title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS19030

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.RS19030
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15628
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9903
****************
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: GSM1101701_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24089.lib-RNA.RS19030.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19030.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-24089 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.16696
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: 46,498,456
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.38
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101701_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24089.lib-RNA.RS19030.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19030.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-24089 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.17159
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 89 30
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-24089 Library lib-RNA.RS19030 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,498,456
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.38
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Fetal Muscle, Arm primary tissue, day 96; RNA.RS19030

value: Fetal Muscle, Arm

value: Primary Tissue

value: UW

value: fetal


title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS19031

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_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.RS19031
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15626
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9899
****************
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: GSM1101702_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24111.lib-RNA.RS19031.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19031.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-24111 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.16701
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: 54,716,847
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.38
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101702_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24111.lib-RNA.RS19031.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19031.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-24111 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.17164
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 11 31
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-24111 Library lib-RNA.RS19031 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,716,847
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.38
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

molecule: total RNA

organism: Homo sapiens

source_name: Fetal Muscle, Arm primary tissue, day 105; RNA.RS19031

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

tag: sample alias

tag: sample common name

tag: disease

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

value: day 105

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 Lung, Right; RNA.RS19412

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Lung, Right
Library name: lib-RNA.RS19412
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15634
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9911
****************
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: GSM1101707_UW.Fetal_Lung_Right.mRNA-Seq.H-24089.lib-RNA.RS19412.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19412.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Lung Right mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Lung Right, Donor H-24089 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.16688
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: 41,535,066
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.6
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

ANALYSIS FILE NAME: GSM1101707_UW.Fetal_Lung_Right.mRNA-Seq.H-24089.lib-RNA.RS19412.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19412.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Lung Right, Donor H-24089 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.17151
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: FLR mRNA 89 12
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right mRNA-Seq Donor H-24089 Library lib-RNA.RS19412 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,535,066
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.6
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

source_name: Fetal Lung, Right primary tissue, day 96; RNA.RS19412

value: Fetal Lung, Right

value: day 96


title: RNA-Seq (Total RNA) Fetal Muscle, Back; RNA.RS18813

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.RS18813
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15674
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8373
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1101696_UW.Fetal_Muscle_Back.mRNA-Seq.H-24005.lib-RNA.RS18813.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18813.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-24005 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.16675
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: 28,143,876
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.43
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: 0.58

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

ANALYSIS FILE NAME: GSM1101696_UW.Fetal_Muscle_Back.mRNA-Seq.H-24005.lib-RNA.RS18813.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18813.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-24005 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.17138
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 05 13
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back mRNA-Seq Donor H-24005 Library lib-RNA.RS18813 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,143,876
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.43
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: 0.58

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

source_name: Fetal Muscle, Back primary tissue, day 105; RNA.RS18813

value: Fetal Muscle, Back

value: Female


title: RNA-Seq (Total RNA) Fetal Lung, Left; RNA.RS19028

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.RS19028
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15645
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9930
****************
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: GSM1101699_UW.Fetal_Lung_Left.mRNA-Seq.H-24089.lib-RNA.RS19028.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19028.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-24089 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.16714
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: 43,961,027
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.84
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

ANALYSIS FILE NAME: GSM1101699_UW.Fetal_Lung_Left.mRNA-Seq.H-24089.lib-RNA.RS19028.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19028.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-24089 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.17177
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 89 28
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left mRNA-Seq Donor H-24089 Library lib-RNA.RS19028 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 43,961,027
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.84
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

source_name: Fetal Lung, Left primary tissue, day 96; RNA.RS19028

value: Fetal Lung, Left

value: Primary Tissue

value: UW


title: RNA-Seq (Total RNA) Fetal Muscle, Lower Limb Skeletal; RNA.RS18814

description:
sample_term_id: UBERON_0003663
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Lower Limb Skeletal
Library name: lib-RNA.RS18814
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15614
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9472
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1101697_UW.Fetal_Muscle_Lower_Limb_Skeletal.mRNA-Seq.H-24042.lib-RNA.RS18814.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18814.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Lower Limb Skeletal mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Lower Limb Skeletal, Donor H-24042 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.16700
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: 33,185,414
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.81
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1101697_UW.Fetal_Muscle_Lower_Limb_Skeletal.mRNA-Seq.H-24042.lib-RNA.RS18814.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18814.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Lower Limb Skeletal mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Lower Limb Skeletal, Donor H-24042 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.17163
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: FMLLS mRNA 42 14
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Lower Limb Skeletal mRNA-Seq Donor H-24042 Library lib-RNA.RS18814 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,185,414
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.81
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Lower, Limb primary tissue, day 120; RNA.RS18814

