Bl6/129S5SvEvBrd

tag: mouse id#

tag: transposon

value: Sleeping beauty


title: Sleeping Beauty induced lymphoma (Shear-splink sample33)

description:
Barcode sequence: GTGACACACG
Shear-splink sample33
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: Lymphosarcoma LUNG


title: Sleeping Beauty induced lymphoma (Shear-splink sample31)

description:
Barcode sequence: GTATACATAG
Shear-splink sample31
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: Lymphosarcoma LYMPH NODE


title: Sleeping Beauty induced lymphoma (Shear-splink sample34)

description:
Barcode sequence: GTGAGCTCGG
Shear-splink sample34
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: Lymphosarcoma THYMUS


title: Sleeping Beauty induced lymphoma (Shear-splink sample28)

description:
Barcode sequence: GCTCACGTAG
Shear-splink sample28
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample27)

description:
Barcode sequence: GCTATCGCGG
Shear-splink sample27
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample24)

description:
Barcode sequence: GCACTGTAGG
Shear-splink sample24
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample26)

description:
Barcode sequence: GCGTCGTCTG
Shear-splink sample26
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample21)

description:
Barcode sequence: GACTCAGCGG
Shear-splink sample21
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample23)

description:
Barcode sequence: GAGCGTCACG
Shear-splink sample23
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample22)

description:
Barcode sequence: GAGAGTGTGG
Shear-splink sample22
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample25)

description:
Barcode sequence: GCGACTAGCG
Shear-splink sample25
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample20)

description:
Barcode sequence: GACTATACTG
Shear-splink sample20
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample29)

description:
Barcode sequence: GTACGCTATG
Shear-splink sample29
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample19)

description:
Barcode sequence: GACGCACTCG
Shear-splink sample19
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample43)

description:
Barcode sequence: TCACGTGCGG
Shear-splink sample43
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

source_name: Lymphoma SPLEEN


title: Sleeping Beauty induced lymphoma (Shear-splink sample17)

description:
Barcode sequence: CTCGCGCACG
Shear-splink sample17
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample18)

description:
Barcode sequence: CTGTACAGTG
Shear-splink sample18
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample16)

description:
Barcode sequence: CTCATCTACG
Shear-splink sample16
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: UChicago_ChipSeq_K562_Input_Control_eGFP-GATA2

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

organism: Homo sapiens

tag: lab

value: UChicago

tag: lab description

value: White - University of Chicago

tag: data type

value: ChipSeq

tag: data type description

value: ChIP-Seq

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control

tag: control description

value: This data represents a control being compared to experiments using antibody eGFP-GATA2

tag: control id

tag: replicate

tag: replicate description

value: tier 1


title: Sleeping Beauty induced lymphoma (Shear-splink sample11)

description:
Barcode sequence: CGCGAGTATG
Shear-splink sample11
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

tag: strain

tag: mouse id#

tag: transposon


title: Sleeping Beauty induced lymphoma (Shear-splink sample12)

description:
Barcode sequence: CGTCTCATCG
Shear-splink sample12
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: UChicago_ChipSeq_K562_Input_Control_eGFP-HDAC8

tag: lab

tag: lab description

tag: data type

tag: data type description

value: This data represents a control being compared to experiments using antibody eGFP-HDAC8


title: Sleeping Beauty induced lymphoma (Shear-splink sample14)

description:
Barcode sequence: CTAGCAGTAG
Shear-splink sample14
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample8)

description:
Barcode sequence: CGAGTGCGTG
Shear-splink sample8
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample10)

description:
Barcode sequence: CGCTCGACAG
Shear-splink sample10
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample9)

description:
Barcode sequence: CGCGATCGAG
Shear-splink sample9
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample7)

description:
Barcode sequence: CGACTACAGG
Shear-splink sample7
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: UChicago_ChipSeq_K562_Input_Control_eGFP-NR4A1

tag: cell

tag: cell organism

tag: cell description

tag: cell karyotype

value: This data represents a control being compared to experiments using antibody eGFP-NR4A1


title: UChicago_ChipSeq_K562_Input_Control_eGFP-JunB

tag: cell lineage

tag: cell sex

tag: antibody

tag: antibody description

value: This data represents a control being compared to experiments using antibody eGFP-JunB


title: UChicago_ChipSeq_K562_Input_Control_eGFP-JunD

tag: control

tag: control description

value: This data represents a control being compared to experiments using antibody eGFP-JunD

