title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS20103

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Arm
Library name: lib-RNA.RS20103
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15670
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9883
****************
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: GSM1101675_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24272.lib-RNA.RS20103.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20103.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Arm mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Arm, Donor H-24272 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.16707
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,847,352
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.03
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

ANALYSIS FILE NAME: GSM1101675_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24272.lib-RNA.RS20103.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20103.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Arm, Donor H-24272 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.17170
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMA mRNA 72 03
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-24272 Library lib-RNA.RS20103 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,847,352
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.03
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

source_name: Fetal Muscle, Arm primary tissue, day 85; RNA.RS20103

value: Fetal Muscle, Arm

value: day 85

value: Female


title: RNA-Seq (Total RNA) Fetal Muscle, Leg; RNA.RS20014

status: Public on Mar 22 2013

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Leg
Library name: lib-RNA.RS20014
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15598
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9827
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: transcriptomic

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

ANALYSIS FILE NAME: GSM1101671_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24259.lib-RNA.RS20014.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20014.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Leg, Donor H-24259 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.16682
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,516,254
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.96
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

ANALYSIS FILE NAME: GSM1101671_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24259.lib-RNA.RS20014.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20014.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Leg, Donor H-24259 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.17145
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FML mRNA 59 14
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg mRNA-Seq Donor H-24259 Library lib-RNA.RS20014 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,516,254
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.96
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

molecule: total RNA

organism: Homo sapiens

source_name: Fetal Muscle, Leg primary tissue, day 97; RNA.RS20014

extract_protocol: Library construction protocol: Illumina TruSeq RNA PART# 15008136 REVISION A

tag: sample alias

tag: sample common name

value: Fetal Muscle, Leg

tag: disease

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

value: Primary Tissue

value: UW

value: fetal

value: day 97

value: Male

value: mRNA-Seq

value: Ambion mirVana miRNA isolation kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Muscle, Back; RNA.RS20105

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Back
Library name: lib-RNA.RS20105
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15618
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9850
****************
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: GSM1101677_UW.Fetal_Muscle_Back.mRNA-Seq.H-24272.lib-RNA.RS20105.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20105.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Back, Donor H-24272 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.16677
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,319,590
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.98
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM1101677_UW.Fetal_Muscle_Back.mRNA-Seq.H-24272.lib-RNA.RS20105.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20105.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Back, Donor H-24272 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.17140
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMB mRNA 72 05
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back mRNA-Seq Donor H-24272 Library lib-RNA.RS20105 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,319,590
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.98
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: Fetal Muscle, Back primary tissue, day 85; RNA.RS20105

value: Fetal Muscle, Back

value: day 85


title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS20101

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Arm
Library name: lib-RNA.RS20101
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15666
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11531
****************
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: GSM1101673_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24244.lib-RNA.RS20101.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20101.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Arm mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Arm, Donor H-24244 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.16720
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,116,624
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.23
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101673_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24244.lib-RNA.RS20101.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20101.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Arm, Donor H-24244 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.17183
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMA mRNA 44 01
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-24244 Library lib-RNA.RS20101 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,116,624
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.23
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Fetal Muscle, Arm primary tissue, day 96; RNA.RS20101

value: Fetal Muscle, Arm

value: day 96


title: RNA-Seq (Total RNA) Fetal Muscle, Leg; RNA.RS20013

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Leg
Library name: lib-RNA.RS20013
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15600
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11474
****************
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: GSM1101670_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24244.lib-RNA.RS20013.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20013.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Leg, Donor H-24244 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.16685
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,860,858
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.25
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.55

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

ANALYSIS FILE NAME: GSM1101670_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24244.lib-RNA.RS20013.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20013.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Leg, Donor H-24244 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.17148
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FML mRNA 44 13
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg mRNA-Seq Donor H-24244 Library lib-RNA.RS20013 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,860,858
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.25
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.55

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

source_name: Fetal Muscle, Leg primary tissue, day 96; RNA.RS20013

value: Fetal Muscle, Leg

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

value: Primary Tissue


title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS20102

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Arm
Library name: lib-RNA.RS20102
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15668
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9889
****************
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: GSM1101674_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24259.lib-RNA.RS20102.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20102.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Arm mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Arm, Donor H-24259 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.16708
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,215,664
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.09
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101674_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24259.lib-RNA.RS20102.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20102.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Arm, Donor H-24259 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.17171
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMA mRNA 59 02
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-24259 Library lib-RNA.RS20102 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,215,664
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.09
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Fetal Muscle, Arm primary tissue, day 97; RNA.RS20102

value: UW

value: fetal

value: day 97


title: RNA-Seq (Total RNA) Fetal Muscle, Leg; RNA.RS20015

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Leg
Library name: lib-RNA.RS20015
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15596
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11467
****************
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: GSM1101672_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24279.lib-RNA.RS20015.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20015.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Leg, Donor H-24279 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.16679
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,218,063
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.94
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

