title: Mouse_TG_Ctrl_RNA-seq

status: Public on Oct 03 2012

first: Weijia

last: Zhang

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

description:
RNA seq of  thyroid gland tissues of transgenic F1H mice immunized that did not develop EAGD
mouse_TGhealthy

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  human hg18 or mouse mm9 exon and exon junction sequences  and contamination datanases using bwa algorithm
After filtering reads mapped to contamination databases, the reads that  have one or no mismatch and are uniquely aligned to each exon and splicing-junction sites were extracted and then counted. The read count for each RefSeq transcript was calculated by combining the counts for exons and splicing junctions of corresponding transcript.
Supplementary_files_format_and_content: tab-delimited txt file including  count values for RefSeq transcripts
Genome_build: hg18 or mm9

source_name: pool of thyroid gland tissues from group

growth_protocol: Human thyroid primary cells were prepared from fresh, non-cancerous thyroid tissue adjacent to thyroid tumors that were removed at surgery. Tissue was minced and digested in a 50 ml falcon tube with type II collagenase at a concentration of 5 mg/ml for three hours at 37 degrees celsius. After three hours, 10ml of medium [DMEM, 4.0 mM L-glutamine and sodium pyruvate, 10% FBS, 1% antibiotic anti-mycotic solution  was added to the tube, and the product was strained through a 70 um cell strainer into another 50 ml falcon tube. The tube was centrifuged at 1000 rpm for 5 minutes. The supernatant was carefully removed from the pellet and the pellet was washed with another 10 ml of medium. Again, the tube was spun at 1000 rpm for 5 minutes. The medium was removed from the pellet. The pellet was suspended in 10 ml of medium, and the cells were plated in a 25 cm2 flask, and placed in an incubator at 37 degrees celsius with 5% CO2.

extract_protocol: According to Illumina mRNA Sequencing Sample Preparation Guide. Briefly, 2ug total RNA hybridized to poly dT magnetic beads to capture polyA mRNA molecules. Chemical fragmentation, first strand synthesis with RTase, randomers second strand synthesis. Then end repair, 3' A overhang, multiplex adapter ligation (from Illumina indexing kit), size selection by electrophoresis and cut at 200bp. 18 cycles of PCR with a primer bearing an indexing barcode.

treatment_protocol: Primary thyroid cell cultures were washed with 10ml PBS after 24 hours, and then 10mL of medium [DMEM, 4.0 mM L-glutamine and sodium pyruvate, 10% FBS, 1% antibiotic anti-mycotic solution (all from Hyclone/Thermo Fisher Waltham, MA)] were added to the flask. This was allowed to incubate at 37oC with 5% CO2 overnight. Cell were washed with PBS, and plated evenly in a 12 well plate. Cells were incubated 24 hours to allow for adherence to the wells. Again, the cells were washed and at this time the cells were treated for 0 or 24 hours with 1 ug of anti-CD40 stimulating antibody (G28.5).

value: thyroid gland

tag: generation

value: F1H (F1, first generation, H hybrid)

value: hybrid C57BL/6xBALB/c

value: CD40 over-expressing transgenic

tag: treatment protocol

value: immunized with thyrotropin receptor A subunit cDNA in an adenovirus construct

tag: immunization outcome

value: healthy


title: Mouse_WT_GD_RNA-seq

type: SRA

city: New York

state: NY

country: USA

description:
RNA seq of  thyroid gland tissues of WT F1H mice immunized that did  develop EAGD
mouse_WTEAGD

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: strain

tag: genotype/variation

value: wild type

value: developed EAGD


title: IRF2-A

status: Public on Oct 04 2012

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) using Illumina software pipeline.  Only ChIP-seq reads that aligned to exactly one location in the reference human genome (UCSC, hg18) were retained for downstream data analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
Genome_build: hg18
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file

molecule: genomic DNA

organism: Homo sapiens

source_name: Human primary adult proerythroblasts (ProEs)

growth_protocol: Primary maturing fetal or adult erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.

extract_protocol: For ChIP-seq analysis using the Illumin HiSeq2000, 10-20 ng of ChIP DNA was processed for library generation using the ChIP-seq Sample Preparation Kit (Illumina) following the manufacturer’s protocol. Raw ChIP-seq data were processed using the Illumina software pipeline. Only ChIP-seq reads that aligned to exactly one location in the reference human genome (UCSC, hg18) were retained for downstream data analysis.

