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Status |
Public on Sep 05, 2012 |
Title |
RNA-Seq analysis of UCSF-4 embryonic stem cell line (A11832) |
Sample type |
SRA |
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Source name |
A11832-1
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Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC172-RNA biomaterial_type: cell line line: UCSF-4 Sex: female body site: Embryo ICM histological type: Embryonic stem cell is tumor: No
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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 UCSF-4 embryonic stem cell line (A11832) using Illumina HiSeq 2000 library name: A11832 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: 10 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 10 LIBRARY_FRAGMENTATION: COVARIS E210 LIBRARY_FRAGMENT_SIZE_RANGE: 221-431 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: GSM958175_UCSF-UBC.UCSF-4star.mRNA-Seq.A11832.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A11832-1.hg19.level.1.release.8 ANALYSIS TITLE: Mapping of UCSF-4* Cell Line mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the UCSF-4* Cell Line, Library A11832 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.13744 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 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 387,057,821 NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22 PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.63 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 55 MAXIMUM_REPLICATE_CORRELATION: 0.65
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ANALYSIS FILE NAME: GSM958175_UCSF-UBC.UCSF-4star.mRNA-Seq.A11832.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A11832-1.hg19.level.2.release.8 ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4star Cell Line mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the UCSF-4star Cell Line, Library A11832 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.13752 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 8 BROWSER_TRACK_NAME: UCSF4* mRNA 32 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line mRNA-Seq Library A11832 EA Release 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 387,057,821 NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22 PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.63 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 55 MAXIMUM_REPLICATE_CORRELATION: 0.65
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Submission date |
Jul 09, 2012 |
Last update date |
May 15, 2019 |
Contact name |
UCSF-UBC CENTER |
Organization name |
UCSF-UBC
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Street address |
UCSF-UBC
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City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94143 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
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Relations |
Named Annotation |
GSM958175_UCSF-UBC.UCSF-4star.mRNA-Seq.A11832.wig.gz |
SRA |
SRX1158130 |
BioSample |
SAMN03416715 |
Supplementary file |
Size |
Download |
File type/resource |
GSM958175_UCSF-UBC.UCSF-4star.mRNA-Seq.A11832.bed.gz |
4.3 Gb |
(ftp)(http) |
BED |
GSM958175_UCSF-UBC.UCSF-4star.mRNA-Seq.A11832.wig.gz |
43.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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