ANALYSIS FILE NAME: GSM1101672_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24279.lib-RNA.RS20015.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20015.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Leg, Donor H-24279 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.17142
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FML mRNA 79 15
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg mRNA-Seq Donor H-24279 Library lib-RNA.RS20015 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,218,063
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.94
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

source_name: Fetal Muscle, Leg primary tissue, day 101; RNA.RS20015

value: day 101

value: Male

value: mRNA-Seq

value: Ambion mirVana miRNA isolation kit


title: RNA-Seq (Total RNA) Fibroblasts, Fetal Skin, Scalp; RNA.RS19986

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fibroblasts, Fetal Skin, Scalp
Library name: lib-RNA.RS19986
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15579
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11432
****************
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: GSM1101668_UW.Fibroblasts_Fetal_Skin_Scalp.mRNA-Seq.H-24259.lib-RNA.RS19986.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19986.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Scalp mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fibroblasts Fetal Skin Scalp, Donor H-24259 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.16684
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,553,126
PERCENT_READS_MAPPING_TO_UCSC_GENES: 96.33
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 97
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101668_UW.Fibroblasts_Fetal_Skin_Scalp.mRNA-Seq.H-24259.lib-RNA.RS19986.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19986.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Scalp mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fibroblasts Fetal Skin Scalp, Donor H-24259 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.17147
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FFSS mRNA 59 86
BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Scalp mRNA-Seq Donor H-24259 Library lib-RNA.RS19986 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,553,126
PERCENT_READS_MAPPING_TO_UCSC_GENES: 96.33
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 97
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Fibroblasts, Fetal Skin, Scalp, day 97 donor; RNA.RS19986

value: Fibroblasts, Fetal Skin, Scalp

value: Primary Cell Culture

tag: markers

value: short term

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA


title: RNA-Seq (Total RNA) Fetal Muscle, Back; RNA.RS19854

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Back
Library name: lib-RNA.RS19854
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15622
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9866
****************
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: GSM1101663_UW.Fetal_Muscle_Back.mRNA-Seq.H-24218.lib-RNA.RS19854.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19854.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Back, Donor H-24218 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.16705
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 50,702,596
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.31
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM1101663_UW.Fetal_Muscle_Back.mRNA-Seq.H-24218.lib-RNA.RS19854.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19854.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Back, Donor H-24218 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.17168
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMB mRNA 18 54
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back mRNA-Seq Donor H-24218 Library lib-RNA.RS19854 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 50,702,596
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.31
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: Fetal Muscle, Back primary tissue, day 96; RNA.RS19854

value: Fetal Muscle, Back

value: day 96

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Muscle, Leg; RNA.RS20012

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Leg
Library name: lib-RNA.RS20012
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15602
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11486
****************
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: GSM1101669_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24198.lib-RNA.RS20012.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20012.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Leg, Donor H-24198 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.16703
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,718,895
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.08
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

ANALYSIS FILE NAME: GSM1101669_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24198.lib-RNA.RS20012.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20012.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Leg, Donor H-24198 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.17166
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FML mRNA 98 12
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg mRNA-Seq Donor H-24198 Library lib-RNA.RS20012 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,718,895
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.08
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

source_name: Fetal Muscle, Leg primary tissue, day 113; RNA.RS20012

value: Fetal Muscle, Leg

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

value: Primary Tissue

value: UW

value: fetal

value: day 113


title: RNA-Seq (Total RNA) Fibroblasts, Fetal Skin, Back; RNA.RS19940

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fibroblasts, Fetal Skin, Back
Library name: lib-RNA.RS19940
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15586
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11359
****************
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: GSM1101665_UW.Fibroblasts_Fetal_Skin_Back.mRNA-Seq.H-24218.lib-RNA.RS19940.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19940.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fibroblasts Fetal Skin Back, Donor H-24218 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.16715
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,356,038
PERCENT_READS_MAPPING_TO_UCSC_GENES: 96.88
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.66

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

ANALYSIS FILE NAME: GSM1101665_UW.Fibroblasts_Fetal_Skin_Back.mRNA-Seq.H-24218.lib-RNA.RS19940.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19940.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fibroblasts Fetal Skin Back, Donor H-24218 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.17178
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FFSB mRNA 18 40
BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Back mRNA-Seq Donor H-24218 Library lib-RNA.RS19940 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,356,038
PERCENT_READS_MAPPING_TO_UCSC_GENES: 96.88
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.66