value: CD34+ HSPC-derived proerythroblasts

tag: developmental stage

value: adult bone marrow

tag: chip antibody

tag: vendor

value: Abcam and Millipore

tag: catalog#

value: ab55331 and ABE115


title: H3K4me1-F

data_processing:
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) using Helisphere software. Only the reads that were uniquely aligned to reference genome with read alignment score higher than 4.5 were retained for further analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
Genome_build: hg18
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file

source_name: Human primary fetal proerythroblasts (ProEs)

extract_protocol: For ChIP-seq analysis using the HeliScope™ Single Molecule Sequencer, ChIP DNA was processed for 3’ polyA tailing followed by 3’ ddATP-blocking. Processing samples by ligation, amplification and size selection are not required by Helicos sequencing. Briefly, 6-9 ng of ChIP DNA or input DNA was used in the 3’ polyA tailing reaction in 14.8 ul containing 2 ul of 2.5 mM CoCl2, 2 ul of 10 x terminal transferase buffer and nuclease-free water. The reaction mixture was denatured in 95C for 5 min, followed by rapid cooling in ice water slurry. Then 1 U of terminal transferase, 4 ul of 50 uM dATP and 0.2 ul of NEB BSA were added to the mixture. Samples were incubated in a thermocycler at 37C for 1 h, 70C 10 min, followed by denaturing at 95C for 5 min and rapid cooling in ice water slurry. For 3’ ddATP-blocking, 0.5 ul of 200 uM ddATP, 1 ul of 10 x terminal transferase, 1 ul of 2.5 mM CoCl2, 1 U of terminal transferase, and 6.5 ul of nuclear-free water were added to the above reaction. Samples were incubated in a thermocycler at 37C for 1 h and 70C for 20 min. Then 2 picomoles of carrier oligonucleotide were added to the reaction, and samples were hybridized to the Helicos flow cells.

value: 2-trimester fetal liver

value: Abcam


title: Mouse_WT_Ctrl_RNA-seq

description:
RNA seq of  thyroid gland tissues of WT F1H mice immunized that did not develop EAGD
mouse_WThealthy


title: Mouse_TG_GD_RNA-seq

description:
RNA seq of  thyroid gland tissues of transgenic F1H mice immunized that did  develop EAGD
mouse_TGEAGD


title: H3K27ac-A


title: HudsonAlpha_MethylSeq_H9ES-EBD

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylSeq

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylSeq

tag: datatype description

value: DNA Methyl Seq

tag: cell

tag: cell organism

value: human

tag: cell description

value: embryonic stem cell (hESC) H9, embryoid body-derived

tag: cell lineage

value: inner cell mass

tag: cell sex

value: F

tag: replicate


title: UW_DnaseDgf_Th1_Wb33676984

extract_protocol: For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwDgf

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

value: Th1 cells in vivo isolation

tag: cell karyotype

value: normal donor is Asian, female 26 year old, primary pheresis of single normal subject

value: mesoderm

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: labexpid

tag: labversion


title: HudsonAlpha_MethylSeq_H9ES-E

value: embryonic stem cell (hESC) H9, endoderm


title: HudsonAlpha_MethylSeq_BG02ES

value: HudsonAlpha

value: embryonic stem cell (hESC), BG02, treatment:H9 conditioned medium

value: normal

value: M


title: HudsonAlpha_MethylSeq_BG02ES-EBD

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylSeq

value: DNA Methyl Seq

value: human

value: embryonic stem cell (hESC), BG02, embryoid body-derived


title: LSD1_ChIPSeq

first: Venugopalan

last: Nair

address: 1 Gustave L. Levy Place

department: Neurology

description: ChIP against LSD1

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 genome (NCBI, Build 37) using the Illumina Genome Analyzer G2 Pipeline. All reads that is uniquely mapped to mm9 with two or fewer mismatches were retained. We kept only one read if multuple reads were mapped to the same position of mm9.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: Embyonic stem cells

growth_protocol: Embryonic stem (R1ES) cells (passage 13-18) were routinely grown on gelatin coated tissue culture plates in complete growth medium in presence of LIF (1000 U/ml) as described in our previous publication (Nair 2006, Apoptosis 11: 955-966).

