title: FAIRE-seq, THP-1 VD 120min

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
V120.FAIRE.THP1
Open chromatin (enhancers).

data_processing:
Library strategy: FAIRE-Seq
Alignment to hg19 using Bowtie v0.12.5 with the following parameters: -n 1 -k 1 -m 1 -l 28 -t -q --best
Visualization in the Integrative Genomics Viewer via conversions from sam to sorted bam (using samtools) and then to tdf (using igvtools).
Peak discovery using Zinba v1.06 and a common Input control. In Zinba, peak refinement was done and default parameters used except for pWinSize=200 and, as suggested for FAIRE-seq analysis, peakconfidence=0.95.
Genome_build: hg19
Supplementary_files_format_and_content: BED6 format, direct Zinba output.

source_name: THP-1 cells, VD, 120min

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol: Standard protocol as suggested by the manufacturer for ChIP-seq libraries (also applicable for FAIRE-seq libraries) as utilized at the EMBL Gene Core in Heidelberg, Germany.

treatment_protocol: Prior to FAIRE sample preparation, cells were grown overnight in phenol red-free medium supplemented with charcoal-stripped fetal bovine serum. Then, cells were treated for the indicated time with vehicle (ethanol, finally 0.1% (v/v)) or 100 nM 1α,25-dihydroxyvitamin D3.

value: monocytic leukemia cells

tag: treatment

value: 1α,25-dihydroxyvitamin D3

value: 120 min


title: A3-1 PolyA+ RNA-seq - untreated

status: Public on Oct 25 2012

type: SRA

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: polya-untreated

library_source: transcriptomic

data_processing: Sequence reads were mapped to a mouse genome assembly (mm9) using GSNAP with maximum 10% mismatches (for CLIP and untreated PolyA RNA-seq) or 5% mismatches (for RPF or the rest of PolyA RNA-seq). The best hits with maximum two mismatches that aligns to single position of genome were counted for RNA-seq transcript level expression. For RPF and CLIP lanes, the reads were aligned again to non redundant subset of RefSeq transcripts with fixed of single nucleotide polymorphisms detected in RNA-seq. 5'-most 26nt of tag reads were used for alignment of RPF and siRNA-treated RNA-seq reads. Transcript-level tag count were calculated using intersectBed with modified annotations of RefSeq, miRBase, RepeatMasker, rfam and tRNAdb. The detailed description of the analysis pipeline is available on supplementary methods section of the paper.

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic stem cell

growth_protocol: Mouse embryonic stem cell were incubated in DMEM media containing 20% FBS, non-essentail amino acid and LIF at 37℃.

extract_protocol:
We purified the RNA using TRIzol according to manufacturer's protocol for PolyA+ RNA-seq samples, and we followed the conventional phenol extraction protocol (Ambion Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1)) for CLIP-seq and ribosome profiling libraries.
RNA purification, oligo-dT enrichment, fragmentation and Illumina sequencing for RNA-seq

treatment_protocol: Mouse embryonic stem cell were treated with siRNA for luciferase or for Lin28a and incubated for 48 hours.

tag: library strategy

value: RNA-Seq

tag: cell line

tag: clip antibody

tag: sirna sequence

tag: rna subset

value: polyA RNA


title: FAIRE-seq, THP-1 VD 100min

description:
V100.FAIRE.THP1
Open chromatin (enhancers).

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: THP-1 cells, VD, 100min

value: 100 min


title: FAIRE-seq, THP-1 VD 80min

description:
V80.FAIRE.THP1
Open chromatin (enhancers).

source_name: THP-1 cells, VD, 80min

value: 80 min


title: C. japonica XO 2

city: College Park

first: Eric

middle: S.

last: Haag

state: MD

address: 4094 Campus Drive

department: Department of Biology

country: USA

institute: University of Maryland

data_processing:
base were called with RTA (specific release indicated for each raw file;  see column E below)
C. briggsae reads were trimmed to 36bp to correspond to data obtained for the other species
reads were used to generate de novo transcriptome assemblies using SOAPdenovo v1.05, k-mer size 23. The contigs shorter than 50bp, at the tips smaller than 2k or whose coverage was low were removed.
reads were aligned to either genome reference sequences using TopHat v1.2.0 (-p 4 -i 40) or to the do novo assemblies using Bowtie v0.12.7 (-v 2 -m 3 -p 4 -q --best)
expression values for contigs were calculated as Reads Per Kilobase of contigs per Million mapped reads, expression values for gene models were assessed using Cufflinks v1.0.3  (default parameters, using gene annotation files from ENSEMBL release 9 and 14 for C. briggsae)
only genes or contigs whose expression were detected consistently across the three biological replicates were considered for further analyses. Statistical differential expression between sexes was assessed by linear regression models taking into account effect of sex and machine variation (HiSeq vs GAII)
Genome_build: C. japonica, C. elegans, C. brenneri, C.remanei, C. briggsae: Wormbase release WS224
C. japonica CJ302, C. elegans WS220, C. brenneri CB601, C.remanei CR2, C. briggsae CB4

organism: Caenorhabditis japonica

source_name: whole animal

growth_protocol: C. remanei, C. japonica, C. brenneri, and C. elegans  were maintained at 20˚C on OP50-seeded NGM agar plates , using 2.2% agar to discourage burrowing. C. briggsae was maintained at 25˚C  to prevent production of intersexual germ cells in the XX sex. To avoid inbreeding depression in obligately outcrossing strains, large populations were maintained by transferring large chunks from two independent plates per passage.

extract_protocol:
Worms were roughly synchronized by hypochlorite / bleach treatment, and at least 400 XX or 600 XO  L4 and young adult worms per replicate were hand-picked.  Worms were washed and resuspended in 50 microliters of RNA-ase free water. 250mL of TRI-Reagent (Molecular Research Center) were added and the samples were frozen at ‑80˚C. Samples were thawed and lysed using a plastic pestle. RNA was purified using phenol/chloroform extractions, isopropanol precipitations, and DNaseI treatment.
Single-ended cDNA libraries were prepared according to manufacturer’s protocol (Illumina)

tag: strain

tag: temperature (deg.c)

tag: developmental stage

value: L4 & adult males

tag: rna

value: poly-A RNA

tag: base calling software version


title: FAIRE-seq, THP-1 VD 40min

description:
V40.FAIRE.THP1
Open chromatin (enhancers).

source_name: THP-1 cells, VD, 40min

value: 40 min


title: FAIRE-seq, THP-1 VD 20min

description:
V20.FAIRE.THP1
Open chromatin (enhancers).

source_name: THP-1 cells, VD, 20min

value: 20 min


title: FAIRE-seq, THP-1 vehicle 100min

description:
E100.FAIRE.THP1
Open chromatin (enhancers).

source_name: THP-1 cells, vehicle, 100min

value: vehicle


title: FAIRE-seq, THP-1 vehicle 20min

description:
E20.FAIRE.THP1
Open chromatin (enhancers).

source_name: THP-1 cells, vehicle, 20min


title: FAIRE-seq, THP-1 input control

description:
ctrl.Input.THP1
input DNA

source_name: THP-1 cells, input


title: C. briggsae XO 3

organism: Caenorhabditis briggsae

value: AF16 (WT)


title: C. briggsae XO 1


title: C. briggsae XO 2


title: C. briggsae XX 3

value: L4 & adult pseudo-females


title: C. briggsae XX 2


title: C. brenneri XO 1

organism: Caenorhabditis brenneri


title: C. briggsae XX 1


title: C. elegans XO 3

organism: Caenorhabditis elegans


title: C.elegans XX 1


title: C. elegans XO 2


title: C. elegans XO 1


title: C.elegans XX 3


title: C.elegans XX 2


title: A3-1 LIN28A CLIP - polyclonal

description: clip-polyclonal

extract_protocol:
We purified the RNA using TRIzol according to manufacturer's protocol for PolyA+ RNA-seq samples, and we followed the conventional phenol extraction protocol (Ambion Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1)) for CLIP-seq and ribosome profiling libraries.
UV-crosslinking, immunoprecipiation, RNA purification and Illumina sequencing for CLIP-seq

value: CLIP-Seq

value: polyclonal (Abcam ab46020)

value: LIN28A-bound RNA


title: FAIRE-seq, THP-1 VD 60min

description:
V60.FAIRE.THP1
Open chromatin (enhancers).