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

source_name: Fibroblasts, Fetal Skin, Back, day 96 donor; RNA.RS19940

value: Fibroblasts, Fetal Skin, Back

value: Male

value: mRNA-Seq

value: Ambion mirVana miRNA isolation kit


title: RNA-Seq (Total RNA) Fetal Ovary; RNA.RS19539

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Ovary
Library name: lib-RNA.RS19539
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15592
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14478
****************
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: GSM1101662_UW.Fetal_Ovary.mRNA-Seq.H23758_H23604.lib-RNA.RS19539.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19539.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Ovary mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Ovary, Donor H23758_H23604 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.16673
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 72,089,243
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.05
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1101662_UW.Fetal_Ovary.mRNA-Seq.H23758_H23604.lib-RNA.RS19539.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19539.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Ovary mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Ovary, Donor H23758_H23604 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.17136
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FO mRNA 04 39
BROWSER_TRACK_DESCRIPTION: UW Fetal Ovary mRNA-Seq Donor H23758_H23604 Library lib-RNA.RS19539 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 72,089,243
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.05
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Ovary primary tissue, pool; RNA.RS19539

value: Fetal Ovary

value: pool

value: Female

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)


title: RNA-Seq (Total RNA) Fetal Lung, Left; RNA.RS18158

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Lung, Left
Library name: lib-RNA.RS18158
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15651
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7242
****************
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: GSM1101685_UW.Fetal_Lung_Left.mRNA-Seq.H-23914.lib-RNA.RS18158.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18158.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Lung Left mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Lung Left, Donor H-23914 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.16722
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,464,796
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.47
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

ANALYSIS FILE NAME: GSM1101685_UW.Fetal_Lung_Left.mRNA-Seq.H-23914.lib-RNA.RS18158.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18158.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Left mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Lung Left, Donor H-23914 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.17185
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FLL mRNA 14 58
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left mRNA-Seq Donor H-23914 Library lib-RNA.RS18158 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,464,796
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.47
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

source_name: Fetal  primary tissue, day 91; RNA.RS18158

value: Fetal Lung, Left

value: day 91

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: TruSeq RNA

value: cDNA

value: Proprietary


title: RNA-Seq (Total RNA) Fibroblasts, Fetal Skin, Back; RNA.RS19941

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fibroblasts, Fetal Skin, Back
Library name: lib-RNA.RS19941
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15584
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11399
****************
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: GSM1101666_UW.Fibroblasts_Fetal_Skin_Back.mRNA-Seq.H-24218.lib-RNA.RS19941.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19941.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fibroblasts Fetal Skin Back, Donor H-24218 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.16716
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,186,581
PERCENT_READS_MAPPING_TO_UCSC_GENES: 96.67
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 99
MAXIMUM_REPLICATE_CORRELATION: 0.66

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

ANALYSIS FILE NAME: GSM1101666_UW.Fibroblasts_Fetal_Skin_Back.mRNA-Seq.H-24218.lib-RNA.RS19941.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19941.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fibroblasts Fetal Skin Back, Donor H-24218 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.17179
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FFSB mRNA 18 41
BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Back mRNA-Seq Donor H-24218 Library lib-RNA.RS19941 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,186,581
PERCENT_READS_MAPPING_TO_UCSC_GENES: 96.67
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 99
MAXIMUM_REPLICATE_CORRELATION: 0.66

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

source_name: Fibroblasts, Fetal Skin, Back, day 96 donor; RNA.RS19941

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

value: Primary Cell Culture

value: day 96

value: short term

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fibroblasts, Fetal Skin, Scalp; RNA.RS19985

description:
sample_term_id: CL_0002620
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fibroblasts, Fetal Skin, Scalp
Library name: lib-RNA.RS19985
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15582
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11325
****************
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: GSM1101667_UW.Fibroblasts_Fetal_Skin_Scalp.mRNA-Seq.H-24259.lib-RNA.RS19985.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19985.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Scalp mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fibroblasts Fetal Skin Scalp, Donor H-24259 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.16683
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 55,369,820
PERCENT_READS_MAPPING_TO_UCSC_GENES: 96.34
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101667_UW.Fibroblasts_Fetal_Skin_Scalp.mRNA-Seq.H-24259.lib-RNA.RS19985.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19985.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Scalp mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fibroblasts Fetal Skin Scalp, Donor H-24259 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.17146
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FFSS mRNA 59 85
BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Scalp mRNA-Seq Donor H-24259 Library lib-RNA.RS19985 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 55,369,820
PERCENT_READS_MAPPING_TO_UCSC_GENES: 96.34
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Fibroblasts, Fetal Skin, Scalp, day 97 donor; RNA.RS19985

value: Fibroblasts, Fetal Skin, Scalp

value: day 97

value: Male

value: mRNA-Seq

value: Ambion mirVana miRNA isolation kit


title: MR7 MM

status: Public on Mar 21 2013

city: Berkeley

first: Wenjun

last: Shao

state: CA

address: 2151 Berkeley Way

department: Molecular and Cell Biology

institute: University of California

description: Indexed and sequenced on Illumina HiSeq sharing with seven other samples in one lane