extract_protocol: ChIP assays were performed using EZ-ChIP kit (Cat#17-371) from Upstate Biotechnology (Millipore) according to the manufacturer's instructions. Briefly, 5 x107 cells were trypsinized, fixed with 1% formaldehyde, resuspended in lysis buffer, and fragmented with a Bioruptor UCD-200 Sonifier (Diagenode Inc. NY) to a size range of 200 to 1,000 bases. Solubilized chromatin was diluted 10-fold in ChIP dilution buffer and after removal of a control aliquot (Input), incubated at 4ºC overnight with antibody against LSD1 (Abcam #07-449) or dimethyl histone H3 Lys4 (Cell Signaling Technology #9753). Control IgG was used as a negative control in all ChIP experiments. Immune-complexes were purified using spin columns and libraries were prepared according to Illumina's  instructions for preparing samples for ChIP sequencing of DNA (Part # 11257047). Approximately 200 bp DNA fragments were purified from the library after ressolving on an agarose gel. DNA was captured on an Illumina flow cell for cluster generation. Libraries were then subjected to sequencing in an Illumina Genome Analyzer II to generate 36 bp reads.

tag: cell type

value: 129SV embryonic stem cells

tag: passages

tag: chip antibody


title: UW_DnaseDgf_CD4+_Naive_Wb11970640

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: CD4+ naive sorted cells, donor is Caucasian, male 26 year old, primary pheresis of single normal subject


title: IgG_ChIPSeq

description: ChIP with Control IgG

value: IgG


title: UW_DnaseDgf_LHCN-M2_DIFF_4d

tag: datatype

tag: datatype description

value: DNase Digital Footprinting

value: skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2:not in 2011 analysis.

value: mesoderm

value: Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam)


title: UW_DnaseDgf_M059J

tag: cell

tag: cell organism

value: malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old

value: cancer

value: ectoderm


title: Input_ChIPSeq

description: Genomic DNA used for ChIP


title: UW_DnaseDgf_T-47D

tag: cell description

value: epithelial cell line derived from a mammary ductal carcinoma.

value: F

value: No special treatment or protocol applies


title: HudsonAlpha_MethylSeq_HFL11W

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylSeq

value: DNA Methyl Seq

value: human

value: fetal liver 11 weeks, consented fetal liver samples were isolated from legally aborted fetuses at 11 weeks gestation

tag: cell lineage

value: endoderm

tag: cell sex

value: U


title: HudsonAlpha_MethylSeq_H9ES-AFP-

value: embryonic stem cell (hESC), H9-derived, treatment:H9 AFP-

value: inner cell mass

tag: replicate


title: UW_DnaseDgf_RPMI-7951

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

value: Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high.

tag: cell karyotype


title: H3K4me2_ChIPSeq

description: ChIP against H3K4me2

value: 129SV embryonic stem cells


title: HudsonAlpha_MethylSeq_H9ES

value: embryonic stem cell (hESC) H9

value: F


title: UW_DnaseDgf_HMVEC-dLy-Neo

source_name: HMVEC-dLy-Neo

value: HMVEC-dLy-Neo

value: neonatal lymphatic microvascular endothelial cells, dermal-derived

value: normal

value: mesoderm

value: M


title: HudsonAlpha_MethylSeq_HAL

source_name: HAL

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylSeq

value: DNA Methyl Seq

value: HAL

value: human

value: adult liver, genomic DNA purified from surgically excised adult human liver

value: endoderm


title: UW_DnaseDgf_HGF

source_name: HGF

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

value: HGF

value: gingival fibroblasts

value: U


title: UW_DnaseDgf_HFF

source_name: HFF

value: HFF

value: foreskin fibroblast

value: normal


title: UW_DnaseDgf_HMVEC-dBl-Neo

source_name: HMVEC-dBl-Neo

value: HMVEC-dBl-Neo

value: neonatal blood microvascular endothelial cells, dermal-derived

value: mesoderm

value: M


title: HudsonAlpha_MethylSeq_H9ES-CM

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylSeq

value: DNA Methyl Seq

value: human

value: embryonic stem cell (hESC) H9, treatment:H9 conditioned medium

value: inner cell mass

value: F


title: UW_DnaseDgf_HCF

source_name: HCF

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

value: HCF

value: cardiac fibroblasts


title: UW_DnaseDgf_Th17

value: T helper cells expressing IL-17, primary pheresis of single normal subject

value: normal

value: B

tag: treatment

tag: treatment description

value: No special treatment or protocol applies


title: HudsonAlpha_MethylSeq_H9ES-AFP+

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: embryonic stem cell (hESC), H9-derived, treatment:H9 AFP+


title: HudsonAlpha_MethylSeq_H9ES-EB

value: MethylSeq

value: DNA Methyl Seq

value: human

value: embryonic stem cell (hESC) H9, embryoid bodies


title: HudsonAlpha_MethylSeq_GM12878

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: mesoderm

value: F

tag: restrictionenzyme

value: hpa,msp


title: UW_DnaseDgf_GM12865

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment:Epstein-Barr Virus transformed

tag: labexpid

tag: labversion


title: UW_DnaseDgf_LHCN-M2

value: skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2:not in 2011 analysis.