value: Fetal Muscle, Lower Limb Skeletal

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

value: Fetal Muscle, Lower Limb

value: fetal

value: day 120


title: RNA-Seq (Total RNA) Fetal Muscle, Back; RNA.RS19033

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.RS19033
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15678
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9875
****************
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: GSM1101704_UW.Fetal_Muscle_Back.mRNA-Seq.H-24111.lib-RNA.RS19033.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19033.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-24111 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.16681
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: 28,502,088
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.32
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM1101704_UW.Fetal_Muscle_Back.mRNA-Seq.H-24111.lib-RNA.RS19033.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19033.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-24111 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.17144
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 11 33
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back mRNA-Seq Donor H-24111 Library lib-RNA.RS19033 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,502,088
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.32
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: Fetal Muscle, Back primary tissue, day 105; RNA.RS19033

value: day 105

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)


title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS18812

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.RS18812
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15660
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8504
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1101695_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24005.lib-RNA.RS18812.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18812.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-24005 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.16690
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: 38,442,907
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.02
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101695_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24005.lib-RNA.RS18812.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18812.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-24005 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.17153
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 05 12
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-24005 Library lib-RNA.RS18812 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,442,907
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.02
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Fetal Muscle, Arm primary tissue, day 105; RNA.RS18812

value: Fetal Muscle, Arm

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, Arm; RNA.RS18773

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.RS18773
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15657
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8508
****************
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: GSM1101694_UW.Fetal_Muscle_Arm.mRNA-Seq.H-23941.lib-RNA.RS18773.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18773.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-23941 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.16698
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: 37,420,512
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.61
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101694_UW.Fetal_Muscle_Arm.mRNA-Seq.H-23941.lib-RNA.RS18773.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18773.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-23941 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.17161
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 41 73
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-23941 Library lib-RNA.RS18773 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,420,512
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.61
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Fetal Muscle, Arm primary tissue, day 120; RNA.RS18773

value: Primary Tissue

value: UW

value: Female


title: RNA-Seq (Total RNA) Fetal Lung, Left; RNA.RS18771

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.RS18771
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15647
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9934
****************
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: GSM1101693_UW.Fetal_Lung_Left.mRNA-Seq.H-24005.lib-RNA.RS18771.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18771.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-24005 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.16709
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: 46,586,296
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.53
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

ANALYSIS FILE NAME: GSM1101693_UW.Fetal_Lung_Left.mRNA-Seq.H-24005.lib-RNA.RS18771.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18771.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-24005 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.17172
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 05 71
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left mRNA-Seq Donor H-24005 Library lib-RNA.RS18771 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,586,296
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.53
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

source_name: Fetal Lung, Left primary tissue, day 105; RNA.RS18771

value: Fetal Lung, Left

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


title: RNA-Seq (Total RNA) Fetal Lung, Right; RNA.RS18769

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Lung, Right
Library name: lib-RNA.RS18769
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15638
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8381
****************
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: GSM1101691_UW.Fetal_Lung_Right.mRNA-Seq.H-23964.lib-RNA.RS18769.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18769.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Lung Right mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Lung Right, Donor H-23964 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.16693
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: 62,025,429
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.86
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

ANALYSIS FILE NAME: GSM1101691_UW.Fetal_Lung_Right.mRNA-Seq.H-23964.lib-RNA.RS18769.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18769.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Lung Right, Donor H-23964 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.17156
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: FLR mRNA 64 69
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right mRNA-Seq Donor H-23964 Library lib-RNA.RS18769 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 62,025,429
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.86
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

source_name: Fetal Lung, Right primary tissue, day 98; RNA.RS18769

value: Fetal Lung, Right

value: fetal

value: day 98


title: RNA-Seq (Total RNA) Fetal Lung, Right; RNA.RS18770

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Lung, Right
Library name: lib-RNA.RS18770
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15636
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8343
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1101692_UW.Fetal_Lung_Right.mRNA-Seq.H-24005.lib-RNA.RS18770.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18770.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Lung Right mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Lung Right, Donor H-24005 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.16718
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: 48,004,744
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.66
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