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
Filter out the reads that did not pass the quality filter by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to MR-7 whole genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1
Peaks were called by counting the total number of reads whose starts mapped to the genome location
Genome_build: Shewanella sp MR-7/ASM1466v1
Supplementary_files_format_and_content: wig file per sample per scaffold per strand

organism: Shewanella sp. MR-7

source_name: Shewanella sp MR-7 grown in D,L-lactate medium till mid-log-phase

growth_protocol: Aerobic growth to mid-log phase at 30C with shaking at 200 rpm

extract_protocol:
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyze.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.
We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends,  blocked the 3'  ends with sodium periodate and we added a sequencing adaptor onto the  5' end with Ambion T4 RNA ligase.  We used random hexamer primers with  a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR  amplified the library to enrich for products that contained both  adaptors and to complete the 5' adaptor. 6-mer index TGACCA was incorporated into the reverse PCR primer. We purified the PCR products  and removed unincorporated nucleotides, primers, and adaptor-only  products with AMPure XP Beads (Agencourt).

tag: treatment

value: 20 mM D,L-lactate, 30 mM PIPES, salts (1.5 g/L NH4Cl, 0.1 g/L KCl, 1.75 g/L NaCl, 0.61 g/L MgCl2.6H20, 0.6 g/L NaH2PO4, Wolfe's vitamins, and Wolfe's minerals, at pH 7

tag: strain


title: MR4 MM

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
Filter out the reads that did not pass the quality filter by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to MR-4 whole genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1
Peaks were called by counting the total number of reads whose starts mapped to the genome location
Genome_build: Shewanella sp MR-4/ASM1468v1
Supplementary_files_format_and_content: wig file per sample per scaffold per strand

organism: Shewanella sp. MR-4

source_name: Shewanella sp MR-4 grown in D,L-lactate medium till mid-log-phase

extract_protocol:
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyze.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.
We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends,  blocked the 3'  ends with sodium periodate and we added a sequencing adaptor onto the  5' end with Ambion T4 RNA ligase.  We used random hexamer primers with  a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR  amplified the library to enrich for products that contained both  adaptors and to complete the 5' adaptor. 6-mer index CTTGTA was incorporated into the reverse PCR primer. We purified the PCR products  and removed unincorporated nucleotides, primers, and adaptor-only  products with AMPure XP Beads (Agencourt).


title: MR4 LB

source_name: Shewanella sp MR-4 grown in LB till mid-log-phase

value: Luria-Bertani broth (LB)


title: MethylC-seq of Fetal Intestine, Small; BiS.DS21178

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: DNA Methylation, whole genome bisulfite sequencing of Fetal Intestine, Small
Library name: lib-BiS.DS21178
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15378
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7055
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing: Various levels of processed data files will be made available as this project proceeds.

molecule: genomic DNA

source_name: Fetal  primary tissue, day 108; BiS.DS21178

value: Fetal Intestine, Small

tag: molecule

value: genomic DNA

value: Primary Tissue

value: UW

value: fetal

value: day 108

value: DNA Methylation

value: Illumina Early access methylation adapter oligo kit (1006132)

value: A 50ul adaptor ligation reaction was set up in a 1.5 ml low bind centrifuge tube.  It was assembled on ice and mixed by gently pipetting up and down 5 times, followed by a quick spin. Water:6 ul DNA sample:10 ul DNA ligase buffer,2X:25ul Illumina Early access methylation adapter:4ul DNA ligase:1U/ul,5ul

value: 60ul of Agencourt AMPure XP beads was added to 50ul of ligation reaction and followed manufacturer's recommendations for purification.

value: Followed the EZ DNA Methylation-Gold Kit protocol.