value: M


title: UW_DnaseDgf_CD20+_RO01778

value: B cells, caucasian, draw number 1, newly promoted to tier 2:not in 2011 analysis

value: normal


title: HudsonAlpha_MethylSeq_HFL24W

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylSeq

value: fetal liver 24 weeks, consented fetal liver samples were isolated from legally aborted fetuses at 24 weeks gestation

value: endoderm

value: U


title: UW_DnaseDgf_AG10803

value: human

value: abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell


title: HudsonAlpha_MethylSeq_HeLa-S3

value: DNA Methyl Seq

value: cervical carcinoma

value: cancer

value: ectoderm

value: F

value: hpa,msp


title: UW_DnaseDgf_Treg_Wb78495824

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

value: T regulatory cells in vivo isolation

value: normal donor is Causasian, female 35 year old, primary pheresis of single normal subject

value: mesoderm

value: No special treatment or protocol applies


title: HudsonAlpha_MethylSeq_K562

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylSeq

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


title: UW_DnaseDgf_Th2_Wb54553204

value: human

value: Th2 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject

value: normal

value: M


title: UW_DnaseDgf_HIPEpiC

source_name: HIPEpiC

value: HIPEpiC

value: iris pigment epithelial cells

value: ectoderm

value: U


title: UW_DnaseDgf_A549

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: cancer

value: endoderm


title: UW_DnaseSeq_Fibroblast_adult-8wks_C57BL/6

source_name: Fibroblast

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeUwDnase

value: UW-m

value: DnaseSeq

value: DNaseI HS Sequencing

value: Fibroblast

value: mouse

tag: age

tag: age description

value: Adult 8 weeks

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: HudsonAlpha_MethylSeq_GM12892

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylSeq

tag: datatype description

value: DNA Methyl Seq

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: mesoderm

value: F

value: hpa,msp


title: UW_DnaseDgf_HUVEC

source_name: HUVEC

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

tag: cell

value: HUVEC

tag: cell organism

tag: cell description

value: umbilical vein endothelial cells

value: normal

tag: cell lineage

value: U


title: HudsonAlpha_MethylSeq_HepG2

value: HudsonAlpha

value: hepatocellular carcinoma

tag: cell karyotype

value: cancer

value: endoderm

tag: cell sex

value: M

tag: replicate


title: UW_DnaseSeq_Retina_adult-1wks_C57BL/6

source_name: Retina

value: UW-m

value: DnaseSeq

value: DNaseI HS Sequencing

value: Retina

value: mouse

value: Adult 1 week

value: C57 black 6, the most common inbred strain of laboratory mouse

tag: labexpid


title: UW_DnaseDgf_HA-h

source_name: HA-h

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

value: HA-h

value: human

value: astrocytes-hippocampal

value: ectoderm

tag: labversion


title: UW_DnaseDgf_HSMM

source_name: HSMM

value: HSMM

value: skeletal muscle myoblasts

value: normal

value: mesoderm

value: U


title: HudsonAlpha_MethylSeq_HCT-116

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylSeq

value: DNA Methyl Seq

value: colorectal carcinoma (PMID:7214343)