tag: control id

tag: replicate


title: UChicago_ChipSeq_K562_eGFP-FOS_Control_eGFP-FOS

value: UChicago

value: eGFP-FOS

tag: antibody antibody description

value: Goat polyclonal

tag: antibody target description

value: Fos

tag: antibody vendor name

value: Kevin White

tag: antibody vendor id

value: (None)

value: This data represents a control being compared to experiments using antibody eGFP-FOS

tag: replicate description


title: Sleeping Beauty induced lymphoma (Shear-splink sample6)

description:
Barcode sequence: CGACAGCTCG
Shear-splink sample6
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

tag: strain

value: mixed C57Bl6/129S5SvEvBrd

tag: mouse id#

tag: transposon

value: Sleeping beauty


title: Sleeping Beauty induced lymphoma (Shear-splink sample5)

description:
Barcode sequence: CATGACGACG
Shear-splink sample5
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: UChicago_ChipSeq_K562_eGFP-GATA2_Control_eGFP-GATA2

tag: lab

tag: lab description

value: White - University of Chicago

tag: data type

value: ChipSeq

tag: data type description

value: ChIP-Seq

tag: cell

tag: cell organism

value: human

tag: cell description

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

tag: cell karyotype

value: cancer

value: mesoderm

value: F


title: Sleeping Beauty induced lymphoma (Shear-splink sample3)

description:
Barcode sequence: CAGTCGTGCG
Shear-splink sample3
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample4)

description:
Barcode sequence: CATACGCGTG
Shear-splink sample4
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: UChicago_ChipSeq_K562_eGFP-HDAC8_Control_eGFP-HDAC8

value: UChicago

tag: cell lineage

tag: cell sex

tag: antibody

tag: control

tag: control description

value: This data represents a control being compared to experiments using antibody eGFP-HDAC8

tag: control id

tag: replicate

value: tier 1


title: UChicago_ChipSeq_K562_eGFP-JunD_Control_eGFP-JunD

value: eGFP-JunD

tag: antibody antibody description

value: Goat polyclonal

tag: antibody target description

value: JunD

tag: antibody vendor name

tag: antibody vendor id

value: This data represents a control being compared to experiments using antibody eGFP-JunD

tag: replicate description


title: Sleeping Beauty induced lymphoma (Shear-splink sample2)

description:
Barcode sequence: CAGTATATAG
Shear-splink sample2
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

tag: strain

value: mixed C57Bl6/129S5SvEvBrd

tag: mouse id#

tag: transposon


title: Sleeping Beauty induced lymphoma (Shear-splink sample1)

description:
Barcode sequence: CACATACGCG
Shear-splink sample1
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR

value: Sleeping beauty


title: Sleeping Beauty induced lymphoma (Shear-splink sample15)

description:
Barcode sequence: CTCACAGAGG
Shear-splink sample15
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: Sleeping Beauty induced lymphoma (Shear-splink sample13)

description:
Barcode sequence: CTACTATGTG
Shear-splink sample13
Processed data file: Insertions_shear.bed
Processed data file build: NCBI m37
Original raw file name: Set1.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR


title: UChicago_ChipSeq_K562_eGFP-NR4A1_Control_eGFP-NR4A1

tag: lab

tag: lab description

value: White - University of Chicago

tag: data type

tag: data type description

tag: cell

tag: cell organism

tag: cell description

value: Kevin White

value: (None)

value: This data represents a control being compared to experiments using antibody eGFP-NR4A1


title: UChicago_ChipSeq_K562_Input_Control_eGFP-FOS

value: ChipSeq

value: ChIP-Seq

value: human

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

tag: cell karyotype

tag: cell lineage

tag: cell sex

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control

tag: control description

value: This data represents a control being compared to experiments using antibody eGFP-FOS

tag: control id


title: 19606S_1

status: Public on Aug 11 2011

city: Clayton

first: Paul

middle: Francis

last: Harrison

state: VIC

address: Building 76, Monash University, Wellington Rd

department: Microbiology

country: Australia

institute: Victorian Bioinformatics Consortium

library_source: transcriptomic

data_processing:
Read pairs were clipped of bases with quality < 20 and adaptor sequences using "nesoni" http://bioinformatics.net.au/software.nesoni.shtml, and aligned using "SHRiMP" http://compbio.cs.toronto.edu/shrimp/. Alignments to coding sequences were then counted. Where a read-pair aligned equally well to multiple locations, it was counted multiple times, but the fact that the alignment was ambiguous was noted (in count.txt).
Processed data file build: NZ_GG704572.1

molecule: total RNA

organism: Acinetobacter baumannii

source_name: bacterial cells

growth_protocol: The lpxA mutant strain 19606R was an LPS-deficient, colistin-resistant derivative of ATCC19606 described previously (30). A. baumannii cultures were grown on Mueller-Hinton (MH) agar, or in cation-adjusted MH broth at 37°C. Colistin sulfate (10 µg/ml) was added to overnight cultures where appropriate.