ANALYSIS FILE NAME: GSM1101692_UW.Fetal_Lung_Right.mRNA-Seq.H-24005.lib-RNA.RS18770.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18770.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Lung Right, Donor H-24005 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.17181
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: FLR mRNA 05 70
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right mRNA-Seq Donor H-24005 Library lib-RNA.RS18770 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,004,744
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.66
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

source_name: Fetal Lung, Right primary tissue, day 105; RNA.RS18770

value: day 105

value: mRNA-Seq


title: RNA-Seq (Total RNA) Fetal Muscle, Back; RNA.RS18238

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.RS18238
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15672
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7285
****************
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: GSM1101690_UW.Fetal_Muscle_Back.mRNA-Seq.H-23964.lib-RNA.RS18238.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18238.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-23964 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.16687
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: 28,276,212
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.09
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM1101690_UW.Fetal_Muscle_Back.mRNA-Seq.H-23964.lib-RNA.RS18238.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18238.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-23964 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.17150
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 64 38
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back mRNA-Seq Donor H-23964 Library lib-RNA.RS18238 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,276,212
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.09
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: Fetal  primary tissue, day 98; RNA.RS18238

value: Fetal Muscle, Back

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

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


title: Histone H3K27ac ChIP-Seq of CD8 Primary Cells; Histone.DS21779

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS21779
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15757
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5352
****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM1102781_UW.CD8_Primary_Cells.H3K27ac.RO_01679.Histone.DS21779.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21779-Histone.DS21779.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD8 Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on CD8 Primary Cells, Donor RO 01679, 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.16862
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: 30,270,350
FINDPEAKS_SCORE: 0.355
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.356
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9993
IROC_PERCENTILE: 87
POISSON_SCORE: 0.409
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102781_UW.CD8_Primary_Cells.H3K27ac.RO_01679.Histone.DS21779.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21779-Histone.DS21779.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from CD8 Primary Cells, Donor RO 01679, 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.16958
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: CD8 H3K27ac 79 79
BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells Histone H3K27ac Donor RO 01679 Library Histone.DS21779 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,270,350
FINDPEAKS_SCORE: 0.355
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.356
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9993
IROC_PERCENTILE: 87
POISSON_SCORE: 0.409
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

source_name: flow sorted CD8+ Cells,year 21; Histone.DS21779

extract_protocol: Library construction protocol: Single read - Illumina

value: CD8 Primary Cells

tag: molecule

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 21

value: Male

value: Caucasian

value: Histone H3K27ac

value: Diagenode Bioruptor

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

value: Invitrogen Dynabeads

value: Active Motif


title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS18237

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.RS18237
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15655
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7249
****************
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: GSM1101689_UW.Fetal_Muscle_Arm.mRNA-Seq.H-23964.lib-RNA.RS18237.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18237.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-23964 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.16712
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: 37,242,455
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.53
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101689_UW.Fetal_Muscle_Arm.mRNA-Seq.H-23964.lib-RNA.RS18237.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18237.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-23964 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.17175
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 64 37
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-23964 Library lib-RNA.RS18237 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,242,455
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.53
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Fetal  primary tissue, day 98; RNA.RS18237

value: Fetal Muscle, Arm

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

value: Primary Tissue

value: UW

value: fetal

value: day 98

value: Female

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, Trunk; RNA.RS18236

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Trunk
Library name: lib-RNA.RS18236
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15594
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7252
****************
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: GSM1101688_UW.Fetal_Muscle_Trunk.mRNA-Seq.H-23941.lib-RNA.RS18236.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18236.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Trunk, Donor H-23941 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.16697
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: 58,105,291
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.19
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1101688_UW.Fetal_Muscle_Trunk.mRNA-Seq.H-23941.lib-RNA.RS18236.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18236.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Trunk, Donor H-23941 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.17160
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: FMT mRNA 41 36
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk mRNA-Seq Donor H-23941 Library lib-RNA.RS18236 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,105,291
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.19
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal  primary tissue, day 120; RNA.RS18236

value: Fetal Muscle, Trunk

value: day 120

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

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


title: RNA-Seq (Total RNA) Fetal Lung, Right; RNA.RS19414

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Lung, Right
Library name: lib-RNA.RS19414
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15632
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9907
****************
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: GSM1101709_UW.Fetal_Lung_Right.mRNA-Seq.H-24111.lib-RNA.RS19414.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19414.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Lung Right mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Lung Right, Donor H-24111 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.16695
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: 41,770,483
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.66
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

ANALYSIS FILE NAME: GSM1101709_UW.Fetal_Lung_Right.mRNA-Seq.H-24111.lib-RNA.RS19414.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19414.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Lung Right, Donor H-24111 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.17158
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: FLR mRNA 11 14
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right mRNA-Seq Donor H-24111 Library lib-RNA.RS19414 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,770,483
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.66
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

source_name: Fetal Lung, Right primary tissue, day 105; RNA.RS19414

value: Fetal Lung, Right

value: day 105

value: Male


title: RNA-Seq (Total RNA) Fetal Muscle, Leg; RNA.RS18831

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.RS18831
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15612
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8497
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1101698_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24078.lib-RNA.RS18831.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18831.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-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.16699
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: 48,940,307
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.37
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