value: cancer

value: endoderm

value: M


title: UW_DnaseDgf_HCM

source_name: HCM

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseDgf

value: DNase Digital Footprinting

value: HCM

value: cardiac myocytes


title: UW_DnaseDgf_HMVEC-LLy

source_name: HMVEC-LLy

value: HMVEC-LLy

value: human

value: lymphatic microvascular endothelial cells, lung-derived

value: normal

value: F


title: UW_DnaseSeq_TReg-Activated_adult-8wks_C57BL/6

source_name: TReg-Activated

value: UW-m

value: DnaseSeq

value: DNaseI HS Sequencing

value: TReg-Activated

value: mouse

value: Activated primary T regulatory cells, isolated ex vivo

tag: age

value: Adult 8 weeks

value: C57 black 6, the most common inbred strain of laboratory mouse


title: UW_DnaseSeq_WholeBrain_E14.5_C57BL/6

source_name: WholeBrain

value: Stamatoyannopoulous - University of Washington

value: tissue

value: Whole Brain

tag: Sex

value: M

tag: age description

value: Embryonic day 14.5


title: UW_DnaseDgf_Th2

value: UW

value: DnaseDgf

value: DNase Digital Footprinting

value: human

value: primary Th2 T cells

value: mesoderm

value: U

tag: treatment

tag: treatment description

value: No special treatment or protocol applies


title: UW_DnaseDgf_HCFaa

source_name: HCFaa

tag: lab

tag: lab description

value: HCFaa

value: cardiac fibroblasts- adult atrial

value: normal

value: F


title: HudsonAlpha_MethylSeq_GM12891

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylSeq

tag: datatype description

value: DNA Methyl Seq

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

tag: restrictionenzyme

value: hpa,msp


title: HudsonAlpha_MethylSeq_H1-hESC

growth_protocol: missing

tag: cell

tag: cell organism

tag: cell description

value: embryonic stem cells

value: inner cell mass

value: M


title: GATA1-A

source_name: Human primary adult proerythroblasts (ProEs)

tag: tissue

value: CD34+ HSPC-derived proerythroblasts

tag: developmental stage

value: adult bone marrow

tag: chip antibody

tag: vendor

value: Abcam

tag: catalog#


title: UW_DnaseSeq_3134_immortalized_RIII

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

value: DNaseI HS Sequencing

value: mouse

value: Mammary

tag: cell sex

tag: age

value: immortalized

value: Immortal cells

tag: strain

value: RIII

tag: strain description

value: High mammary tumor incidence in unfostered substrains.

tag: labversion

tag: replicate


title: UW_DnaseDgf_HMVEC-LBl

source_name: HMVEC-LBl

tag: lab

value: UW

tag: lab description

tag: datatype

value: DnaseDgf

value: DNase Digital Footprinting

value: HMVEC-LBl

value: human

value: blood microvascular endothelial cells, lung-derived

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

value: F

tag: labexpid


title: UW_DnaseDgf_NHDF-neo

source_name: NHDF-neo

value: Stamatoyannopoulous - University of Washington

tag: datatype description

tag: cell

value: NHDF-neo

tag: cell organism

tag: cell description

value: neonatal dermal fibroblasts

value: U


title: UW_DnaseDgf_NB4

value: acute promyelocytic leukemia cell line. (PMID:1995093)

value: cancer


title: UW_DnaseSeq_Kidney_adult-8wks_C57BL/6

source_name: Kidney

value: UW-m

value: DnaseSeq

value: DNaseI HS Sequencing

value: Kidney

value: mouse

value: M

tag: age description

value: Adult 8 weeks

value: C57 black 6, the most common inbred strain of laboratory mouse


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Neural Progenitor Cells; renlab.H3K4me3.NPC.04.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY26
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13940
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM1013151_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me3.CY26.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.NPC.04.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library CY26, 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.16461
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,550,006
FINDPEAKS_SCORE: 0.4431
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4642
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4585
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM1013151_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me3.CY26.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.NPC.04.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library CY26, 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.16615
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP H3K4me3 26
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me3 Library CY26 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,550,006
FINDPEAKS_SCORE: 0.4431
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4642
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4585
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K4me3.NPC.04.01

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

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

tag: passage

tag: medium

tag: Sex

value: Male

tag: batch

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: UW_DnaseSeq_B-cell_(CD19+)_adult-8wks_C57BL/6

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

value: DNaseI HS Sequencing

value: mouse

value: B Cell , CD19+

tag: cell sex

tag: age

tag: strain

tag: strain description

tag: labversion

tag: replicate


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

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY27
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13950
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM1013158_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.CY27.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.NPC.03.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library CY27, 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.16495
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,621,160
FINDPEAKS_SCORE: 0.1025
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.191
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.8776
IROC_PERCENTILE: 79
POISSON_SCORE: 0.3439
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM1013158_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.CY27.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.NPC.03.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library CY27, 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.16649
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP H3K9me3 27
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library CY27 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,621,160
FINDPEAKS_SCORE: 0.1025
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.191
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.8776
IROC_PERCENTILE: 79
POISSON_SCORE: 0.3439
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K9me3.NPC.03.01

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Histone H3K9me3

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in Mesenchymal Stem Cells; renlab.H2BK15ac.MSC.01.01

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK15ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY42
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13934
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10198
****************
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: Various levels of processed data files will be made available as this project proceeds.