title: MR7 LB

source_name: Shewanella sp MR-7 grown in LB till mid-log-phase


title: MethylC-seq of Fetal Intestine, Large; BiS.DS21177

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: DNA Methylation, whole genome bisulfite sequencing of Fetal Intestine, Large
Library name: lib-BiS.DS21177
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15376
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7041
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal  primary tissue, day 108; BiS.DS21177

value: Fetal Intestine, Large

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


title: MR1 MM

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
Filter out the reads that did not pass the quality filter by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to MR-1 whole genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1
Peaks were called by counting the total number of reads whose starts mapped to the genome location
Genome_build: Shewanella oneidensis MR-1/ASM14616v2
Supplementary_files_format_and_content: wig file per sample per scaffold per strand

organism: Shewanella oneidensis MR-1

source_name: S. oneidensis MR-1 grown in D,L-lactate medium till mid-log-phase

extract_protocol:
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyze.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.
We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends,  blocked the 3'  ends with sodium periodate and we added a sequencing adaptor onto the  5' end with Ambion T4 RNA ligase.  We used random hexamer primers with  a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR  amplified the library to enrich for products that contained both  adaptors and to complete the 5' adaptor. For indexed samples (2 and 4) a 6-mer index GCCAAT was incorporated into the reverse PCR primer. We purified the PCR products  and removed unincorporated nucleotides, primers, and adaptor-only  products with AMPure XP Beads (Agencourt).


title: CN32 MM

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
Filter out the reads that did not pass the quality filter by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to Shewanella putrefaciens CN-32 genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1
Peaks were called by counting the total number of reads whose starts mapped to the genome location
Genome_build: Shewanella putrefaciens CN-32/ASM1658v1
Supplementary_files_format_and_content: wig file per sample per scaffold per strand

organism: Shewanella putrefaciens CN-32

source_name: Shewanella putrefaciens CN-32 grown in D,L-lactate medium till mid-log-phase

extract_protocol:
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyze.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.
We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends,  blocked the 3'  ends with sodium periodate and we added a sequencing adaptor onto the  5' end with Ambion T4 RNA ligase.  We used random hexamer primers with  a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR  amplified the library to enrich for products that contained both  adaptors and to complete the 5' adaptor. 6-mer index CGATGT was incorporated into the reverse PCR primer. We purified the PCR products  and removed unincorporated nucleotides, primers, and adaptor-only  products with AMPure XP Beads (Agencourt).


title: ANA3 MM

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
Filter out the reads that did not pass the quality filter by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to ANA-3 whole genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1
Peaks were called by counting the total number of reads whose starts mapped to the genome location
Genome_build: Shewanella sp. ANA-3/ASM20393v1
Supplementary_files_format_and_content: wig file per sample per scaffold per strand

organism: Shewanella sp. ANA-3

source_name: Shewanella sp ANA-3 grown in D,L-lactate medium till mid-log-phase

extract_protocol:
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyze.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.
We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends,  blocked the 3'  ends with sodium periodate and we added a sequencing adaptor onto the  5' end with Ambion T4 RNA ligase.  We used random hexamer primers with  a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR  amplified the library to enrich for products that contained both  adaptors and to complete the 5' adaptor. 6-mer index CAGATC was incorporated into the reverse PCR primer. We purified the PCR products  and removed unincorporated nucleotides, primers, and adaptor-only  products with AMPure XP Beads (Agencourt).


title: ANA3 LB

source_name: Shewanella sp ANA-3 grown in LB till mid-log-phase


title: Leukocyte LCMRRBS 1ng

city: St. Louis

first: Maximiliaan

last: Schillebeeckx

state: MO

address: 4444 Forest Parkway

department: Genetics

institute: Washington University in St. Louis

data_processing:
Basecalls performed using CASAVA version 1.4
All analysis was performed using the February 2009 (GrCh37/hg19) build of the human genome and the July 2007 (NCBI37/mm9) build of the mouse genome. On average 25 million single-end 42-bp raw high quality reads per sample were either aligned to the cytosine-poor strand reference using the bisulfite mode of MAQ (41) or aligned to the reduced reference using RRBSMAP (42) filtering against reads that contain adapter sequence. Reads that showed less than 90% bisulfite conversion (~1 unconverted non-CpG cytosine per read) were filtered to remove those that resulted from incomplete bisulfite converted molecules. Aligned reads with a mapping quality of zero were also discarded. The resulting high quality uniquely mapped reads were used for methylation calling. We identified the genomic coordinates of all CpGs in the reference sequence and assessed percent DNA methylation by calculating the fraction of reads that had an unconverted cytosine at the CpG position relative to the total reads. We required that each read have either a “TG” or “CG” dinucleotide at the expected CpG coordinate to be considered for analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed tab-delimited txt files containing methylation calls for all CpGs