extract_protocol: Total RNA was purified using the Qiagen RNeasy Purification Kit. Sequencing was conducted on an Illumina GAIIx by the Micromon High Throughput Sequencing Facility (Monash University). ATCC19606 and 19606R cDNA samples were multiplexed into a single lane and sequenced using a 75 bp paired-end DNA-sequencing protocol as per the manufacturer's instructions (Illumina). GSM773505 had mean fragment size 154, standard deviation 31. GSM773506 had mean fragment size 238, standard deviation 48. GSM773507 had mean fragment size 158, standard deviation 40. GSM773508 had mean fragment size 319, standard deviation 56.

tag: strain

tag: growth stage

value: mid-log

tag: antibiotic

value: No selection


title: 19606S_2


title: 19606R_2

value: colistin 10mg/mL


title: 19606R_1


title: smallRNA_S.cerevisiae_AGO1DCR1

status: Public on Aug 10 2011

city: Cambridge

first: Ines

middle: Anna

last: Drinnenberg

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Small RNA sequencing, 18-30 nt size selection.

data_processing: After removing the adaptor sequences, reads representing the small RNAs were collapsed to a non-redundant set, and 14-30-nt sequences were mapped to the appropriate genome, allowing no mismatches and recovering all hits. The processed files are collapsed to unique sequences (1 line per sequence); the second (numeric) value in each column is the number of times each unique sequence was sequenced.

organism: Saccharomyces cerevisiae

source_name: log-phase liquid culture, AGO1DCR1

growth_protocol: Liquid cultures were grown at 30ºC to log-phase.

extract_protocol: Total RNA was isolated using hot phenol from log-phase YPD cultures. Small-RNA cDNA libraries were prepared as described in Grimson et al. (2008).

tag: genotype/variation


title: RNAseq_S.cerevisiae_AGO1DCR1

description: Small RNA sequencing by mRNA fragmentation, 5' and 3' adaptor ligation, and RT-PCR

data_processing: The first 25 nt of each 36-nt read were isolated and collapsed into a non-redundant set of 25-nt sequences with occurrence counts. Sequences were mapped to the reference genome, allowing no mismatches and recovering all hits. The processed files are collapsed to unique sequences (1 line per sequence); the second (numeric) value in each column is the number of times each unique sequence was sequenced.

extract_protocol: Total RNA was isolated using hot phenol from log-phase YPD cultures and treated with DNaseI. Poly-(A)+ mRNA was purified from total RNA using magnetic oligo-dT beads (2 rounds of poly-(A)+ selection), and then fragmented by alkaline hydrolysis. RNA-Seq cDNA libraries were prepared as described in Drinnenberg et al. (2009).


title: cFOS_ChIP-seq_B

city: Palo Alto

first: Philip

last: Cayting

address: 1501 S California Ave

department: Genetics

institute: Stanford University

description: Chromatin IP against cFOS

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (February, 2009) genomes 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)

source_name: Chromatin IP against cFOS

growth_protocol: 1.Thaw Primary Human Umbilical Vein Endothelial Cells (HUVECs)  (~0.5-1 x 105 cells) from liquid nitrogen and thaw it in 37 degree waterbath.Suspend the washed cells in cell-type specific medium (BulletKits â Lonza Biosciences)  2. Centrifuge at 700 rpm for 5 min.  3. Suspend the cells in cell-type specific medium and seed flasks at 5,000 cells/cm2 to be incubated in CO2 incubator.  4. Change media the day after seeding and every OTHER day thereafter. Increase media volume as confluency increases.  5. Propagate cells until density reaches 70-80% confluence. Subculturing protocol: decant medium, wash cells with warm 1X PBS, add 8mLs of Accutase and return to incubator for 10-15 minutes, immediately remove cells and pellet at 500 xg for 3 minutes (4C), wash cells 2X with 1X PBS, gently re-suspend cell pellet in warm medium, count cells with hemocytometer, add warmed medium to flasks and seed flasks at 5,000 cells/cm2.  6. Pass cells 3-4 times until the desired cell number is achieved (primary cells will senesce after 4-5  passages).

