|
Status |
Public on Mar 31, 2011 |
Title |
RNA-Seq analysis of breast progenitor enriched cell from RM080 (A01031) |
Sample type |
SRA |
|
|
Source name |
A01031-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC74-RNA donor_id: RM080 Sex: female body site: Breast histological type: Progenitor enriched cell is tumor: No biomaterial_type: primary cell cell_type: breast progenitor enriched cell
|
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/)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
design description: RNA-Seq analysis of breast progenitor enriched cell from RM080 (A01031) using Illumina Genome Analyzer IIx library name: A01031 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 7.3 RNA_PREPARATION_INITIAL_RNA_QNTY: N/A LIBRARY_FRAGMENTATION: COVARIS E210 LIBRARY_FRAGMENT_SIZE_RANGE: 233-440 bp **************** 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: GSM669622_UCSF-UBC.Breast_Stem_Cells.mRNA-Seq.RM080.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A01031-1.hg19.level.1.release.3 ANALYSIS TITLE: Mapping of Breast Stem Cells mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Breast Stem Cells, Donor RM080 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.6318 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 3
QUALITY SCORES: NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7 PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.4 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 14
**********************************************************************
ANALYSIS FILE NAME: GSM669622_UCSF-UBC.Breast_Stem_Cells.mRNA-Seq.RM080.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A01031-1.hg19.level.2.release.3 ANALYSIS TITLE: Raw Signal Density Graphs of Breast Stem Cells mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast Stem Cells, Donor RM080 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.6325 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 3 BROWSER_TRACK_NAME: BSC mRNA 80 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Stem Cells mRNA-Seq Donor RM080 Library A01031-1 EA Release 3
QUALITY SCORES: NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 7 PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.4 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 14
**********************************************************************
|
|
|
Submission date |
Feb 07, 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 |
GPL10999 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
Relations |
Named Annotation |
GSM669622_UCSF-UBC.Breast_Stem_Cells.mRNA-Seq.RM080.wig.gz |
SRA |
SRX1158045 |
BioSample |
SAMN03416883 |