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H2BK15ac.MSC.01.01

value: H1 Derived Mesenchymal Stem Cells

tag: disease

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Publication in progress

value: Male

value: Histone H2BK15ac


title: UW_DnaseDgf_HVMF

source_name: HVMF

value: UW

value: DnaseDgf

tag: datatype description

value: DNase Digital Footprinting

tag: cell

value: HVMF

tag: cell organism

value: human

tag: cell description

value: villous mesenchymal fibroblast cells

tag: cell karyotype

value: normal

value: U

tag: labexpid


title: UW_DnaseSeq_T-Naive_adult-8wks_C57BL/6

source_name: T-Naive

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

value: DNaseI HS Sequencing

value: T-Naive

value: mouse

value: Naive T cells:CD4+, CD25-

tag: cell sex

value: M

tag: age

tag: age description

value: Adult 8 weeks

value: C57 black 6, the most common inbred strain of laboratory mouse


title: UW_DnaseSeq_Retina_newborn-1days_C57BL/6

source_name: Retina

value: Retina

value: Newborn 1 day

tag: strain

tag: strain description

tag: labversion

tag: replicate


title: UW_DnaseSeq_MEL_immortalized_Unknown

source_name: MEL

tag: line

value: MEL

value: Leukemia (K562 analog)

value: immortalized

value: immortalized cell line

value: Unknown

value: Unknown strain origin


title: UW_DnaseSeq_Liver_E14.5_C57BL/6

source_name: Liver

value: UW-m

value: Stamatoyannopoulous - University of Washington

tag: datatype description

value: tissue

value: liver

tag: Sex

value: Embryonic day 14.5


title: Reference Epigenome: ChIP-Seq Analysis of H3K23ac in Neural Progenitor Cells; renlab.H3K23ac.NPC.02.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY12
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14058
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM1013121_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K23ac.CY12.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.NPC.02.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K23ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library CY12, 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.16376
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,272,751
FINDPEAKS_SCORE: 0.174
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3127
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9272
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4558
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1013121_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K23ac.CY12.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.NPC.02.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K23ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library CY12, 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.16530
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP H3K23ac 12
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K23ac Library CY12 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,272,751
FINDPEAKS_SCORE: 0.174
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3127
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9272
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4558
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K23ac.NPC.02.01

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

tag: passage

tag: medium

value: Male

tag: batch

value: Histone H3K23ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Upstate


title: UW_DnaseSeq_ES-CJ7_E0_129S1/SVImJ

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

value: DNaseI HS Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.)

tag: cell sex

value: M

tag: age

value: Embryonic day 0 (stem cell)

value: Control inbred strain of the steel-derived ES cells.


title: UW_DnaseSeq_Thymus_adult-8wks_C57BL/6

source_name: Thymus

tag: datatype description

value: tissue

value: thymus

tag: Sex

tag: age description

value: Adult 8 weeks

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse

tag: labexpid

tag: labversion

tag: replicate


title: UW_DnaseSeq_LgIntestine_adult-8wks_C57BL/6

source_name: LgIntestine

value: LgIntestine

value: Large Intestine


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Neural Progenitor Cells; renlab.H3K36me3.NPC.03.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY23
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13938
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM1013141_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K36me3.CY23.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.NPC.03.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library CY23, 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.16363
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,160,834
FINDPEAKS_SCORE: 0.1797
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9542
IROC_PERCENTILE: 35
POISSON_SCORE: 0.405
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM1013141_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K36me3.CY23.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.NPC.03.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library CY23, 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.16517
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP H3K36me3 23
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library CY23 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,160,834
FINDPEAKS_SCORE: 0.1797
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9542
IROC_PERCENTILE: 35
POISSON_SCORE: 0.405
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K36me3.NPC.03.01

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

tag: passage

tag: medium

value: Male

tag: batch

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Neural Progenitor Cells; renlab.H3K4me1.NPC.03.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY25
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13942
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM1013146_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me1.CY25.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.NPC.03.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library CY25, 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.16430
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,263,415
FINDPEAKS_SCORE: 0.1783
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2796
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9386
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4417
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM1013146_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me1.CY25.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.NPC.03.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library CY25, 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.16584
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HDNP H3K4me1 25
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library CY25 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,263,415
FINDPEAKS_SCORE: 0.1783
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2796
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9386
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4417
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K4me1.NPC.03.01

