|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jul 15, 2013 |
Title |
RNA-Seq analysis of breast myoepithelial cell from RM084 (A17919) |
Sample type |
SRA |
|
|
Source name |
A17919-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC197-RNA donor_id: RM084 Sex: female body site: Breast histological type: Myoepithelial cell is tumor: No biomaterial_type: primary cell cell_type: breast myoepithelial 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 HiSeq 2000 |
|
|
Description |
design description: RNA-Seq analysis of breast myoepithelial cell from RM084 (A17919) using Illumina HiSeq 2000 library name: A17919 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: 13 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 8 RNA_PREPARATION_INITIAL_RNA_QNTY: 4 ug LIBRARY_FRAGMENTATION: COVARIS E210 LIBRARY_FRAGMENT_SIZE_RANGE: 213-451 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: GSM1127093_UCSF-UBC.Breast_Myoepithelial_Cells.mRNA-Seq.RM084.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A17919-1.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Breast Myoepithelial Cells, Donor RM084 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.16999 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: 342,389,922 PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.98 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 32 MAXIMUM_REPLICATE_CORRELATION: 0.56
**********************************************************************
ANALYSIS FILE NAME: GSM1127093_UCSF-UBC.Breast_Myoepithelial_Cells.mRNA-Seq.RM084.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A17919-1.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast Myoepithelial Cells, Donor RM084 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.17015 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: BMC mRNA 84 19 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Myoepithelial Cells mRNA-Seq Donor RM084 Library A17919 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 342,389,922 PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.98 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 32 MAXIMUM_REPLICATE_CORRELATION: 0.56
**********************************************************************
|
|
|
Submission date |
Apr 22, 2013 |
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 |
|
Relations |
Named Annotation |
GSM1127093_UCSF-UBC.Breast_Myoepithelial_Cells.mRNA-Seq.RM084.wig.gz |
SRA |
SRX1158069 |
BioSample |
SAMN03416839 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1127093_UCSF-UBC.Breast_Myoepithelial_Cells.mRNA-Seq.RM084.bed.gz |
3.8 Gb |
(ftp)(http) |
BED |
GSM1127093_UCSF-UBC.Breast_Myoepithelial_Cells.mRNA-Seq.RM084.wig.gz |
33.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
|
|
|
|
|