|
Status |
Public on Jul 27, 2011 |
Title |
RNA-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A03500) |
Sample type |
SRA |
|
|
Source name |
A03500-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC091-RNA donor_id: HuFGM02 Sex: male body site: Brain histological type: Germinal matrix tissue is tumor: No biomaterial_type: primary tissue tissue_type: brain (germinal matrix) tissue
|
Extracted molecule |
total RNA |
Extraction protocol |
library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
design description: RNA-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A03500) using Illumina HiSeq 2000 library name: A03500 EXPERIMENT_TYPE: mRNA-Seq EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions. LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle 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: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT LIBRARY_GENERATION_PCR_TEMPLATE: cDNA EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.1 RNA_PREPARATION_INITIAL_RNA_QNTY: 3 ug LIBRARY_FRAGMENTATION: COVARIS E210 LIBRARY_FRAGMENT_SIZE_RANGE: 300-400 bp **************** 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: GSM751275_UCSF-UBC.Brain_Germinal_Matrix.mRNA-Seq.HuFGM02.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A03500-1.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of Brain Germinal Matrix mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Brain Germinal Matrix, Donor HuFGM02 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.7980 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 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 98,462,099 NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10 PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.66 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 30 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM751275_UCSF-UBC.Brain_Germinal_Matrix.mRNA-Seq.HuFGM02.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A03500-1.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 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.7990 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 4 BROWSER_TRACK_NAME: BGM mRNA 02 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix mRNA-Seq Donor HuFGM02 Library A03500-1 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 98,462,099 NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10 PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.66 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 30 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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Submission date |
Jun 29, 2011 |
Last update date |
May 15, 2019 |
Contact name |
UCSF-UBC CENTER |
Organization name |
UCSF-UBC
|
Street address |
UCSF-UBC
|
City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94143 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
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Relations |
Named Annotation |
GSM751275_UCSF-UBC.Brain_Germinal_Matrix.mRNA-Seq.HuFGM02.wig.gz |
SRA |
SRX1158052 |
BioSample |
SAMN03416897 |