ANALYSIS FILE NAME: GSM1101698_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24078.lib-RNA.RS18831.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18831.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-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.17162
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 78 31
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg mRNA-Seq Donor H-24078 Library lib-RNA.RS18831 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,940,307
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.37
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

source_name: Fetal Muscle, Leg primary tissue, day 127; RNA.RS18831

value: Fetal Muscle, Leg

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

value: Primary Tissue

value: UW

value: day 127


title: RNA-Seq (Total RNA) Fetal Muscle, Upper Limb Skeletal; RNA.RS18159

description:
sample_term_id: UBERON_0003662
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Upper Limb Skeletal
Library name: lib-RNA.RS18159
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15630
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7255
****************
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: GSM1101686_UW.Fetal_Muscle_Upper_Limb_Skeletal.mRNA-Seq.H-23887.lib-RNA.RS18159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18159.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Upper Limb Skeletal mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Upper Limb Skeletal, Donor H-23887 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.16713
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: 44,808,930
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.39
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1101686_UW.Fetal_Muscle_Upper_Limb_Skeletal.mRNA-Seq.H-23887.lib-RNA.RS18159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18159.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Upper Limb Skeletal mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Upper Limb Skeletal, Donor H-23887 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.17176
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: FMULS mRNA 87 59
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Upper Limb Skeletal mRNA-Seq Donor H-23887 Library lib-RNA.RS18159 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,808,930
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.39
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal  primary tissue, day 108; RNA.RS18159

value: Fetal Muscle, Upper Limb Skeletal

value: fetal

value: day 108

value: Female

value: Random Primers(hexamers)

value: TruSeq RNA


title: RNA-Seq (Total RNA) Fetal Lung, Left; RNA.RS18157

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.RS18157
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15653
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7236
****************
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: GSM1101684_UW.Fetal_Lung_Left.mRNA-Seq.H-23887.lib-RNA.RS18157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18157.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-23887 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.16676
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: 45,161,001
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.81
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

ANALYSIS FILE NAME: GSM1101684_UW.Fetal_Lung_Left.mRNA-Seq.H-23887.lib-RNA.RS18157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18157.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-23887 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.17139
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 87 57
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left mRNA-Seq Donor H-23887 Library lib-RNA.RS18157 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,161,001
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.81
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

source_name: Fetal  primary tissue, day 108; RNA.RS18157

value: Fetal Lung, Left

value: mRNA-Seq

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 Lung, Right; RNA.RS18156

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Lung, Right
Library name: lib-RNA.RS18156
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15640
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7245
****************
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: GSM1101683_UW.Fetal_Lung_Right.mRNA-Seq.H-23887.lib-RNA.RS18156.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18156.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Lung Right mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Lung Right, Donor H-23887 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.16702
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: 69,794,603
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.87
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

ANALYSIS FILE NAME: GSM1101683_UW.Fetal_Lung_Right.mRNA-Seq.H-23887.lib-RNA.RS18156.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18156.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Right mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Lung Right, Donor H-23887 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.17165
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: FLR mRNA 87 56
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Right mRNA-Seq Donor H-23887 Library lib-RNA.RS18156 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 69,794,603
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.87
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

source_name: Fetal  primary tissue, day 108; RNA.RS18156

value: Fetal Lung, Right

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

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


title: RNA-Seq (Total RNA) Fetal Lung, Left; RNA.RS18216

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.RS18216
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15649
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7239
****************
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: GSM1101687_UW.Fetal_Lung_Left.mRNA-Seq.H-23964.lib-RNA.RS18216.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18216.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-23964 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.16692
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: 59,985,501
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.72
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