source_name: THP-1 cells, VD, 60min

value: monocytic leukemia cells

value: 60 min


title: A3-1 LIN28A CLIP - 35L33G (mAb)

value: 35L33G (anti-LIN28A, custom mAb manufactured in-house)


title: Digital Genomic Footprinting assay of Penis Foreskin Melanocytes Primary Cells; DGF.DS18590

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: CL_2000045
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS18590
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14205
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.7321
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1024610_UW.Penis_Foreskin_Melanocyte_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18590.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18590.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Penis Foreskin Melanocyte Primary Cells, Donor skin01, Library DGF.DS18590 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.15150
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 230,373,033
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4924
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.5171
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9898
IROC_PERCENTILE: 27
POISSON_SCORE: 0.5488
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1024610_UW.Penis_Foreskin_Melanocyte_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18590.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18590.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  Penis Foreskin Melanocyte Primary Cells, Donor skin01, Library DGF.DS18590 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.15161
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFM DGF 01 90
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Melanocyte Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18590 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 230,373,033
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4924
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.5171
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9898
IROC_PERCENTILE: 27
POISSON_SCORE: 0.5488
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA

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

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

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: Penis, Foreskin, Melanocyte skin01

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: SFVAMC Dermatology

value: Primary Cell Culture

value: Melanocyte

tag: markers

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

value: Neonate

value: Disease Free

value: Male

tag: karyotype

tag: parity

value: Digital Genomic Footprinting

value: Qiagen minElut


title: A3-1 LIN28A CLIP - 2J3 (mAb)

tag: library strategy

value: CLIP-Seq

value: 2J3 (anti-LIN28A, custom mAb manufactured in-house)


title: Chromatin accessibility assay of Fetal Kidney, Right; DS20917

description:
sample_term_id: UBERON_0004539
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20917
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14152
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14151
****************
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: GSM1024607_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24568.DS20917.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20917.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Right, Donor H-24568, Library DS20917 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.17633
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,236,145
FINDPEAKS_SCORE: 0.4172
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4074
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9916
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4651
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1024607_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24568.DS20917.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20917.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Right, Donor H-24568, Library DS20917 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.17587
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FKR DNase 68 17
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Right DNase Hypersensitivity Donor H-24568 Library DS20917 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,236,145
FINDPEAKS_SCORE: 0.4172
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4074
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9916
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4651
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, Right primary tissue, day 98; DS20917

value: Fetal Kidney, Right

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

value: Primary Tissue

value: UW

value: fetal

value: day 98

value: Female

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Kidney; DS20987

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20987
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14147
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14146
****************
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: GSM1024608_UW.Fetal_Kidney.ChromatinAccessibility.H-24584.DS20987.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20987.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-24584, Library DS20987 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.17607
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,220,703
FINDPEAKS_SCORE: 0.3934
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3899
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9936
IROC_PERCENTILE: 63
POISSON_SCORE: 0.4537
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1024608_UW.Fetal_Kidney.ChromatinAccessibility.H-24584.DS20987.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20987.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney, Donor H-24584, Library DS20987 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.17561
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FK DNase 84 87
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-24584 Library DS20987 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,220,703
FINDPEAKS_SCORE: 0.3934
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3899
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9936
IROC_PERCENTILE: 63
POISSON_SCORE: 0.4537
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney primary tissue, day 113; DS20987

value: Fetal Kidney

value: genomic DNA

value: day 113


title: Digital Genomic Footprinting assay of Breast vHMEC; DGF.DS18406

description:
sample_term_id: CL_0002327
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS18406
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14170
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.2872
****************
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: GSM1024609_UW.Breast_vHMEC.Digital_Genomic_Footprinting.RM035.DGF.DS18406.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18406.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast vHMEC Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Breast vHMEC, Donor RM035, Library DGF.DS18406 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.15145
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 346,018,292
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4046
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.4816
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5142
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1024609_UW.Breast_vHMEC.Digital_Genomic_Footprinting.RM035.DGF.DS18406.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18406.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  Breast vHMEC, Donor RM035, Library DGF.DS18406 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.15156
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Bv DGF 35 06
BROWSER_TRACK_DESCRIPTION: UW Breast vHMEC Digital Genomic Footprinting Donor RM035 Library DGF.DS18406 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 346,018,292
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4046
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.4816
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5142
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Breast, vHMEC, RM035; DGF.DS18406

value: Breast vHMEC RM035

value: Breast, vHMEC

value: Tlsty Lab, University of California, San Francisco

value: Primary Cell Culture

value: Variant Human Mammary Epithelial Cells

value: spilt 1:5 in MEGM medium (Lonza Inc.)

value: Disease Free

value: Caucasian


title: IMR90_CrKD

city: Los Angeles

first: Jing-Yu

last: Li

address: 615 Charles E. Young Dr. South BSRB 357

institute: University of California, Los Angeles

description: mRNA-seq

data_processing:
Unique sequences were aligned to human genome reference HG19 by using TopHat-1.3.2 (default setting). Reads per kb per million reads (RPKM) of each RefSeq genes were calculated for expression comparison.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files containing RPKM for each refseq genes

source_name: IMR90 human lung fibroblasts

growth_protocol: IMR90 human primary lung embryo fibroblasts (purchased from ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO2. Growing cells with 50~70% confluence were used for further assay.

extract_protocol:
Total RNA were extracted by using TriZol reagent (Invitrogen).
5 µg of total RNA from control knockdown and H1.5 knockdown IMR90 fibroblasts were used to prepare libraries for mRNA-seq by using mRNA-seq Sample Preparation Kit (Illumina).

treatment_protocol: Control siRNAs or iRNAs targeting H1.5 (MU-012049-00) were purchased from Dharmacon. 1.5 µg of siRNAs were transfected to 2x106 cells by using Lipofectamine RNAiMAX (Invitrogen Cat # 13778075). Cells were collected 48 hours after transfection.

tag: cell line

tag: passages

tag: transfection

value: control siRNA


title: C. remanei XO 3

organism: Caenorhabditis remanei

value: L4 & adult males

value: poly-A RNA


title: IMR90_H1.5KD

description: mRNA-seq

value: siRNA targeting H1.5


title: C. remanei XX 3

value: L4 & adult females


title: C. remanei XO 2


title: C. remanei XX 2


title: low c-Myc. P493-6 T=0HR - RNA-Seq

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 2 -n 2 -l 40 --best.
Genome_build: hg18
Supplementary_files_format_and_content: Final expression counts were calculated as Reads Per KB per Million mapped read (RPKM) (Mortazavi et al., 2008). RPKM values were then re-normalized based on values for synthetic spike-ins. See manuscript for details.

source_name: P493-6 cells with low c-Myc expression

growth_protocol: RPMI 1640 + FBS. Tetracycline repressed c-Myc transgene expression. c-Myc expression released for 0 hours.

