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Status |
Public on Mar 22, 2013 |
Title |
RNA-Seq (Total RNA) Fetal Lung, Left; RNA.RS18216 |
Sample type |
SRA |
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Source name |
Fetal primary tissue, day 98; RNA.RS18216
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Organism |
Homo sapiens |
Characteristics |
sample alias: fLung_Left.H-23964d98 sample common name: Fetal Lung, Left disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Lung, Left tissue_depot: UW collection_method: fetal donor_id: H-23964 donor_age: day 98 donor_health_status: NA donor_sex: Female donor_ethnicity: NA experiment_type: mRNA-Seq extraction_protocol: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit extraction_protocol_mrna_enrichment: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit rna_preparation_initial_rna_qnty: 1ug rna_preparation_reverse_transcription_primer_sequence: Random Primers(hexamers) rna_preparation_reverse_transcription_protocol: TruSeq RNA library_generation_pcr_template: cDNA library_fragmentation: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit library_fragment_size_range: 120-200bp library_generation_pcr_polymerase_type: Proprietary library_generation_pcr_thermocycling_program: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold library_generation_pcr_number_cycles: 15 library_generation_pcr_f_primer_sequence: Proprietary library_generation_pcr_r_primer_sequence: Proprietary library_generation_pcr_primer_conc: Proprietary library_generation_pcr_product_isolation_protocol: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit
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Extracted molecule |
total RNA |
Extraction protocol |
Library construction protocol: Illumina TruSeq RNA PART# 15008136 REVISION A
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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 ****************
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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
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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
**********************************************************************
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Submission date |
Mar 19, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Northwest REMC |
E-mail(s) |
rharris1@bcm.tmc.edu
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Organization name |
University of Washington
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Street address |
-
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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Relations |
SRA |
SRX252265 |
BioSample |
SAMN00254283 |
Named Annotation |
GSM1101687_UW.Fetal_Lung_Left.mRNA-Seq.H-23964.lib-RNA.RS18216.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM1101687_UW.Fetal_Lung_Left.mRNA-Seq.H-23964.lib-RNA.RS18216.bed.gz |
811.0 Mb |
(ftp)(http) |
BED |
GSM1101687_UW.Fetal_Lung_Left.mRNA-Seq.H-23964.lib-RNA.RS18216.wig.gz |
18.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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