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Sample GSM751279 Query DataSets for GSM751279
Status Public on Jul 27, 2011
Title RNA-Seq analysis of cortex neural stem and progenitor cells from HuFNSC03 (A04599)
Sample type SRA
 
Source name A04599-1
Organism Homo sapiens
Characteristics submitted sample id: JOC106-RNA
donor_id: HuFNSC03
body site: Brain
histological type: Cortex neurosphere culture
is tumor: No
biomaterial_type: primary cell culture
cell type: cortex neural stem and progenitor cells
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 cortex neural stem and progenitor cells from HuFNSC03 (A04599) using Illumina HiSeq 2000
library name: A04599
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 9.2
RNA_PREPARATION_INITIAL_RNA_QNTY: 6 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
****************
Data processing **********************************************************************

ANALYSIS FILE NAME: GSM751279_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.mRNA-Seq.HuFNSC03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A04599-1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC03 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.7986
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: 118,213,421
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.28
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM751279_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.mRNA-Seq.HuFNSC03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A04599-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC03 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.7996
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: NCD mRNA 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived mRNA-Seq Donor HuFNSC03 Library A04599-1 EA Release 4


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 118,213,421
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.28
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

 
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
Relations
Named Annotation GSM751279_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.mRNA-Seq.HuFNSC03.wig.gz
SRA SRX1158056
BioSample SAMN03416933

Supplementary file Size Download File type/resource
GSM751279_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.mRNA-Seq.HuFNSC03.bed.gz 1.4 Gb (ftp)(http) BED
GSM751279_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.mRNA-Seq.HuFNSC03.wig.gz 24.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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