extract_protocol:
Total RNA was purified using mirVana miRNA isolation kit (Life technologies) following the manufacturer instructions. Synthetic RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added to each population based on cell number. See manuscript for details.
Polyadenylated RNA was purified from the total RNA by two rounds of selection using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA (Life Technologies) following the manufacturer instructions and sequenced using a standard Illumina mRNA-Seq protocol with the following modifications. Briefly, polyadenylated RNA was fragmented with divalent cations under elevated temperature. First strand cDNA synthesis was performed with random hexamers and Superscript III reverse transcriptase. Second strand cDNA synthesis was performed using RNAse H and DNA Polymerase I. In the second-strand synthesis reaction, dTTP was replaced with dUTP. Following cDNA synthesis, the double stranded products were end repaired, a single “A” base was added, and Illumina PE adaptors were ligated onto the cDNA products. The ligation products with an average size of 300 bp were purified using agarose gel electrophoresis. Following gel purification, the strand of cDNA containing dUTP was selectively destroyed during incubation of purified double-stranded DNA with HK-UNG (Epicentre). The adapter ligated single-stranded cDNA was then amplified with 15 cycles of PCR and PCR products were purified using gel electrophoresis.

treatment_protocol: c-Myc expression released for 0 hours.

tag: cell type

value: B-cell lymphoma


title: UW_DnaseSeq_NT2-D1Rep2

status: Public on Oct 24 2012

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=wgEncodeUwDnase

value: immortalized cell line

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: line

tag: cell organism

value: human

tag: cell description

value: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

tag: cell karyotype

value: cancer

tag: cell lineage

value: inner cell mass

tag: cell sex

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: labexpid

tag: labversion

tag: replicate


title: UW_DnaseSeq_RPMI-7951Rep2

tag: cell

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.

value: ectoderm

value: F


title: UW_DnaseSeq_Monocytes-CD14+_RO01746Rep2

value: primary cell

value: CD14-positive monocyte

value: Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2:not in 2011 analysis

value: normal

value: mesoderm


title: UW_DnaseSeq_M059JRep2

value: UW

value: Stamatoyannopoulous - University of Washington

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


title: UW_DnaseSeq_Th2Rep2

value: DnaseSeq

value: DNaseI HS Sequencing

value: human

value: primary Th2 T cells

value: U


title: UW_DnaseSeq_Th17Rep1

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

value: B

value: No special treatment or protocol applies


title: UW_DnaseSeq_LHCN-M2Rep1

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_DnaseSeq_CD4+_Naive_Wb11970640Rep1

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


title: UW_DnaseSeq_bone_marrow_HS27aRep1

value: HS27a Human Marrow Stromal Cells are fibroblastoid cells immortalized with HPV16 E6/E7 genes as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005, insert DNA is LXSN-16 E6E7 packaged in PA31.


title: UW_DnaseSeq_MCF-7_Estradiol_100nM_1hrRep2

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: cancer

value: ectoderm

value: F

value: 1 h with 100 nM Estradiol, hormone treatment (Stam)


title: UW_DnaseSeq_HSMMtubeRep2

source_name: HSMMtube

value: UW

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

value: HSMMtube

value: skeletal muscle myotubes differentiated from the HSMM cell line

value: normal

value: mesoderm


title: UW_DnaseSeq_CD4+_Naive_Wb78495824Rep1

value: DNaseI HS Sequencing

value: human

value: CD4+ naive sorted cells, donor is Causasian, female 35 year old, primary pheresis of single normal subject

value: No special treatment or protocol applies


title: UW_DnaseSeq_RPMI-7951Rep1

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.


title: high c-Myc. P493-6 T=24HR - RNA-Seq

source_name: P493-6 cells with high c-Myc expression

growth_protocol: RPMI 1640 + FBS. Tetracycline repressed c-Myc transgene expression. c-Myc expression released for 24 hours.

treatment_protocol: c-Myc expression released for 24 hours.

tag: cell line

tag: cell type

value: B-cell lymphoma


title: UW_DnaseSeq_GM04503Rep2

tag: lab

tag: lab description

value: adult twin pair fibroblasts, monozygotic twin of GM04504


title: UW_DnaseSeq_NHBE_RARep1

tag: datatype

tag: datatype description

value: bronchial epithelial cells with retinoic acid


title: UW_DnaseSeq_GM04504Rep2

tag: cell organism

value: adult twin pair fibroblasts, monozygotic twin of GM04503, 13% of the cells examined show random chromosome loss

value: F


title: UW_DnaseSeq_GM04503Rep1

value: UW

tag: cell description


title: Chromatin accessibility assay of Fetal Stomach; DS19933

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19933
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14163
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14162
****************
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: GSM1024606_UW.Fetal_Stomach.ChromatinAccessibility.H-24342.DS19933.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19933.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-24342, Library DS19933 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.17599
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,416,933
FINDPEAKS_SCORE: 0.3102
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.299
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9874
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3705
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1024606_UW.Fetal_Stomach.ChromatinAccessibility.H-24342.DS19933.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19933.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-24342, Library DS19933 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.17553
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FS DNase 42 33
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-24342 Library DS19933 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,416,933
FINDPEAKS_SCORE: 0.3102
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.299
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9874
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3705
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Stomach primary tissue, day 96; DS19933

tag: sample alias

tag: sample common name

value: Fetal Stomach

tag: molecule

value: genomic DNA

tag: disease

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

value: Primary Tissue

value: fetal

value: day 96

value: Female

value: Chromatin Accessibility

value: Qiagen minElut


title: UW_DnaseSeq_GM04504Rep1

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

value: DNaseI HS Sequencing

value: human

tag: cell karyotype

value: normal

tag: cell sex

tag: treatment

tag: treatment description

value: No special treatment or protocol applies


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS19439

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19439
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14158
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14157
****************
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: GSM1024605_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24279.DS19439.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19439.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24279, Library DS19439 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.17588
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,179,977
FINDPEAKS_SCORE: 0.3338
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.328
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9922
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3961
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1024605_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24279.DS19439.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19439.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Arm, Donor H-24279, Library DS19439 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.17542
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMA DNase 79 39
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24279 Library DS19439 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,179,977
FINDPEAKS_SCORE: 0.3338
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.328
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9922
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3961
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Arm primary tissue, day 101; DS19439

value: Fetal Muscle, Arm

value: day 101

value: Male


title: UW_DnaseSeq_M059JRep1

value: UW

tag: cell

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

tag: cell lineage

value: ectoderm

value: M

tag: labexpid

tag: labversion

tag: replicate


title: UW_DnaseSeq_H7-hESC_diffProtA_2dRep1

value: in vitro differentiated cells

value: cardiac mesoderm

tag: lab

tag: lab description

tag: datatype

value: undifferentiated embryonic stem cells

value: inner cell mass

value: U

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage:mesoderm


title: UW_DnaseSeq_H7-hESC_diffProtA_9dRep1

value: Stamatoyannopoulous - University of Washington

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell organism

value: human

tag: cell description

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage:mesoderm


title: UW_DnaseSeq_LHCN-M2_DIFF_4dRep1

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_DnaseSeq_CD34+_MobilizedRep1

value: UW

value: hematopoietic progenitor cells- mobilized, from donor RO01679.

value: No special treatment or protocol applies


title: UW_DnaseSeq_LHCN-M2_DIFF_4dRep2

value: M


title: UW_DnaseSeq_MCF-7_Estradiol_100nM_1hrRep1

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: cancer

value: ectoderm

value: F

value: 1 h with 100 nM Estradiol, hormone treatment (Stam)


title: UW_DnaseSeq_HBVSMCRep1

source_name: HBVSMC

value: Stamatoyannopoulous - University of Washington

value: HBVSMC

value: brain vascular smooth muscle cells.