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

tag: passage


title: RNAseq_S.cerevisiae_DCR1

source_name: log-phase liquid culture, DCR1


title: GATA2_ChIP-seq_B

description: Chromatin IP against GATA2

source_name: Chromatin IP against GATA2


title: GATA2_ChIP-seq_A

description: Chromatin IP against GATA2


title: input

description: control input sample

source_name: control input sample


title: smallRNA_S.cerevisiae_WT

source_name: log-phase liquid culture, WT

value: WT


title: RNAseq_S.cerevisiae_WT


title: E_histolytica_BSSeq

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

data_processing: Alignment: Sequence reads were obtained and mapped to the genome of Entamoeba histolytica (amoebadb.org) using the program BSMAP 2.0. All reads mapping with four or fewer mismatches were retained.

organism: Entamoeba histolytica

source_name: Amoeba cells

extract_protocol: 5 ug of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 ul. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 ul using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 ul using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the "Size Select" program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95C for 15 s, 50C for 1 h, repeat from step 1, 15x, 4C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95C for 2 min, 95C for 30 s, 65C for 20 s, 72C for 30 s, then repeat from step 2, 11x, 72C for 7min, hold at 4C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 ul elution buffer (Qiagen). The average fragment size is 196.7 and the standard deviation is 37.2.

tag: cell type

value: Amoeba cells


title: UChicago_ChipSeq_K562_eGFP-JunB_Control_eGFP-JunB

tag: lab

value: UChicago

tag: lab description

value: White - University of Chicago

tag: data type

tag: data type description

tag: cell

tag: cell organism

value: cancer

value: mesoderm

value: F

value: eGFP-JunB

tag: antibody antibody description

value: Goat polyclonal

tag: antibody target description

value: JunB

tag: antibody vendor name

tag: antibody vendor id

value: This data represents a control being compared to experiments using antibody eGFP-JunB

tag: replicate

tag: replicate description

value: tier 1


title: Thielavia_terrestris_Glucose_34C_rep2

status: Public on Aug 08 2011

city: Montreal

first: Ian

last: Reid

state: QC

address: 7141 Sherbrooke West

department: Biology

country: Canada

institute: Concordia University

data_processing: Short reads from C. globosum were aligned to the assembly of the Chaetomium globosum CBS 148.51 genome from the Broad Institute using TopHat v1.0.13. Reads from M. thermophila were aligned with BowTie v0.12.7 to the Sporotrichum thermophile genome assembly v2.0 from the DOE Joint Genome Institute, augmented with splice junction sequences. Introns were first located by mapping the pooled reads to the genomic sequence with BLAT; reads that aligned with >95% identity and coverage, but with gaps, were examined for the presence of plausible introns in the gaps. Splice junction sequences were constructed by concatenating 35 bases of sequence from the two flanks of the introns thus identified. Read alignments to the splice junction sequences were translated into gapped alignments to the genome. Reads that mapped equally well to more than one location were randomly assigned to one of the locations with probability proportional to the local depth of coverage by uniquely-mapped reads. Reads from T. terrestris were mapped to the Thielavia terrestris genome v2.0 from JGI.

molecule: polyA RNA

organism: Thermothielavioides terrestris

source_name: Mycelium

growth_protocol: Spores of each filamentous fungus were inoculated at a final concentration of 10^6/mL into 10x Trametes Defined Medium containing 2% carbon source.  Liquid cultures were grown with shaking at 150 rpm at 34C or 45C.  Mycelia were harvested by filtering through Miracloth (Calbiochem) and ground in liquid nitrogen.  RNA was extracted with Trizol (Invitrogen, Carlsbad CA, USA) according to the manufacturer's protocol.

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the mRNA-Seq Sample Prep Kit
gel-based size selection

tag: carbon source

value: Glucose

tag: growth temperature


title: Thielavia_terrestris_Barley_45C_rep2

value: Barley straw


title: Thielavia_terrestris_Glucose_45C_rep1


title: Thielavia_terrestris_Glucose_34C_rep1


title: IMR90_Young

status: Public on Aug 09 2011

city: Los Angeles

first: Dario

last: Boffelli

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

description: 18-30nt fraction of small RNA

data_processing: Sequence reads were called with the Illumina Pipeline v1.4. Called reads were processed to trim 5' and 3' adapter sequences (GTTCAGAGTTCTACAGTCCGACGATC and TCGTATGCCGTCTTCTGCTTG, respectively), and discarded reads shorter than 4 nucleotides. The remaining reads were aligned against the human genome (NCBI36/hg18) with bowtie version  0.12.5 using the following parameters: -v 2 -a -m 10 --best --strata.   Aligned reads were used to create BedGraph coverage files with the genomeCoverageBed utility from BEDTools.