source_name: Leukocyte LCMRRBS 1ng

extract_protocol:
Full details can be found in Schillebeeckx et al. (2013). Briefly, human tumor specimens were collected under an Institutional Review Board (IRB)-approved protocol. Immediately after surgery, a human endometrial tumor was divided in half. One half was fresh frozen while the other was formalin-fixed and paraffin-embedded (FFPE). 50 mg of fresh frozen endometrial tumor was cut into small pieces with a sterile scalpel blade and DNA extracted using the Maxwell 16 Tissue DNA Purification Kit (AS1030, Promega). The formalin-fixed paraffin-embedded preserved portion was cut into 6-µm sections onto microscope slides. Four 4 mm2 slices were scratched off the slide with a sterile scalpel blade, combined in 80 µl buffer and proteinase K (740901.50, Clontech), and incubated overnight at 65°C. Liver tissue was harvested from C57BL/6J mice and divided in half. One half was preserved in Tissue-tek optimal cutting temperature (O.C.T.) compound (25608-930, VWR) and snap frozen, while the other half was formalin-fixed and paraffin-embedded for downstream bulk DNA extraction and LCM. Fresh frozen, FFPE, and LCM samples were purified using NucleoSpin Tissue XS columns (740901.5, Clontech) following the protocol for laser-microdissected tissue and eluted in 20 μl of nuclease-free water.
Full details can be found in Schillebeeckx et al. (2013). For RRBS, genomic DNA was digested with MspI, size selected, end-repaired, 3'-terminal A extended and ligated to Illumina adapters containing methylated cytosines, bilsufite converted using the EZ DNA Methylation Gold Kit (ZYMO), PCR amplified with 18-24 cycles and sequenced. For LCM-RRBS , genomic DNA was digested with MspI, size selected, end-repaired, 3'-terminal A extended and ligated to Illumina adapters containing methylated cytosines, bilsufite converted using the EZ DNA Methylation Gold Kit (ZYMO), PCR amplified with 12 cycles and indexed primers, pooled, gel extracted, PCR amplifed with universal primers and 14 cycles, and sequenced

tag: method

value: LCM-RRBS

tag: tissue

value: Leukocytes


title: MR1 LB exp1

description: Sequenced in one lane on Illumina HiSeq

source_name: S. oneidensis MR-1 grown in LB till mid-log-phase


title: CN32 LB

source_name: Shewanella putrefaciens CN-32 grown in LB till mid-log-phase


title: Endometrial Fresh Frozen Rep 1

source_name: Endometrial Fresh Frozen Rep 1

value: Endometrial Tumor


title: MR1 LB exp2

value: Luria-Bertani broth (LB)


title: Endometrial Fresh Frozen Rep 2

source_name: Endometrial Fresh Frozen Rep 2


title: Endometrial FFPE Rep 2

source_name: Endometrial FFPE Rep 2


title: Leukocyte RRBS 400ng

source_name: Leukocyte RRBS 400ng

value: RRBS


title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS19029

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Arm
Library name: lib-RNA.RS19029
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15662
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11571
****************
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: GSM1101700_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24078.lib-RNA.RS19029.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19029.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Arm mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Arm, Donor H-24078 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.16711
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,181,532
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.39
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101700_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24078.lib-RNA.RS19029.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19029.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Arm, Donor H-24078 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.17174
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMA mRNA 78 29
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-24078 Library lib-RNA.RS19029 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,181,532
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.39
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Fetal Muscle, Arm primary tissue, day 127; RNA.RS19029

value: Fetal Muscle, Arm

value: day 127

value: Male

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Muscle, Back; RNA.RS20106

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Back
Library name: lib-RNA.RS20106
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15616
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11514
****************
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: GSM1101678_UW.Fetal_Muscle_Back.mRNA-Seq.H-24279.lib-RNA.RS20106.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20106.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Back, Donor H-24279 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.16704
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,504,741
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.98
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM1101678_UW.Fetal_Muscle_Back.mRNA-Seq.H-24279.lib-RNA.RS20106.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20106.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Back, Donor H-24279 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.17167
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMB mRNA 79 06
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back mRNA-Seq Donor H-24279 Library lib-RNA.RS20106 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,504,741
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.98
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: Fetal Muscle, Back primary tissue, day 101; RNA.RS20106

value: Fetal Muscle, Back

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

value: Primary Tissue

value: UW

value: fetal

value: day 101

value: Ambion mirVana miRNA isolation kit


title: Endometrial FFPE Rep 1

source_name: Endometrial FFPE Rep 1

value: LCM-RRBS

value: Endometrial Tumor


title: IMR90duplicate

city: Atlanta

first: Tao

last: Wang

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

data_processing:
Bowtie aligned
remove duplicate reads
MACS peak calling
Genome_build: hg18/NCBI36
Supplementary_files_format_and_content: bed files with 5hmC enrichment peaks

source_name: fibroblasts

growth_protocol: The fibroblasts were cultured in DMEM medium containing 10% FBS, 1× Non-Essential amino acids, 1× glutamine, and 1× Pen/Strep.  The stem cells were maintained in hESC/hiPSC standard medium (DMEM/F12, 20% KnockOut Serum Replacement, 1× MEM Non-Essential Amino Acids, 1× glutamine, 0.11 mM 2-mercaptoethanol, 10 ng/ml bFGF) on irradiated MEF feeders.