value: normal


title: UW_DnaseSeq_MCF-7_Estradiol_ctrl_0hrRep1

value: DnaseSeq

value: DNaseI HS Sequencing

value: human

value: No hormone control, zero timepoint, used to distinguish untreated sample in series (Stam)


title: UW_DnaseSeq_LHCN-M2Rep2

value: UW

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


title: UW_DnaseSeq_MCF-7_Estradiol_ctrl_0hrRep2


title: UW_DnaseSeq_HPAECRep1

source_name: HPAEC

value: HPAEC

value: pulmonary artery endothelial cells.

value: No special treatment or protocol applies


title: UW_DnaseSeq_CD20+_RO01778Rep1

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


title: UW_DnaseSeq_T-47DRep2

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

value: cancer

value: F


title: UW_DnaseSeq_T-47DRep1

value: Stamatoyannopoulous - University of Washington


title: ML-05_RNAseq

first: Ana

middle: C

last: Maretti-Mira

address: 1450 Biggy Street, NRT 3514

department: Medicine

institute: USC

data_processing: Alignment: reads were aligned to human (USCS-hg19) and Leishmania braziliensis (Wellcome Trust Sanger Institute - V2_29072008) using BOWTIE and TOPHAT. The parameters used allowed up to 2 mismatches for read alignment to genome, zero mismatches for read alignment to splice junctions, and inclusion of reads that assigned up to 30 regions (unique and multi-hit reads). SAMTools was used for quality control and processing of the reads. The quality control step filtered out reads with the FLAGS 0x4, 0x100, 0x200, 0x400. Afterwards, the reads were sorted and converted to .BAM files.

molecule: polyA RNA

source_name: skin lesion

extract_protocol: Total RNA was isolated from the tissue fragments using acid guanidinium-chloroform-phenol method, then treated with DNAse and cleaneup with Rneasy micro kit (Qiagen). cDNA libraries were prepared according to Illumina's instructions. Briefly, mRNA was purified using magnetic beads covered with oligo-dT, fragmented under enzymatic and heat actions, and precipitated with glycogen. Superscript II kit (Invitrogen) and radom primers were used for sinthesize the first-strand of the cDNA, the RNA templates were removed by RNAse H, and the second-strand of cDNA was synthesized by DNA polymerase I and dNTP. The double-strand cDNA was repaired using T4 DNA polymerase and Klenow DNA polymerase. Afterward, a poly-A tail was added at the 3' end of the DNA and adaptors were bound at both extremities. Fragments with 200bp were purified by 2% agarose gel and extracted using QIAquick Gele Extraction kit (Qiagen). Finally, these fragments were amplified by PCR and evaluated by Bioanalyzed (Agilent Technologies).

treatment_protocol: Fragments of leishmaniasis cutaneous lesions where embebbed in OCT medium (Tissue-Tek, Sakura Finetek, USA) and preserved in liquid nitrogen.

tag: tissue

value: skin

tag: clinical form

value: Mucosal leishmaniasis

tag: parasite

value: Leishmania braziliensis


title: ML-04_RNAseq


title: UW_DnaseSeq_NHBE_RARep2

value: DnaseSeq

value: DNaseI HS Sequencing

value: bronchial epithelial cells with retinoic acid

tag: cell karyotype

value: normal

tag: cell sex


title: UW_DnaseSeq_bone_marrow_MSCRep1

value: UW

value: human

value: These cells are primary fibroblastoid cells obtained from human bone marrow of normal donors as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005.

value: M

tag: treatment

tag: treatment description


title: ML-03_RNAseq


title: UW_DnaseSeq_CD20+_RO01778Rep2

value: primary cell

value: B cell

tag: cell

tag: cell lineage

value: mesoderm

value: No special treatment or protocol applies


title: UW_DnaseSeq_HBVSMCRep2

value: HBVSMC

value: brain vascular smooth muscle cells.

value: F

tag: labexpid

tag: labversion


title: UW_DnaseSeq_H7-hESC_diffProtA_5dRep2

tag: lab

value: Stamatoyannopoulous - University of Washington

value: undifferentiated embryonic stem cells

value: inner cell mass

value: U

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage:mesoderm

tag: replicate


title: UW_DnaseSeq_Th1_Wb54553204Rep1

tag: lab description

tag: datatype

value: DnaseSeq

value: DNaseI HS Sequencing

value: Th1 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject

value: normal


title: UW_DnaseSeq_Th1Rep2

value: UW

tag: datatype description

tag: cell organism

value: human

value: primary Th1 T cells


title: UW_DnaseSeq_HBVPRep1

source_name: HBVP

value: HBVP

tag: cell description

value: brain vascular pericytes

value: mesoderm


title: ML-01_RNAseq

tag: tissue

value: skin

tag: clinical form

value: Mucosal leishmaniasis

value: Leishmania braziliensis


title: ML-02_RNAseq

tag: parasite


title: UW_DnaseSeq_H7-hESC_diffProtA_14dRep2

value: Stamatoyannopoulous - University of Washington

value: undifferentiated embryonic stem cells

tag: cell sex

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage:mesoderm


title: UW_DnaseSeq_bone_marrow_MSCRep2

value: These cells are primary fibroblastoid cells obtained from human bone marrow of normal donors as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005.

tag: cell karyotype

value: M

tag: treatment

value: No special treatment or protocol applies


title: UW_DnaseSeq_Th1_Wb54553204Rep2

value: DnaseSeq

value: DNaseI HS Sequencing

tag: cell

value: Th1 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject

tag: treatment description


title: UW_DnaseSeq_H7-hESC_diffProtA_5dRep1

value: UW

value: human

tag: cell lineage

value: inner cell mass

value: U

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage:mesoderm

tag: labexpid


title: LCL-05_RNAseq

value: skin

value: Localized cutaneous leishmaniasis


title: LCL-04_RNAseq

value: Leishmania braziliensis


title: UW_DnaseSeq_HMVEC-dAdRep2

source_name: HMVEC-dAd

tag: lab

value: Stamatoyannopoulous - University of Washington

value: HMVEC-dAd

value: adult dermal microvascular endothelial cells.

value: normal

value: F

tag: labversion


title: UW_DnaseSeq_H7-hESC_diffProtA_14dRep1

tag: lab description

value: undifferentiated embryonic stem cells

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage:mesoderm

tag: replicate


title: UW_DnaseSeq_bone_marrow_HS5Rep1

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

value: HS5 Human Marrow Stromal Cells are fibroblastoid cells immortalized with HPV16 E6/E7 genes as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005, insert DNA is LXSN-16 E6E7 packaged in PA31.

value: M

value: No special treatment or protocol applies


title: LCL-03_RNAseq


title: LCL-02_RNAseq


title: UW_DnaseSeq_Treg_Wb78495824Rep1

value: UW

tag: cell organism

value: human

tag: cell description

value: T regulatory cells in vivo isolation

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

value: mesoderm


title: UW_DnaseSeq_HMVEC-dAdRep1

value: Stamatoyannopoulous - University of Washington


title: UW_DnaseSeq_PrECRep2

source_name: PrEC

value: PrEC

value: prostate epithelial cell line

value: epithelial

value: U


title: UW_DnaseSeq_PrECRep1

value: normal


title: UW_DnaseSeq_Treg_Wb83319432Rep1

value: T regulatory cells in vivo isolation, donor is Caucasian, male 28 year old, primary pheresis of single normal subject


title: LCL-01_RNAseq

tag: tissue

value: skin

tag: clinical form

value: Localized cutaneous leishmaniasis

value: Leishmania braziliensis


title: UW_DnaseSeq_NT2-D1Rep1

value: DnaseSeq

value: DNaseI HS Sequencing

value: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

value: cancer

value: inner cell mass

tag: cell sex

value: M


title: PTB_MI12_R2

status: Public on Oct 22 2012

city: New York

first: Andre

last: Kahles

state: New York

address: 1275 York Avenue

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

description: 529 R2 (mi_1+2)

data_processing:
Illumina Raw Data processing with SHORE 4.1 pipeline with application 'mRNA' and disabled Illumina filter
fastq files were aligned to the TAIR10 reference genome with the spliced aligner PALMapper (version 4)
Alignment postprocessing (filtering and multimapper resolution) using RNAgeeq
Reads were counted as overlapping to a gene, if they shared at least one exonic position
Expression values were transformed to RPKM (Reads per kilobase per million mapped reads)
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text-file, with following columns: (1) gene id; (2) WT; (3) MI12; (4) MI3; (5) OE1; (6) OE2; (7) OE3