value: Histone H3K4me1


title: UW_DnaseSeq_WholeBrain_E18.5_C57BL/6

source_name: WholeBrain

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell

value: WholeBrain

tag: cell organism

value: mouse

tag: cell description

value: Whole Brain

tag: cell sex

value: M

tag: age

value: Embryonic day 18.5

value: C57 black 6, the most common inbred strain of laboratory mouse


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in BMP4 Mesendoderm Cells; renlab.H2BK15ac.BMP4M.02.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK15ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK418
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13936
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11184
****************
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: GSM1013119_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK15ac.AK418.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.BMP4M.02.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK15ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK418, 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.16429
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,521,186
FINDPEAKS_SCORE: 0.0031
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0933
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.5196
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2249
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1013119_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK15ac.AK418.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.BMP4M.02.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK15ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK418, 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.16583
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HBDM H2BK15ac 18
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK15ac Library AK418 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,521,186
FINDPEAKS_SCORE: 0.0031
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0933
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.5196
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2249
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H2BK15ac.BMP4M.02.01

tag: sample alias

tag: sample common name

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

tag: Sex

value: Male

value: Histone H2BK15ac


title: UW_DnaseSeq_Spleen_adult-8wks_C57BL/6

source_name: Spleen

value: UW-m

value: Stamatoyannopoulous - University of Washington

value: tissue

value: Spleen

tag: age description

value: Adult 8 weeks

tag: strain

tag: strain description

tag: labexpid

tag: labversion

tag: replicate


title: UW_DnaseSeq_Liver_adult-8wks_C57BL/6

tag: lab

tag: lab description

value: DnaseSeq

value: DNaseI HS Sequencing

value: mouse

value: liver


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: ChIP-Seq input analysis of foreskin fibroblast from skin03 (A15571) using Illumina HiSeq 2000
library name: A15571
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 90-360 bp
****************
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: GSM958168_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.Input.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15571-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13922
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,019,451
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0618
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0832
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM958168_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.Input.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15571-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13973
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFF Input 03 71
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin03 Library A15571 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,019,451
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0618
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0832
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: male

tag: body site

value: Penis

tag: histological type

value: Fibroblast

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: foreskin fibroblast


description:
design description: ChIP-Seq input analysis of foreskin keratinocyte from skin03 (A15578) using Illumina HiSeq 2000
library name: A15578
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 49-391 bp
****************
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: GSM958167_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Input.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15578-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13923
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,000,153
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.0037
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.0163
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0532
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM958167_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Input.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15578-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13974
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFK Input 03 78
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15578 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,000,153
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.0037
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.0163
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0532
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Keratinocyte

value: foreskin keratinocyte


title: UW_DnaseDgf_HEEpiC

source_name: HEEpiC

value: UW

tag: datatype

value: DnaseDgf

tag: datatype description

value: DNase Digital Footprinting

tag: cell

value: HEEpiC

tag: cell organism

value: human

tag: cell description

value: esophageal epithelial cells

tag: cell karyotype

value: normal

tag: cell lineage

value: endoderm

tag: cell sex

value: U


title: UW_DnaseDgf_NHLF

source_name: NHLF

value: Stamatoyannopoulous - University of Washington

value: NHLF

value: lung fibroblasts

tag: labexpid

tag: labversion


title: UW_DnaseSeq_Lung_adult-8wks_C57BL/6

source_name: Lung

tag: lab

value: UW-m

value: DnaseSeq

value: DNaseI HS Sequencing

value: Lung

value: mouse

value: M

tag: age

tag: age description

value: Adult 8 weeks

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse

tag: replicate


title: UW_DnaseDgf_HA-sp

source_name: HA-sp

value: UW

tag: lab description

value: DnaseDgf

value: DNase Digital Footprinting

value: HA-sp

value: astrocytes spinal cord

value: ectoderm


title: UW_DnaseSeq_mG/ER_adult-8wks_diffProtC_24hr_C57BL/6

source_name: mG/ER

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: mG/ER

value: MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with Β-estradiol treatment

tag: treatment

tag: treatment description

value: 24 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam)


title: UW_DnaseSeq_SkMuscle_adult-8wks_C57BL/6

source_name: SkMuscle

value: UW-m

value: DnaseSeq

tag: datatype description

tag: cell

value: SkMuscle

tag: cell organism

value: Skeletal Muscle


description:
design description: ChIP-Seq input analysis of foreskin melanocyte from skin03 (A15585) using Illumina HiSeq 2000
library name: A15585
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 88-407 bp
****************
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: GSM958166_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.Input.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15585-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13913
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 57,996,366
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.0035
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.0079
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0496
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM958166_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.Input.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15585-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13964
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFM Input 03 85
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15585 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 57,996,366
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
FINDPEAKS_SCORE: 0.0035
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.0079
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0496
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Penis