source_name: Fetal lung fibroblasts

growth_protocol: IMR90 were maintained in DMEM (Hyclone, South Logan, UT) with 10% FBS (Hyclone) supplemented with penicillin (10 U/ml) and streptomycin (10 U/ml) in a humidified 95% air-5% CO2 atmosphere.

extract_protocol: Total RNA including small RNAs was extracted from young and senescent IMR90 cells with the QIAGEN miRNeasy Mini Kit and separated by electrophoresis on an 18% polyacrylamide gel. The region corresponding to the 18–30 nucleotide bands in the marker lane was excised, extracted from the gel, and used for library construction. Libraries were prepared according to Illumina's Small RNA Sample Preparation Guide (Part # 1004239 RevB).

treatment_protocol: Young IMR90 fetal lung fibroblasts were grown for 14 passagings and senescent cells were passaged 34 times, and had ceased further growth.

tag: cell line name

tag: passages


title: Myceliophthora_thermophila_Glucose_34C_rep1

organism: Thermothelomyces thermophilus


title: Myceliophthora_thermophila_Barley_45C_rep2


title: Myceliophthora_thermophila_Glucose_45C_rep2


title: Thielavia_terrestris_Alfalfa_45C_rep2

value: Alfalfa hay


title: IMR90_Senescent

description: 18-30nt fraction of small RNA


title: Thielavia_terrestris_Barley_45C_rep1


title: cFOS_ChIP-seq_A

description: Chromatin IP against cFOS

tag: cell-type

tag: passage


title: Myceliophthora_thermophila_Alfalfa_45C_rep1


title: Thielavia_terrestris_Alfalfa_45C_rep1


title: Chaetomium_globosum_Barley_34C_rep2

organism: Chaetomium globosum


title: Myceliophthora_thermophila_Glucose_45C_rep1


title: RNAseq_S.cerevisiae_AGO1

source_name: log-phase liquid culture, AGO1

tag: strain

tag: genotype/variation


title: Chaetomium_globosum_Alfalfa_34C_rep2


title: Myceliophthora_thermophila_Barley_45C_rep1


title: P. tricornutum_N-limited_48h

city: Qingdao

first: Guangce

last: Wang

address: Nanhai Road 7

country: China

institute: Institute of Oceanology, the Chinese Academy of Sciences (IOCAS)

description: small RNA

data_processing: Low-quality reads were filtered strictly. 3' adaptor sequences were trimmed and 5' adaptor contaminants were removed. Too small and polyA sequences were removed. The proccess data (.clean.fa) includes sequenc id, counts for clean tags (18-30 nt) and unique RNA sequence. The software we used was  wrote in perl by BGI (Beijing Genome Institute).

organism: Phaeodactylum tricornutum

source_name: Phaeodactylum tricornutum cells

growth_protocol: Axenic cultures of P. tricornutum were grown in f/2 medium made with steam-sterilized local seawater supplemented with inorganic nutrients and f/2 vitamins (filter sterilized)at 20C under cool white fluorescent lights at 24 umol.m-1.s-1 with a 12-h photoperiod for one week.

extract_protocol: Total RNA was extracted from P. tricornutum cells using the Trizol method according to manufacturer's protocol (Invitrogen). Basically, sRNAs were separated by size fractionation on denaturing polyacrylamide gels. Fragments of 18-28 nt were gel-purified then ligated to a 5'-adaptor and a 3'-adaptor and then RT-PCR-amplified using SuperScript II Reverse Transcription Kit (Invitrogen). RT-PCR product was then sequenced directly using a Solexa 1G Genome Analyzer according to the manufacturer's protocols.

treatment_protocol: Cells were harvested by centrifugation for 10 min at 4000 g, washed with sterilized seawater, aliquoted into a 500-mL conical flask and then incubated in normal, nitrogen-free and silicon-free f/2 media made with artificial seawater  for 48 h.

value: Bohlin

tag: development stage

value: log phase cells

tag: treatment

value: nitrogen-limited


title: P. tricornutum_Si-limited_48h

description: small RNA

value: silicon-limited


title: MOLF backcross animal 4461

status: Public on Aug 06 2011

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

state: MD

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

description: mean insert size : 254.8

data_processing: Illumina software pipeline ( Basecalls was done by using Illumina RTA 1.6 for GAIIx run, RTA 1.7 for HiSeq run , Alignment was done by using Illumina CASAVA1.6, CASAVA_v1.7.0 pipelines)

source_name: PyMT-induced mammary tumor

extract_protocol: Illumina mRNA Library Preparation Protocol  (Total RNA extracted from mammary tissue, Purify mRNA by poly-A selection, Fragment mRNA, Synthesize the First Strand cDNA, Synthesize the Second Strand cDNA, Perform End Repair, Adenylate 3' ends, Ligate the Adapters, Purify the cDNA Templates on a gel to select a size range)