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seeds were surface sterilized and plated on 1/2 MS medium containing 2% sucrose and 0.8% phytoagar. Following stratification for 2 days in darkness at 4°C plates were transferred to continuous light (~20°C, ~60% humidity). Seedlings were sampled after cultivation for 11 days.

extract_protocol:
Total RNA was extracted from ∼100 mg of plant tissue using the Universal RNA Purification kit (EURx), including an on-column DNaseI treatment performed according to the manufacturer's instructions.
Libraries were prepared using the Illumina TruseqTM sample prep kit (Illumina) according to the manufacturer's instructions (TruSeqTM RNA Sample Preparation v2 Guide, version: November 2010). For the adapter ligation step, the RNA Adapter Indexes 10 (AR010) and 13 (AR013) were used. Following the PCR enrichment step using half the sample volume, libraries were subjected to an additional gel purification step. A size range of 250-350 bp was extracted from a 2% agarose gel and purified using the MinElute Gel Extraction Kit (Qiagen).

tag: ecotype

value: Columbia

tag: genotype

value: At3g01150 & At5g53180 downregulation via miRNA

tag: developmental stage

value: 11 days old seedlings


title: PTB_OE1_R2

description: 382 R2 (oe_1)

value: At3g01150 overexpression


title: PTB_WT_R2

description: WT  R3

value: wild type


title: UW_DnaseSeq_Th2_Wb54553204Rep1

value: UW

value: Stamatoyannopoulous - University of Washington

tag: cell

value: human

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

tag: cell karyotype

value: mesoderm

tag: treatment

tag: treatment description

value: No special treatment or protocol applies


title: PTB_OE1_R1

description: 382 R1 (oe_1)


title: PTB_OE3_R2

description: 440 R2 (oe_3)

value: At1g43190 overexpression


title: PTB_WT_R1

description: WT  R1 (Col-0)


title: PTB_MI12_R1

description: 529 R1 (mi_1+2)


title: PTB_OE2_R1

description: 429 R1 (oe_2)

value: At5g53180 overexpression


title: LS287

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

data_processing:
Sequencing reads were processed using TopHat (Trapnell et al., 2009), a junction mapping alignment program designed to identify splice junctions from RNA-Seq reads. Briefly, the program aligns reads to a reference genome, identifying regions of coverage that correspond to transcribed RNA. The underlying sequence of adjacent regions is joined together to create a spliced reference, and reads that did not initially align to the reference genome are aligned to identify sequencing reads that originated from potential splice junctions (e.g. exon-exon junctions).
Genome_build: hg19
Supplementary_files_format_and_content: Feature counts were computed using the Python program HT-Seq (http://wwwhuber. embl.de/users/anders/HTSeq). Given a SAM file with alignments and a GFF file with genomic features, the htseq-counts script counts how many reads map to each feature. This files are in txt format

extract_protocol: RNA was extracted from skin samples frozen in liquid nitrogen using the RNeasy Mini Kit (Qiagen, Valencia, CA). Total RNA from paired lesional and nonlesional skin samples from three patients was reverse transcribed and amplified by using the Ovation RNA-seq kit (NuGEN Technologies, Inc.). The cDNA was subsequently subjected to fragmentation, linker adapter ligation, and further  mplification by using the Encore NGS Library System I kit (NuGEN Technologies, Inc.) in  conjunction with the Covaris S-series Sonication System (Covaris, Inc., Woburn, MA). Samples were amplified onto flowcells using the standard Illumina cluster station per manufacturer protocol. Cluster kits used were version 4 single read cluster amplification kits. Samples were sequenced on the Illumina Genome Analyzer IIx platform (Illumina, San Diego, CA) for 80 cycles, and raw sequencing data was processed using the onboard SCS/RTA software version 2.8 yielding 80bp reads. Sequencing kits used were Tru-Seq version 5 sequencing kits.

tag: patient

value: Patient 2

tag: group

value: lesional

value: skin


title: LS292

value: Patient 3


title: LS252

value: Patient 1


title: NL286

value: non-lesional


title: NL251


title: NPCtotalRNA1

status: Public on Oct 21 2012

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

data_processing:
For RNA-seq, reads were aligned with TopHat to the mouse mm9 genome build. Only unique hits were accepted. Further expression analysis was with the Genomatix software suite (Genomatix, Munich, Germany) and the Eldorado gene annotation. For each transcript a normalized expression value was calculated from the read distribution that accounts for the length differences using the program DEseq for the analysis of differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: bed files

source_name: Neuronal progenitor cells

extract_protocol: The Total RNA from ESCs, NPCs and MEFs was extracted by guanidinisothiocyanat/phenol extraction with the Trifast kit (Peqlab). Total RNA preparations were treated with DNase I, phenol/chloroform extracted and precipitated before further processing. RNAs were depleted of 5S, 5.8S, 18S and 28S rRNAs using the Human/Mouse/Rat Ribo-Zero rRNA Removal Kit (Epicentre) according to the manufacturer’s protocol. After rRNA depletion, RNAs were fragmented with a kit from Ambion. Libraries for Solexa sequencing were generated according to the standard Illumina protocol that comprised first strand cDNA synthesis, second strand cDNA synthesis, end repair, addition of a single A base, and adapter ligation. Sequencing was performed on the Illumina GAIIx (replicate 1) and Illumina HiSeq 2000 (replicate 2) at the sequencing core facilities of the BioQuant in Heidelberg, Germany.

tag: strain

tag: cell type

value: ES derived neuronal progenitor

tag: passage


title: ESCtotalRNA1

source_name: Embryonic stem cells

value: mouse embryonic stem cells

value: blastocyst, E3.5


title: PTB_OE2_R2

description: 429 R2 (oe_2)

value: Columbia

value: 11 days old seedlings


title: HeLa mRNA-seq

city: PARIS

first: Herve

last: LE HIR

address: 46 rue d'Ulm

department: Functional Genomics

country: France

institute: IBENS

data_processing:
Illumina Casava1.7 software used for basecalling.
CLIP-seq reads were trimmed for adaptor sequence using the Btrim software (parameters -3 -v7 -l 15).
CLIP-seq and mRNA-seq reads were mapped to hg19 genome assembly (Ensembl 63) using Novoalign V2.07.11 (parameters -F ILMFQ -o SAM) and BLAT version 34 (parameter -minScore=15).
All uniquely mapped reads with Novoalign and BLAT were used in subsequent processing.
bedGraph files were generated using the genomeCoverageBed function v2.12.0 from BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files

source_name: HeLa mRNA-seq

growth_protocol: HeLa cells were cultivated in 15 cm dishes in Dulbecco’s modified Eagle’s medium (DMEM) with 4,5g l-1 D-glucose supplemented with 10% FCS and antibiotics (streptomycin 100 ug ml-1 and penicillin 100 U ml-1).

