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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 05, 2012 |
| Title |
RNA-Seq (Total RNA) Moblized CD34 Primary Cells; RNA.RS18745 |
| Sample type |
SRA |
| |
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| Source name |
flow sorted CD34+ cells from cord blood; RNA.RS18745
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: RO 01549
sample common name: CD34 Primary Cells
disease: None
biomaterial_provider: FHCRC HEIMFELD
biomaterial_type: Primary Cell
cell_type: CD34 Primary Cells
markers: CD34+
donor_id: RO 01549
donor_age: 33 years
donor_health_status: NA
donor_sex: Female
donor_ethnicity: Caucasian
passage_if_expanded: NA
experiment_type: mRNA-Seq
extraction_protocol: Ambion Ribopure
extraction_protocol_mrna_enrichment: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit
rna_preparation_initial_rna_qnty: 1ug
rna_preparation_reverse_transcription_primer_sequence: Random Primers(hexamers)
rna_preparation_reverse_transcription_protocol: TruSeq RNA
library_generation_pcr_template: cDNA
library_fragmentation: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit
library_fragment_size_range: 120-200bp
library_generation_pcr_polymerase_type: Proprietary
library_generation_pcr_thermocycling_program: 98C 30 sec, 15 cycles 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: Proprietary
library_generation_pcr_r_primer_sequence: Proprietary
library_generation_pcr_primer_conc: Proprietary
library_generation_pcr_product_isolation_protocol: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit
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| Extracted molecule |
total RNA |
| Extraction protocol |
Library construction protocol: Illumina TruSeq RNA PART# 15008136 REVISION A
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
sample_term_id: CL_0000837
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Moblized CD34 Primary Cells
Library name: lib-RNA.RS18745
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12162
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2401
****************
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: GSM909310_UW.Mobilized_CD34_Primary_Cells.mRNA-Seq.RO_01549.lib-RNA.RS18745.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18745.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Mobilized CD34 Primary Cells, Donor RO 01549 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.13741
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: 346,073,864
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.3
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM909310_UW.Mobilized_CD34_Primary_Cells.mRNA-Seq.RO_01549.lib-RNA.RS18745.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS18745.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 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.13742
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: MCD34 mRNA 49 45
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells mRNA-Seq Donor RO 01549 Library lib-RNA.RS18745 EA Release 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 346,073,864
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.3
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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| Submission date |
Apr 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Northwest REMC |
| E-mail(s) |
rharris1@bcm.tmc.edu
|
| Organization name |
University of Washington
|
| Street address |
-
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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| Relations |
| Reanalyzed by |
GSE84999 |
| Reanalyzed by |
GSE99453 |
| SRA |
SRX135562 |
| BioSample |
SAMN00113441 |
| Named Annotation |
GSM909310_UW.Mobilized_CD34_Primary_Cells.mRNA-Seq.RO_01549.lib-RNA.RS18745.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM909310_UW.Mobilized_CD34_Primary_Cells.mRNA-Seq.RO_01549.lib-RNA.RS18745.bed.gz |
4.4 Gb |
(ftp)(http) |
BED |
| GSM909310_UW.Mobilized_CD34_Primary_Cells.mRNA-Seq.RO_01549.lib-RNA.RS18745.wig.gz |
31.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
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