tag: strain background

value: ((MOLF x PyMT) x FVB) backcross animal

tag: tissue

value: MOLF x PyMT backcross mammary tumor


title: MOLF backcross animal 4492

description: mean insert size : 233.8


title: MOLF backcross animal 4488

description: mean insert size : 242.8


title: MOLF backcross animal 4459

description: mean insert size : 224.3


title: MOLF backcross animal 4511

description: mean insert size : 247


title: MOLF backcross animal 4042

description: mean insert size : 238.4


title: MOLF backcross animal 4036

description: mean insert size : 234.7


title: MOLF backcross animal 4016

description: mean insert size : 244.4


title: MOLF backcross animal 4038

description: mean insert size : 231.1


title: MOLF backcross animal 3654

description: mean insert size : 205.9


title: MOLF backcross animal 4030

description: mean insert size : 242.5


title: MOLF backcross animal 3871

description: mean insert size : 201.8


title: MOLF backcross animal 4139

description: mean insert size : 234.2


title: MOLF backcross animal 4020

description: mean insert size : 230.6


title: Chaetomium_globosum_Barley_34C_rep1


title: Chromatin accessibility assay of Fetal Muscle, Leg; DS18386

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18386
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8498
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8497
****************
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: GSM774242_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24078.DS18386.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18386.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-24078, Library DS18386 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.10398
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,394,239
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.5551
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5468
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9938
IROC_PERCENTILE: 51
POISSON_SCORE: 0.5913
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.83

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

ANALYSIS FILE NAME: GSM774242_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24078.DS18386.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18386.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Leg, Donor H-24078, Library DS18386 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.10351
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FML DNase 78 86
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24078 Library DS18386 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,394,239
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.5551
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5468
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9938
IROC_PERCENTILE: 51
POISSON_SCORE: 0.5913
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.83

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

source_name: Fetal Muscle, Leg primary tissue, day 127; DS18386

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Muscle, Leg

tag: molecule

value: genomic DNA

tag: disease

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 127

value: Male

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Muscle, Lower Limb; DS18174

description:
sample_term_id: UBERON_0003663
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18174
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9473
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9472
****************
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: GSM774238_UW.Fetal_Muscle_Lower_Limb_Skeletal.ChromatinAccessibility.H-24042.DS18174.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18174.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Muscle Lower Limb Skeletal Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Lower Limb Skeletal, Donor H-24042, Library DS18174 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.10403
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 79,521,454
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.5285
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.5157
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9922
IROC_PERCENTILE: 32
POISSON_SCORE: 0.5792
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM774238_UW.Fetal_Muscle_Lower_Limb_Skeletal.ChromatinAccessibility.H-24042.DS18174.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18174.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Lower Limb Skeletal Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Lower Limb Skeletal, Donor H-24042, Library DS18174 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.10356
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FMLLS DNase 42 74
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Lower Limb Skeletal DNase Hypersensitivity Donor H-24042 Library DS18174 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 79,521,454
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.5285
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.5157
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9922
IROC_PERCENTILE: 32
POISSON_SCORE: 0.5792
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Lower, Limb primary tissue, day 120; DS18174

value: Fetal Muscle, Lower Limb Skeletal

value: Fetal Muscle, Lower Limb

value: day 120


title: Chromatin accessibility assay of Penis Foreskin Fibroblast Primary Cells; DS18229

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18229
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8469
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.7320
****************
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: GSM774241_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin01.DS18229.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18229.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin01, Library DS18229 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.10373
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,194,310
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.6313
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.6375
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9982
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6592
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM774241_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin01.DS18229.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18229.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Fibroblast Primary Cells, Donor skin01, Library DS18229 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.10326
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: PFF DNase 01 29
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin01 Library DS18229 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,194,310
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.6313
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.6375
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9982
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6592
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Penis, Foreskin, Fibroblast Primary Cells skin01; DS18229

value: Penis, Foreskin, Fibroblast skin01

value: SFVAMC Dermatology

value: Primary Cell Culture

value: Fibroblast

tag: markers

value: Invitrogen 154CF + HKGS + .07mM Ca

value: Neonate

value: Disease Free

tag: karyotype

tag: parity


title: P. tricornutum_normal_48h

description: small RNA

value: Bohlin

value: log phase cells

value: normal


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS18176

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18176
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8501
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8500
****************
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: GSM774239_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24042.DS18176.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18176.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24042, Library DS18176 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.10404
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,249,585
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3866
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.3717
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9908
IROC_PERCENTILE: 23
POISSON_SCORE: 0.4297
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM774239_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24042.DS18176.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18176.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Arm, Donor H-24042, Library DS18176 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.10357
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FMA DNase 42 76
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24042 Library DS18176 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,249,585
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3866
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.3717
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9908
IROC_PERCENTILE: 23
POISSON_SCORE: 0.4297
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Arm primary tissue, day 120; DS18176