extract_protocol: Total RNA was harvested from HeLa cells using TRI Reagent (Ambion). cDNA library was generated from polyA+ selected mRNAs using Illumina TruSeq(TM) SBS v5 kit.

treatment_protocol: HeLa cells were crosslinked on ice with UV-C (254 nm) at 400 mJ per cm2 in presence of cold PBS (4 ml per 15 cm dish).

tag: cell line

value: HeLa


title: UW_DnaseSeq_Th2_Wb33676984Rep1

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell organism

value: human

tag: cell description

value: Th2 cells in vivo isolation, donor is Asian, female 26 year old, primary pheresis of single normal subject

value: normal

tag: cell lineage

value: F

tag: labexpid

tag: labversion

tag: replicate


title: ESC_H3K27ac

data_processing:
For ChIP-seq, reads were aligned with Bowtie to the mouse mm9 genome build allowing up to two mismatches. Only unique hits were accepted. Sequenced 50 bp reads were mapped with Bowtie and subsequently clustered with MACS 55 implemented in the Genomatix software suite (Genomatix, Munich, Germany) using a p-value of 10-5.
Genome_build: mm9
Supplementary_files_format_and_content: peaks.bed

extract_protocol: For chromatin immunoprecipitation, for each sample, 1 x 106 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). Chromatin was sheared to mononucleosomal fragments. After IgG preclearance the sheared chromatin was incubated with 4 µg of either a H3K9ac (Abcam, ab4441), a H3K27ac (Abcam, ab4729), or a H3K9me3 (Abcam ab8898) antibody over night. After washes with sonication (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5% N-lauroylsarcosine, 0.1% Na-deoxycholate), high-salt- (50 mM Hepes pH 7.9, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), lithium- (20 mM Tris-HCl pH 8.0, 1mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and 10 mM Tris-HCl, chromatin was eluted from the protein G magnetic beads and the crosslink was reversed over night. After RNase A and proteinase K digestion, the DNA was purified and subsequently cloned into a multiplexed Illumina library according to standard protocols.

tag: antibody

value: H3K27ac (Abcam, ab4729)


title: ESC_H3K9me3

value: H3K9me3 (Abcam ab8898)


title: ESCtotalRNA2

tag: developmental stage


title: ESC_H3K9ac

value: H3K9ac (Abcam, ab4441)


title: PTB_MI3_R1

description: 536 R1 (mi3)

tag: ecotype

tag: genotype

value: At1g43190 downregulation via miRNA


title: NPCtotalRNA2

tag: strain

tag: cell type

value: ES derived neuronal progenitor


title: MEF merged mononucleosomes

data_processing:
DNA reads were aligned on the mm9 assembly version of the mouse genome with Bowtie reporting unique hits with up to two mismatches.
The nucleosome occupancy maps were calculated with custom made Perl scripts by counting how many paired-end reads covered a given DNA base pair.
Sites with artificially high coverage were considered as artifacts and excluded from the analysis.
No further peak calling or smoothing was conducted. In addition, no assumptions on the length of the nucleosomal DNA had to be made to derive the nucleosome occupancy maps, since nucleosome boundaries were determined on both sides of the nucleosome.
Genome_build: mm9
Supplementary_files_format_and_content: Nucleosome Nucleosome positioning data are in tab separated text files with four columns: (1) Chromosome #, (2) nucleosome start site, (3) nucleosome end site, (4) MNase-protected fragment length.

source_name: Mouse fibroblast cells

extract_protocol: 129P2/Ola embryonic stem cells were cultured in ESGRO Complete (Millipore). Differentiation of ESC into neuronal precursors was induced via formation of embryoid bodies in embryoid body formation medium (Millipore) and treatment with 5 µM retinoic acid for four days. Neuronal embryoid bodies were dissociated and seeded on matrigel in neuronal stem cell medium (PAN) for four days. 129P2/Ola mouse embryonic fibroblasts (MEFs) were generated from pregnant E13.5 mice and cultured in DMEM supplemented with 10% fetal calf serum and glutamine up to passage five. For MNase digestion, cells were harvested and resuspended in low salt buffer (10 mM Hepes, pH 8, 10 mM KCl, 0.5 mM DTT) at 4 °C. After disruption of the cells with a douncer the nuclei were collected by centrifugation and washed once with the MNase Buffer (10 mM Tris-HCl, pH 7.5, 10 mM CaCl2), resuspended in the MNase Buffer and digested with 0.5 Units MNase/µl (Fermentas) and incubation for 6-11 minutes at 37°C. The MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM. After digestion with 0.1 µg/µl RNase A (Fermentas) and removal of protein by phenol/chloroform extraction, the DNA was ethanol precipitated and the resulting DNA pellet was dissolved in H2O. DNA fragments corresponding to mononucleosomes or dinucleosomes were separated on a 2% agarose gel using an E-Gel electrophoresis system (Life Technologies, Carlsbad, CA, USA). The libraries for sequencing were prepared according to the standard protocol for the Illumina HiSeq2000 sequencing platform.

value: primary mouse embryonic fibroblast

tag: passage

value: embryo, E14


title: MEFtotalRNA


title: HeLa eIF4AIII CLIP-seq 2

data_processing:
Library strategy: CLIP-seq
Illumina Casava1.7 software used for basecalling.
CLIP-seq reads were trimmed for adaptor sequence (Adapter 5’ 5'-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACGATC-3'; Adapter 3’
5'-ATCTCGTATGCCGTCTTCTGCTTG-3) using the Btrim software (parameters -3 -v7 -l 15).
CLIP-seq and mRNA-seq reads were mapped to hg19 genome assembly (Ensembl 63) using Novoalign V2.07.11 (parameters -F ILMFQ -o SAM) and BLAT version 34 (parameter -minScore=15).
All uniquely mapped reads with Novoalign and BLAT were used in subsequent processing.
bedGraph files were generated using the genomeCoverageBed function v2.12.0 from BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files

source_name: HeLa eIF4AIII CLIP-seq

extract_protocol: HeLa cell lysate were treated with RNAse T1 and mRNP-containing eIF4AIII were immunoprecipitated by using rabbit polyclonal anti-human eIF4AIII antibodies. eIF4AIII-RNAs complexes were resolved on SDS-PAGE and transferred to nitrocellulose membrane. RNAs were extracted by proteinase K treatment. cDNAs libraries were prepared with the small RNA kit (v1.5, Illumina).