extract_protocol:
Genomic DNA was extracted and purified with the DNeasy Kit (Qiagen). Genomic DNA (20ug-30ug) from each cell line was sonicated to an average size of 200bp by the Covaris sonicator.  5hmC labeling reactions were performed according to the previous protocol (Song et al., 2011) with some modifications. Briefly, the UDPG-N3 transfer was carried out with 1X reaction buffer containing 50 mM HEPES (pH 7.9) and 25 mM MgCl2, 100 uM of UDP-6-N3-Glu, and 2 uM of wild-type beta-glucose transferase for 1 h at 37° C. The labeled DNA was purified by the QIAquick PCR purification kit (Qiagen). The click chemistry was performed with the addition of 150 uM of disulfide-biotin linker, and the mixture was incubated for 2 h at 37° C.  The DNA samples were then purified by the Pierce Monomeric Avidin Kit (Thermo) following the manufacturerâ€™s recommendations. Subsequently, the 5hmC enriched DNA was concentrated by 10 K Amicon Ultra-0.5 mL Centrifugal Filters (Millipore), then purified and eluted with 12ul H2O by the MinElute PCR Purification Kit (Qiagen).
Approximately 50ng (5ul) of each 5hmC enriched DNA was used for Illumina SR library preparation by NEBNext ChIP-Seq Sample Prep Reagent Set 1(NEB) according to the manufacturer's standard protocol.

tag: cell line

tag: cell type

value: fibroblasts

tag: modification

value: 5hmC-chemical label pull down


title: IMR90


title: iPSB23

source_name: hiPSCs

value: hiPSCs


title: GM0011


title: iPSS3


title: ChIP-Seq Input of Fetal Muscle, Trunk; Histone.DS23031

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS23031
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15687
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15686
****************
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: GSM1102809_UW.Fetal_Muscle_Trunk.Input.H-24854.Histone.DS23031.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23031-Histone.DS23031-Histone.DS23031.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Fetal Muscle Trunk, Donor H-24854, 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.16812
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,760,287
FINDPEAKS_SCORE: 0.0062
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.0329
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.873
IROC_PERCENTILE: 43
POISSON_SCORE: 0.051
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102809_UW.Fetal_Muscle_Trunk.Input.H-24854.Histone.DS23031.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23031-Histone.DS23031-Histone.DS23031.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Fetal Muscle Trunk, Donor H-24854, 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.16908
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMT Input 54 31
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk ChIP-Seq Input Donor H-24854 Library Histone.DS23031 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,760,287
FINDPEAKS_SCORE: 0.0062
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.0329
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.873
IROC_PERCENTILE: 43
POISSON_SCORE: 0.051
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, trunk primary tissue, day 115; Histone.DS23031

extract_protocol: Library construction protocol: Single read - Illumina

value: Fetal Muscle, Trunk

value: genomic DNA

value: day 115

value: Female

value: ChIP-Seq Input

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Input


title: iPSAG2.3


title: RNA-Seq (Total RNA) Fetal Muscle, Back; RNA.RS19459

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Back
Library name: lib-RNA.RS19459
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15680
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9871
****************
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: GSM1101661_UW.Fetal_Muscle_Back.mRNA-Seq.H-24143.lib-RNA.RS19459.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19459.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Back, Donor H-24143 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.16717
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,840,505
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.88
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM1101661_UW.Fetal_Muscle_Back.mRNA-Seq.H-24143.lib-RNA.RS19459.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19459.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Back, Donor H-24143 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.17180
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMB mRNA 43 59
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back mRNA-Seq Donor H-24143 Library lib-RNA.RS19459 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,840,505
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.88
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: Fetal Muscle, Back primary tissue, day 115; RNA.RS19459

value: Fetal Muscle, Back

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

value: Primary Tissue

value: UW

value: mRNA-Seq

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: GM0011duplicate

value: fibroblasts

value: 5hmC-chemical label pull down


title: iPSIMR90

value: hiPSCs


title: iPSB22


title: CRL2097


title: CRL2097duplicate


title: iPSS2


title: HUES53

source_name: hESCs

value: hESCs


title: W3-18-1 LB

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
Filter out the reads that did not pass the quality filter by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to Shewanella sp W3-18-1 genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1
Peaks were called by counting the total number of reads whose starts mapped to the genome location
Genome_build: Shewanella sp. W3-18-1/ASM1518v1
Supplementary_files_format_and_content: wig file per sample per scaffold per strand

organism: Shewanella sp. W3-18-1

source_name: Shewanella sp W3-18-1 grown in LB till mid-log-phase

extract_protocol:
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyze.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.
We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends,  blocked the 3'  ends with sodium periodate and we added a sequencing adaptor onto the  5' end with Ambion T4 RNA ligase.  We used random hexamer primers with  a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR  amplified the library to enrich for products that contained both  adaptors and to complete the 5' adaptor. 6-mer index ACAGTG was incorporated into the reverse PCR primer. We purified the PCR products  and removed unincorporated nucleotides, primers, and adaptor-only  products with AMPure XP Beads (Agencourt).