value: Fetal Muscle, Arm

value: genomic DNA

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: Male


title: Myceliophthora_thermophila_Barley_34C_rep1

tag: carbon source

value: Barley straw

tag: growth temperature


title: Chaetomium_globosum_Alfalfa_34C_rep1

value: Alfalfa hay


title: Chromatin accessibility assay of Penis Foreskin Fibroblast Primary Cells; DS18224

description:
sample_term_id: CL_1001608
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18224
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8472
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.7320
****************
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: GSM774240_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin01.DS18224.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18224.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin01, Library DS18224 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.10372
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 91,961,019
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.6709
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6743
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9982
IROC_PERCENTILE: 100
POISSON_SCORE: 0.697
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM774240_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin01.DS18224.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18224.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Fibroblast Primary Cells, Donor skin01, Library DS18224 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.10325
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: PFF DNase 01 24
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin01 Library DS18224 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 91,961,019
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.6709
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6743
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9982
IROC_PERCENTILE: 100
POISSON_SCORE: 0.697
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Penis, Foreskin, Fibroblast Primary Cells skin01; DS18224

value: Penis, Foreskin, Fibroblast skin01

value: SFVAMC Dermatology

value: Primary Cell Culture

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Muscle, Back; DS18083

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18083
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8374
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8373
****************
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: GSM774235_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24005.DS18083.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18083.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-24005, Library DS18083 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.10370
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 90,158,122
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4913
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.4711
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.991
IROC_PERCENTILE: 26
POISSON_SCORE: 0.5293
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM774235_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24005.DS18083.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18083.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-24005, Library DS18083 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.10323
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FMB DNase 05 83
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-24005 Library DS18083 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 90,158,122
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4913
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.4711
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.991
IROC_PERCENTILE: 26
POISSON_SCORE: 0.5293
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Back primary tissue, day 105; DS18083

value: Fetal Muscle, Back

value: day 105

value: Female


title: Chromatin accessibility assay of Fetal Lung, Left; DS18170

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18170
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8391
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8390
****************
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: GSM774237_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23640.DS18170.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18170.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Left, Donor H-23640, Library DS18170 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.10402
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 90,417,058
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.6549
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.6406
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9964
IROC_PERCENTILE: 83
POISSON_SCORE: 0.6535
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM774237_UW.Fetal_Lung_Left.ChromatinAccessibility.H-23640.DS18170.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18170.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Left, Donor H-23640, Library DS18170 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.10355
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FLL DNase 40 70
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left DNase Hypersensitivity Donor H-23640 Library DS18170 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 90,417,058
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.6549
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.6406
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9964
IROC_PERCENTILE: 83
POISSON_SCORE: 0.6535
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Fetal Lung, Left primary tissue, day 115; DS18170

value: Fetal Lung, Left

value: genomic DNA

value: day 115


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS18080

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18080
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8505
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8504
****************
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: GSM774234_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24005.DS18080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18080.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24005, Library DS18080 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.10368
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 84,357,139
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4669
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.441
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.99
IROC_PERCENTILE: 13
POISSON_SCORE: 0.5145
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774234_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24005.DS18080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18080.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Arm, Donor H-24005, Library DS18080 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.10321
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FMA DNase 05 80
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24005 Library DS18080 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 84,357,139
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4669
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.441
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.99
IROC_PERCENTILE: 13
POISSON_SCORE: 0.5145
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Arm primary tissue, day 105; DS18080

value: Fetal Muscle, Arm

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW


title: Chromatin accessibility assay of Fetal Renal Pelvis; DS18088

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18088
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8348
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8347
****************
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: GSM774236_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24005.DS18088.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18088.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis, Donor H-24005, Library DS18088 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.10371
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,026,022
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.2824
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.2917
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.988
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3469
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM774236_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24005.DS18088.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18088.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis, Donor H-24005, Library DS18088 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.10324
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FRP DNase 05 88
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24005 Library DS18088 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,026,022
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.2824
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.2917
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.988
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3469
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Fetal Kidney, renal, pelvis primary tissue, day 105; DS18088

value: Fetal Renal Pelvis

value: fetal


title: Chromatin accessibility assay of Penis Foreskin Melanocytes Primary Cells; DS18601