ANALYSIS FILE NAME: GSM1101687_UW.Fetal_Lung_Left.mRNA-Seq.H-23964.lib-RNA.RS18216.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18216.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-23964 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.17155
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 64 16
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left mRNA-Seq Donor H-23964 Library lib-RNA.RS18216 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 59,985,501
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.72
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

source_name: Fetal  primary tissue, day 98; RNA.RS18216

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

value: Primary Tissue

value: day 98


title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS20235

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.RS20235
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15624
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8500
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1101682_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24042.lib-RNA.RS20235.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20235.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-24042 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.16689
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: 53,413,739
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.69
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101682_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24042.lib-RNA.RS20235.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20235.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-24042 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.17152
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 42 35
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-24042 Library lib-RNA.RS20235 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,413,739
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.69
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: Fetal Muscle, Arm primary tissue, day 120; RNA.RS20235

value: Fetal Muscle, Arm

value: UW

value: day 120

value: Male

value: Ambion mirVana miRNA isolation kit


title: RNA-Seq (Total RNA) Fibroblasts, Fetal Skin, Abdomen; RNA.RS20159

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, Abdomen
Library name: lib-RNA.RS20159
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15588
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11389
****************
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: GSM1101681_UW.Fibroblasts_Fetal_Skin_Abdomen.mRNA-Seq.H-24259.lib-RNA.RS20159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20159.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Abdomen mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fibroblasts Fetal Skin Abdomen, 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.16721
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: 47,913,848
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.91
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

ANALYSIS FILE NAME: GSM1101681_UW.Fibroblasts_Fetal_Skin_Abdomen.mRNA-Seq.H-24259.lib-RNA.RS20159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20159.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Abdomen mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fibroblasts Fetal Skin Abdomen, 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.17184
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: FFSA mRNA 59 59
BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Abdomen mRNA-Seq Donor H-24259 Library lib-RNA.RS20159 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,913,848
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.91
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

source_name: Fibroblasts, Fetal Skin, Abdomen, day 97 donor; RNA.RS20159

value: Fibroblasts, Fetal Skin, Abdomen

value: Primary Cell Culture

value: day 97

value: short term

value: Random Primers(hexamers)

value: TruSeq RNA


title: RNA-Seq (Total RNA) Fibroblasts, Fetal Skin, Abdomen; RNA.RS20158

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, Abdomen
Library name: lib-RNA.RS20158
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15590
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11370
****************
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: GSM1101680_UW.Fibroblasts_Fetal_Skin_Abdomen.mRNA-Seq.H-24259.lib-RNA.RS20158.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20158.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Abdomen mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fibroblasts Fetal Skin Abdomen, 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.16719
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: 67,065,600
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.96
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

ANALYSIS FILE NAME: GSM1101680_UW.Fibroblasts_Fetal_Skin_Abdomen.mRNA-Seq.H-24259.lib-RNA.RS20158.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20158.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Abdomen mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fibroblasts Fetal Skin Abdomen, 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.17182
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: FFSA mRNA 59 58
BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Abdomen mRNA-Seq Donor H-24259 Library lib-RNA.RS20158 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,065,600
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.96
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

source_name: Fibroblasts, Fetal Skin, Abdomen, day 97 donor; RNA.RS20158

value: mRNA-Seq

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 Spinal Cord; RNA.RS20108

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Spinal Cord
Library name: lib-RNA.RS20108
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15573
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14295
****************
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: GSM1101679_UW.Fetal_Spinal_Cord.mRNA-Seq.H-24244.lib-RNA.RS20108.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20108.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Spinal Cord mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Spinal Cord, 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.16678
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: 33,373,507
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.73
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.58

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

ANALYSIS FILE NAME: GSM1101679_UW.Fetal_Spinal_Cord.mRNA-Seq.H-24244.lib-RNA.RS20108.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20108.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Spinal Cord mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Spinal Cord, 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.17141
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: FSC mRNA 44 08
BROWSER_TRACK_DESCRIPTION: UW Fetal Spinal Cord mRNA-Seq Donor H-24244 Library lib-RNA.RS20108 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,373,507
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.73
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.58

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

source_name: Fetal Spinal, Cord primary tissue, day 96; RNA.RS20108

value: Fetal Spinal Cord

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

value: Primary Tissue

value: fetal

value: day 96

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


title: RNA-Seq (Total RNA) Fetal Muscle, Back; RNA.RS20104

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.RS20104
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15620
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10155
****************
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: GSM1101676_UW.Fetal_Muscle_Back.mRNA-Seq.H-24244.lib-RNA.RS20104.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20104.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-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.16691
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: 43,598,723
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.33
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM1101676_UW.Fetal_Muscle_Back.mRNA-Seq.H-24244.lib-RNA.RS20104.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS20104.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-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.17154
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 44 04
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back mRNA-Seq Donor H-24244 Library lib-RNA.RS20104 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 43,598,723
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.33
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: Fetal Muscle, Upper, back primary tissue, day 96; RNA.RS20104

value: Fetal Muscle, Back

value: UW

value: Male

value: Ambion mirVana miRNA isolation kit