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Sample GSM669616 Query DataSets for GSM669616
Status Public on Mar 31, 2011
Title RNA-Seq analysis of peripheral mononuclear cell from TC014 (A01025)
Sample type SRA
 
Source name A01025-1
Organism Homo sapiens
Characteristics submitted sample id: JOC68-RNA
donor_id: TC014
Sex: male
body site: Blood
histological type: Peripheral blood mononuclear cell
is tumor: No
biomaterial_type: primary cell
cell_type: Peripheral blood mononuclear 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 peripheral mononuclear cell from TC014 (A01025) using Illumina Genome Analyzer IIx
library name: A01025
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 9.1
RNA_PREPARATION_INITIAL_RNA_QNTY: N/A
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 293-492 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: GSM669616_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.mRNA-Seq.TC014.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A01025-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC014 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.6314
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: 93.4
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 86

**********************************************************************

ANALYSIS FILE NAME: GSM669616_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.mRNA-Seq.TC014.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A01025-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC014 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.6321
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: PBM mRNA 14
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells mRNA-Seq Donor TC014 Library A01025-1 EA Release 3


QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 7
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.4
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 86

**********************************************************************

 
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
Reanalyzed by GSE99453
Named Annotation GSM669616_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.mRNA-Seq.TC014.wig.gz
SRA SRX1158039
BioSample SAMN03416733

Supplementary file Size Download File type/resource
GSM669616_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.mRNA-Seq.TC014.bed.gz 644.3 Mb (ftp)(http) BED
GSM669616_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.mRNA-Seq.TC014.wig.gz 18.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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