value: Luria-Bertani broth (LB)


title: SB2B LB

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
Filter out the reads that did not pass the quality filter by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to Shewanella amazonensis SB2B genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1
Peaks were called by counting the total number of reads whose starts mapped to the genome location
Genome_build: Shewanella amazonensis SB2B/ASM1524v1
Supplementary_files_format_and_content: wig file per sample per scaffold per strand

organism: Shewanella amazonensis SB2B

source_name: Shewanella amazonensis SB2B grown in LB till mid-log-phase

extract_protocol:
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyze.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.
We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends,  blocked the 3'  ends with sodium periodate and we added a sequencing adaptor onto the  5' end with Ambion T4 RNA ligase.  We used random hexamer primers with  a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR  amplified the library to enrich for products that contained both  adaptors and to complete the 5' adaptor. 6-mer index GATCAG was incorporated into the reverse PCR primer. We purified the PCR products  and removed unincorporated nucleotides, primers, and adaptor-only  products with AMPure XP Beads (Agencourt).


title: Liver RRBS 400 ng Replicate 2

data_processing:
Basecalls performed using CASAVA version 1.4
All analysis was performed using the February 2009 (GrCh37/hg19) build of the human genome and the July 2007 (NCBI37/mm9) build of the mouse genome. On average 25 million single-end 42-bp raw high quality reads per sample were either aligned to the cytosine-poor strand reference using the bisulfite mode of MAQ (41) or aligned to the reduced reference using RRBSMAP (42) filtering against reads that contain adapter sequence. Reads that showed less than 90% bisulfite conversion (~1 unconverted non-CpG cytosine per read) were filtered to remove those that resulted from incomplete bisulfite converted molecules. Aligned reads with a mapping quality of zero were also discarded. The resulting high quality uniquely mapped reads were used for methylation calling. We identified the genomic coordinates of all CpGs in the reference sequence and assessed percent DNA methylation by calculating the fraction of reads that had an unconverted cytosine at the CpG position relative to the total reads. We required that each read have either a “TG” or “CG” dinucleotide at the expected CpG coordinate to be considered for analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bed tab-delimited txt files containing methylation calls for all CpGs

organism: Mus musculus

source_name: Liver RRBS 400 ng Replicate 2

value: RRBS

value: Liver


title: iPSA2


title: IMR90input

description: input

value: input


title: iPSRX35i


title: Liver RRBS 400 ng Replicate 3

source_name: Liver RRBS 400 ng Replicate 3


title: HUES48


title: HUES49


title: RNA-Seq (Total RNA) Fetal Muscle, Leg; RNA.RS19855

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Leg
Library name: lib-RNA.RS19855
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15604
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9833
****************
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: GSM1101664_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24218.lib-RNA.RS19855.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19855.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Leg, Donor H-24218 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.16694
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,518,073
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.03
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

ANALYSIS FILE NAME: GSM1101664_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24218.lib-RNA.RS19855.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19855.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Leg, Donor H-24218 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.17157
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FML mRNA 18 55
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg mRNA-Seq Donor H-24218 Library lib-RNA.RS19855 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,518,073
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.03
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

source_name: Fetal Muscle, Leg primary tissue, day 96; RNA.RS19855

value: Fetal Muscle, Leg

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

value: Primary Tissue

value: fetal

value: day 96

value: Male

value: Ambion mirVana miRNA isolation kit


title: W3-18-1 MM

source_name: Shewanella sp W3-18-1 grown in D,L-lactate medium till mid-log-phase

value: 20 mM D,L-lactate, 30 mM PIPES, salts (1.5 g/L NH4Cl, 0.1 g/L KCl, 1.75 g/L NaCl, 0.61 g/L MgCl2.6H20, 0.6 g/L NaH2PO4, Wolfe's vitamins, and Wolfe's minerals, at pH 7


title: SB2B MM

source_name: Shewanella amazonensis SB2B grown in D,L-lactate medium till mid-log-phase


title: Liver RRBS 400 ng Replicate 1

source_name: Liver RRBS 400 ng Replicate 1


title: Liver LCMRRBS Fresh Frozen 5mm2

source_name: Liver LCMRRBS Fresh Frozen 5mm2

value: LCM-RRBS