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18601
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8463
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.7321
****************
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: GSM774244_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18601.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18601.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin01, Library DS18601 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.10393
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,263,473
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4665
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4705
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9945
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5365
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM774244_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18601.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18601.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Melanocyte Primary Cells, Donor skin01, Library DS18601 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.10346
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: PFM DNase 01 01
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Melanocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18601 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,263,473
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4665
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4705
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9945
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5365
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Penis, Foreskin, Melanocyte Primary Cells skin01; DS18601

value: Penis, Foreskin, Melanocyte skin01

value: SFVAMC Dermatology

value: Melanocyte

value: Invitrogen 154CF + HKGS + .07mM Ca

value: Neonate

value: Disease Free

value: Male


title: Chromatin accessibility assay of Fetal Stomach; DS17963

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17963
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8484
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8483
****************
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: GSM774232_UW.Fetal_Stomach.ChromatinAccessibility.H-24005.DS17963.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17963.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-24005, Library DS17963 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.10389
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,657,032
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3493
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.3471
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9903
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4353
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM774232_UW.Fetal_Stomach.ChromatinAccessibility.H-24005.DS17963.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17963.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-24005, Library DS17963 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.10342
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FS DNase 05 63
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-24005 Library DS17963 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,657,032
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3493
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.3471
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9903
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4353
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Fetal Stomach primary tissue, day 105; DS17963

value: Fetal Stomach

value: day 105

value: Female

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Intestine, Large; DS17990

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17990
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8427
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8426
****************
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: GSM774233_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24005.DS17990.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17990.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Intestine Large, Donor H-24005, Library DS17990 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.10363
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,168,060
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4052
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.4078
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9923
IROC_PERCENTILE: 34
POISSON_SCORE: 0.4536
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774233_UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24005.DS17990.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17990.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Intestine Large, Donor H-24005, Library DS17990 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.10316
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FIL DNase 05 90
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large DNase Hypersensitivity Donor H-24005 Library DS17990 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,168,060
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4052
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.4078
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9923
IROC_PERCENTILE: 34
POISSON_SCORE: 0.4536
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Intestine, Large primary tissue, day 105; DS17990

value: Fetal Intestine, Large

value: genomic DNA

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue


title: Chromatin accessibility assay of Penis Foreskin Melanocytes Primary Cells; DS18590

description:
sample_term_id: CL_2000045
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18590
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8466
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.7321
****************
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: GSM774243_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18590.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18590.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin01, Library DS18590 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.10395
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,409,921
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.483
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.5131
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9945
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5383
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM774243_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18590.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18590.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Melanocyte Primary Cells, Donor skin01, Library DS18590 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.10348
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: PFM DNase 01 90
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Melanocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18590 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,409,921
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.483
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.5131
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9945
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5383
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Penis, Foreskin, Melanocyte Primary Cells skin01; DS18590

value: Penis, Foreskin, Melanocyte skin01

value: Primary Cell Culture


title: Chromatin accessibility assay of Fetal Thymus; DS17876

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17876
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8475
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7180
****************
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: GSM774230_UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17876.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17876.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Thymus, Donor H-23964, Library DS17876 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.10401
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 78,106,015
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3354
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.3208
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9965
IROC_PERCENTILE: 85
POISSON_SCORE: 0.3607
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774230_UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17876.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17876.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Thymus, Donor H-23964, Library DS17876 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.10354
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FT DNase 64 76
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-23964 Library DS17876 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 78,106,015
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.3354
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.3208
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9965
IROC_PERCENTILE: 85
POISSON_SCORE: 0.3607
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal  primary tissue, day 98; DS17876

value: Fetal Thymus

value: UW

value: fetal

value: day 98


title: Chromatin accessibility assay of Fetal Lung, Right; DS17954

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS17954
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8344
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8343
****************
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: GSM774231_UW.Fetal_Lung_Right.ChromatinAccessibility.H-24005.DS17954.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17954.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung Right, Donor H-24005, Library DS17954 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.10394
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,885,773
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.5502
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.5343
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9945
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5976
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM774231_UW.Fetal_Lung_Right.ChromatinAccessibility.H-24005.DS17954.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS17954.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Lung Right, Donor H-24005, Library DS17954 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.10347
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: FLR DNase 05 54
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right DNase Hypersensitivity Donor H-24005 Library DS17954 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,885,773
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.5502
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.5343
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9945
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5976
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Lung, Right primary tissue, day 105; DS17954

value: Fetal Lung, Right