tag: cell line


title: NPC merged mononucleosomes


title: ESC merged mononucleosomes

value: mouse embryonic stem cells

value: blastocyst, E3.5


title: UW_ChipSeq_NHDF-neo_CTCFRep2

status: Public on Oct 19 2012

source_name: NHDF-neo

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=wgEncodeUwTfbs

tag: lab

value: UW

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: NHDF-neo

value: neonatal dermal fibroblasts

tag: cell karyotype

value: mesoderm

tag: cell sex

value: U

value: CTCF

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid


title: HeLa eIF4AIII CLIP-seq 1

value: HeLa


title: UW_ChipSeq_NHDF-neo_CTCFRep1

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

tag: cell organism

value: human

tag: cell description

value: normal

tag: cell lineage

tag: antibody

tag: labexpid

tag: labversion

tag: replicate


title: UW_ChipSeq_HAc_InputRep1

source_name: HAc

tag: lab

value: UW

tag: lab description

value: ChipSeq

tag: cell

value: HAc

value: astrocytes-cerebellar

tag: cell karyotype

value: ectoderm

tag: cell sex

value: Input

tag: antibody description

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


title: UW_ChipSeq_HCM_CTCFRep2

source_name: HCM

value: Chromatin IP Sequencing

value: HCM

value: cardiac myocytes

value: mesoderm

value: U

value: CTCF

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: treatment

tag: treatment description

tag: control

tag: control description


title: NL291

tag: patient

value: Patient 3

tag: group

value: non-lesional

tag: tissue

value: skin


title: UW_ChipSeq_H7-hESC_Input_diffProtA_2dRep1

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

tag: cell organism

value: human

tag: cell description

value: undifferentiated embryonic stem cells

tag: cell lineage

value: inner cell mass

tag: antibody

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage:mesoderm

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid

tag: labversion

tag: replicate


title: UW_ChipSeq_HFF-Myc_CTCFRep1

source_name: HFF-Myc

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: HFF-Myc

value: foreskin fibroblast cells expressing canine cMyc

tag: cell karyotype

value: normal

value: fibroblast

tag: cell sex

value: M

tag: antibody antibodydescription

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies


title: UW_ChipSeq_A549_InputRep1

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

tag: cell organism

tag: cell description

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

value: Input

tag: antibody description

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

tag: control

tag: control description


title: PTB_OE3_R1

description: 440 R1 (oe_3)

tag: ecotype

value: Columbia

tag: genotype

value: At1g43190 overexpression

tag: developmental stage

value: 11 days old seedlings


title: UW_ChipSeq_HFF-Myc_CTCFRep2

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: HFF-Myc

value: human

value: foreskin fibroblast cells expressing canine cMyc

tag: cell karyotype

tag: cell lineage

tag: cell sex

tag: antibody

value: CTCF

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid

tag: labversion

tag: replicate


title: UW_DnaseSeq_Th1_Wb33676984Rep1

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell organism

tag: cell description

value: Th1 cells in vivo isolation

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

value: mesoderm

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies


title: UW_ChipSeq_HA-sp_CTCFRep2

source_name: HA-sp

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: HA-sp

value: astrocytes spinal cord

value: normal

value: ectoderm

value: U

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: control

tag: control description


title: UW_ChipSeq_RPTEC_CTCFRep1

source_name: RPTEC

value: UW

value: Stamatoyannopoulous - University of Washington

value: RPTEC

value: human

value: renal proximal tubule epithelial cells

tag: cell karyotype

tag: cell sex

tag: antibody

value: CTCF

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid


title: UW_ChipSeq_HRPEpiC_CTCFRep2

source_name: HRPEpiC

tag: lab

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: HRPEpiC

tag: cell organism

value: retinal pigment epithelial cells

tag: cell lineage

value: No special treatment or protocol applies

tag: labversion

tag: replicate


title: UW_ChipSeq_RPTEC_CTCFRep2

tag: lab description

tag: cell

tag: cell description

value: normal

value: U

tag: antibody targetdescription

tag: antibody vendorname

tag: treatment

tag: treatment description


title: UW_ChipSeq_MCF-7_CTCFRep2

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

value: ectoderm

tag: cell sex

value: F

tag: antibody

tag: antibody antibodydescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

tag: antibody vendorid

tag: control

tag: control description


title: UW_ChipSeq_H7-hESC_Input_diffProtA_9dRep1

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

tag: cell organism

value: human

value: undifferentiated embryonic stem cells

tag: cell lineage

value: inner cell mass

value: Input

tag: antibody description

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

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage:mesoderm

tag: controlid

tag: labexpid


title: UW_ChipSeq_Monocytes-CD14+_RO01746_InputRep1

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell description

value: Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2:not in 2011 analysis

value: mesoderm

tag: treatment

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

tag: labversion

tag: replicate


title: UW_ChipSeq_MCF-7_CTCFRep1

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

value: ectoderm

tag: cell sex

value: F

tag: antibody

value: CTCF

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

tag: antibody vendorid

tag: treatment description


title: UW_ChipSeq_HAc_CTCFRep2

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: HAc

tag: cell organism

value: human

value: astrocytes-cerebellar

value: normal

tag: cell lineage

value: U

value: Millipore

tag: control

tag: control description


title: UW_ChipSeq_HAc_CTCFRep1

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell description

tag: treatment

value: No special treatment or protocol applies

value: std

tag: controlid

tag: labexpid

tag: labversion


title: UW_ChipSeq_LNCaP_InputRep1

source_name: LNCaP

value: LNCaP

value: prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.)

tag: cell karyotype

value: cancer

value: endoderm

tag: cell sex

value: M

tag: antibody

value: Input

tag: antibody description

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

value: Standard input signal for most experiments.

tag: replicate


title: UW_ChipSeq_HCM_CTCFRep1

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: HCM

value: human

value: cardiac myocytes

value: mesoderm

value: CTCF

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

tag: antibody vendorid

tag: treatment description


title: UW_ChipSeq_BE2_C_CTCFRep1

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

value: neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy.

tag: cell lineage

value: ectoderm

value: Millipore

tag: treatment

value: No special treatment or protocol applies

tag: control

value: std

tag: control description


title: UW_ChipSeq_HCT-116_CTCFRep1

value: colorectal carcinoma (PMID:7214343)

tag: cell karyotype

value: cancer

value: endoderm

tag: cell sex

value: M

tag: antibody

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid

tag: labversion

tag: replicate


title: UW_ChipSeq_WI-38_Input_4OHTAM_20nM_72hrRep1

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

tag: datatype

tag: datatype description

value: human

value: embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct

value: normal

value: F

value: Input

tag: antibody description

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

value: 72 hours with 20 nM 4-hydroxytamoxifen (Stam)


title: UW_ChipSeq_HFF-Myc_InputRep1

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: HFF-Myc

tag: cell organism

value: foreskin fibroblast cells expressing canine cMyc

value: fibroblast

tag: treatment description


title: UW_ChipSeq_H7-hESC_Input_diffProtA_5dRep1

tag: cell description

value: undifferentiated embryonic stem cells

tag: cell lineage

value: inner cell mass

value: U

tag: treatment

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage:mesoderm

tag: control

value: std


title: UW_ChipSeq_H7-hESC_Input_diffProtA_14dRep1

value: UW

value: Stamatoyannopoulous - University of Washington

value: human

tag: cell sex

tag: antibody

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage:mesoderm

tag: control description

value: Standard input signal for most experiments.


title: UW_ChipSeq_CD20+_RO01794_InputRep1

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

tag: cell karyotype

value: normal

value: mesoderm

value: F

value: Input

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

value: No special treatment or protocol applies

tag: controlid

tag: labexpid

tag: labversion


title: UW_ChipSeq_WI-38_InputRep1

tag: lab

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct

value: endoderm

tag: replicate


title: UW_ChipSeq_SKMC_InputRep1

source_name: SKMC

tag: lab description

tag: cell

value: SKMC

tag: cell organism

value: skeletal muscle cells

value: U

tag: antibody description

value: std


title: UW_ChipSeq_BE2_C_CTCFRep2

value: UW

value: Stamatoyannopoulous - University of Washington

value: human

tag: cell description

value: neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy.