tag: histological type

value: Melanocyte

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: foreskin melanocyte


description:
design description: H3K4me1 ChIP-Seq analysis of foreskin fibroblast from skin03 (A15565) using Illumina HiSeq 2000
library name: A15565
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 111-411 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
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: GSM958164_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me1.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15565-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13926
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,659,491
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.1658
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.2433
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9406
IROC_PERCENTILE: 27
POISSON_SCORE: 0.4397
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM958164_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K4me1.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15565-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13977
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFF H3K4me1 03 65
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin03 Library A15565 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,659,491
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.1658
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.2433
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9406
IROC_PERCENTILE: 27
POISSON_SCORE: 0.4397
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: Fibroblast

value: foreskin fibroblast


title: UW_DnaseSeq_mG/ER_adult-8wks_diffProtC_48hr_C57BL/6

tag: lab

value: DNaseI HS Sequencing

value: mouse

tag: cell description

tag: cell sex

value: M

tag: age

tag: age description

value: Adult 8 weeks

value: 48 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam)

value: C57 black 6, the most common inbred strain of laboratory mouse

tag: labexpid

tag: labversion


description:
design description: H3K27ac ChIP-Seq analysis of foreskin fibroblast from skin03 (A15570) using Illumina HiSeq 2000
library name: A15570
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 122-443 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
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: GSM958163_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K27ac.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15570-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13927
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,241,365
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 24
FINDPEAKS_SCORE: 0.1162
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.1597
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9753
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3215
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM958163_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K27ac.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15570-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13978
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFF H3K27ac 03 70
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27ac Donor skin03 Library A15570 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,241,365
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 24
FINDPEAKS_SCORE: 0.1162
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.1597
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9753
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3215
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: NA

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


title: UW_DnaseSeq_Mesoderm_E11.5_CD-1

source_name: Mesoderm

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

value: Mesoderm

value: axial somatic and lateral plate mesoderm from eviscerated headless, limbless embryos

value: Embryonic day 11.5

tag: strain

tag: strain description

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.

tag: replicate


description:
design description: H3K9me3 ChIP-Seq analysis of foreskin melanocyte from skin03 (A15581) using Illumina HiSeq 2000
library name: A15581
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 74-385 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
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: GSM958165_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K9me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15581-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13924
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,037,550
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 18
FINDPEAKS_SCORE: 0.1262
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1711
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9114
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3597
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM958165_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K9me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15581-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13975
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFM H3K9me3 03 81
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15581 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,037,550
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 18
FINDPEAKS_SCORE: 0.1262
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1711
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9114
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3597
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

tag: submitted sample id

tag: Sex

value: male

value: Penis

value: Melanocyte

value: No

value: primary cell culture


title: UW_DnaseSeq_HindlimbBud_E11.5_CD-1

source_name: HindlimbBud

tag: datatype description

value: DNaseI HS Sequencing

tag: cell

value: HindlimbBud

tag: cell organism

value: mouse

value: embryo hindlimb buds


description:
design description: H3K36me3 ChIP-Seq analysis of foreskin keratinocyte from skin03 (A15576) using Illumina HiSeq 2000
library name: A15576
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 115-446 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
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: GSM958159_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K36me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15576-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13915
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 90,479,845
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.435
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.2981
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9895
IROC_PERCENTILE: 73
POISSON_SCORE: 0.6292
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM958159_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K36me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15576-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13966
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFK H3K36me3 03 76
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15576 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 90,479,845
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.435
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.2981
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9895
IROC_PERCENTILE: 73
POISSON_SCORE: 0.6292
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

tag: body site

tag: histological type

value: Keratinocyte

tag: is tumor

tag: cell type

value: foreskin keratinocyte


description:
design description: H3K36me3 ChIP-Seq analysis of foreskin melanocyte from skin03 (A15583) using Illumina HiSeq 2000
library name: A15583
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 93-369 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
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: GSM958160_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K36me3.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15583-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13919
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,318,843
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.3612
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.2988
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9824
IROC_PERCENTILE: 53
POISSON_SCORE: 0.5544
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM958160_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K36me3.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15583-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13970
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: PFM H3K36me3 03 83
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15583 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,318,843
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.3612
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.2988
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9824
IROC_PERCENTILE: 53
POISSON_SCORE: 0.5544
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: foreskin melanocyte