value: cancer

tag: cell lineage

value: ectoderm

value: M

value: CTCF

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description


title: UW_ChipSeq_HCT-116_CTCFRep2

value: ChipSeq

value: Chromatin IP Sequencing

value: colorectal carcinoma (PMID:7214343)

tag: cell karyotype

tag: cell sex

tag: antibody

value: No special treatment or protocol applies

tag: control

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid

tag: labversion


title: UW_ChipSeq_HFF_CTCFRep1

source_name: HFF

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: cell

value: HFF

tag: cell organism

value: foreskin fibroblast

value: normal

value: std

tag: replicate


title: UW_ChipSeq_GM12864_CTCFRep3

value: UW

value: Stamatoyannopoulous - University of Washington

value: human

tag: cell description

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

tag: cell lineage

value: mesoderm

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: treatment


title: UW_ChipSeq_NB4_CTCFRep1

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

tag: cell karyotype

value: cancer

tag: cell sex

value: U

tag: antibody

value: CTCF

value: Rabbit polyclonal. Antibody Target:CTCF

tag: treatment description

tag: control

tag: control description

tag: controlid


title: UW_ChipSeq_NHLF_InputRep1

source_name: NHLF

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: NHLF

value: lung fibroblasts

value: endoderm

value: Input

tag: antibody description

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

tag: labexpid

tag: labversion


title: UW_ChipSeq_A549_CTCFRep2

value: UW

tag: cell organism

tag: cell description

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

tag: cell lineage

value: M

tag: antibody antibodydescription

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

value: No special treatment or protocol applies

value: std

value: Standard input signal for most experiments.

tag: replicate


title: UW_ChipSeq_RPTEC_InputRep1

value: Stamatoyannopoulous - University of Washington

value: RPTEC

value: human

value: renal proximal tubule epithelial cells

tag: cell karyotype

value: normal

tag: cell sex

value: U

tag: antibody

tag: treatment

tag: treatment description

tag: control

tag: control description

tag: controlid


title: UW_ChipSeq_WI-38_CTCFRep1

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct

value: endoderm

value: F

value: CTCF

value: Rabbit polyclonal. Antibody Target:CTCF

tag: labexpid

tag: labversion


title: UW_ChipSeq_GM12865_CTCFRep3

value: UW

tag: cell organism

tag: cell description

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

tag: cell lineage

value: mesoderm

tag: antibody antibodydescription

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid


title: UW_ChipSeq_AG04450_CTCFRep2

value: Stamatoyannopoulous - University of Washington

value: fetal lung fibroblast

tag: cell karyotype

tag: cell sex

value: M

tag: antibody

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

value: Standard input signal for most experiments.

tag: replicate


title: UW_ChipSeq_WI-38_CTCFRep2

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: human

value: normal

tag: control description

tag: controlid


title: UW_ChipSeq_HVMF_CTCFRep1

source_name: HVMF

value: HVMF

tag: cell organism

tag: cell description

value: villous mesenchymal fibroblast cells

value: U

value: CTCF

tag: antibody antibodydescription

tag: antibody targetdescription

tag: labexpid

tag: labversion


title: UW_ChipSeq_PANC-1_InputRep1

value: UW

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

tag: antibody

value: Input

tag: antibody description

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

tag: treatment


title: UW_ChipSeq_GM12872_CTCFRep3

tag: lab

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

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

value: mesoderm

value: M

value: Rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment description

value: No special treatment or protocol applies

tag: control

tag: replicate


title: UW_ChipSeq_GM12873_CTCFRep3

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

value: F

tag: antibody antibodydescription

tag: antibody targetdescription

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid


title: UW_ChipSeq_HMEC_CTCFRep2

source_name: HMEC

value: UW

value: HMEC

value: mammary epithelial cells

tag: cell karyotype

value: normal

tag: cell lineage

value: ectoderm

tag: cell sex

value: U

tag: antibody

value: CTCF

tag: treatment

tag: labexpid

tag: labversion


title: UW_ChipSeq_HVMF_CTCFRep2

tag: lab

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: HVMF

value: villous mesenchymal fibroblast cells

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody vendorname

tag: antibody vendorid

tag: treatment description

tag: control


title: UW_ChipSeq_CD20+_RO01778_InputRep1

value: ChipSeq

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

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

value: mesoderm

value: Input

tag: antibody description

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

value: No special treatment or protocol applies

tag: replicate


title: UW_ChipSeq_HFF_InputRep1

value: UW

value: Chromatin IP Sequencing

value: HFF

value: human

value: foreskin fibroblast

tag: cell karyotype

tag: cell sex

value: M

tag: antibody

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid


title: UW_ChipSeq_NHLF_CTCFRep1

tag: lab

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: NHLF

value: lung fibroblasts

value: normal

tag: cell lineage

value: endoderm

value: U

value: CTCF

tag: antibody antibodydescription

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

tag: treatment

tag: labexpid

tag: labversion


title: UW_ChipSeq_BE2_C_InputRep1

value: UW

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

tag: cell organism

value: neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy.

value: cancer

value: ectoderm

value: Input

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

tag: treatment description

value: No special treatment or protocol applies

tag: control


title: Dot1l_wildtype

city: Boston

first: Amit

last: Sinha

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: messenger RNA

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mm9 whole genome.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: intestinal villus epithelium, wildtype

growth_protocol: Intestinal villus cells from 4- to 6-week-old mice.

extract_protocol:
NEB magnetic oligo-dT beads was used to extract mRNA from total RNA prepared by the Qiagen RNeasy Mini Kit.
RNA libraries were prepared for sequencing using Encore® Complete RNA-Seq IL Multiplex Library Systems protocols.

treatment_protocol: Tamoxifen (2mg/day for 5 days) was injected in Dot1 f/f (control) and Villin-Cre, Dot1 f/f (mutant) mice. Villus cells were collected at least 5 days after injection was finished.

tag: strain

tag: genotype

value: Dot1l f/f

tag: tissue

value: intestinal villus epithelium

tag: age

value: 4-6 weeks


title: DF-NCCIT_NP

city: Augusta

first: Keith

last: robertson

address: 1120 15th street

institute: Georgia Health Sciences University

description: Nucleosome-Seq

data_processing:
Novoalign V2.07.00 (-F ILMFQ -r All 10 -o SAM)
MACS 1.4 (-w -f AUTO --call-subpeaks)
DANPOS 0.7.0
Genome_build: hg19
Supplementary_files_format_and_content: All peaks are generated using MACS 1.4 against input.

Each file (except DF-NP.bed and UD-NP.bed) has five columns as following:
1). Chromosome
2). 0-index starting position (inclusive)
3). 0-index end position (exclusive)
4). MACS statistics
5). Peak score

DF-NP.bed and UD-NP.bed have seven columns as following:
1). Chromosome
2). 0-index starting position (inclusive)
3). 0-index end position (exclusive)
4). summit position
5). summit value
6). strand
7). -log(p value)

growth_protocol: NCCIT cells were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone).

extract_protocol: To prepare mononucleosomes, purified nucleosomes were digested with 4000 gel units/ml of micrococcal nuclease _New England Biolabs, M0247_ at 37oC for 15 min. DNA was purified with phenol/chloroform extraction and the fragments of approximately 150 bp were collected from 2% agarose gel. Libraries were constructed according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303) and sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Treatment of NCCIT cells with 10 μM all-trans retinoic acid (RA) was performed for up to 7 days

tag: cell type

value: embroynic cancer

tag: cell line

value: NCCIT

tag: cell status

value: differentiated


title: UD-NCCIT_NP

description: Nucleosome-Seq

value: undifferentiated


title: UD-NCCIT_MBD

extract_protocol: Enrichment for methylated DNA is essentially based on the MIRA _methylated CpG island recovery assay_ described in {Rauch, 2005 #4114} with the following modifications, using the MethylMagnet mCpG DNA Isolation Kit (RiboMed).  Libraries were constructed according to Illumina's instructions accompanying the DNA Sample Kit _Part# 0801-0303_ and sequenced on the Genome Analyzer following the manufacturer's protocols.


title: Dot1l_mutant

description: messenger RNA

source_name: intestinal villus epithelium, Dot1l mutant

value: Villin-Cre, Dot1 f/f