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Status |
Public on Apr 13, 2011 |
Title |
Shotgun sequencing of polyA+ RNA from the iPS cell line clone 19.11; mRNA-Seq_ff_ips_19_11_r1 |
Sample type |
SRA |
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Source name |
iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts, biological replicate 1 (r1); mRNA-Seq_ff_ips_19_11_r1
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Organism |
Homo sapiens |
Characteristics |
sample alias: ff_ips_19_11_r1 sample common name: iPS DF 19.11 Cell Line disease: None biomaterial_provider: Thomson Laboratory biomaterial_type: Cell Line line: iPS DF 19.11 lineage: NA differentiation_stage: induced pluripotent stem cell differentiation_method: NA passage: 32 medium: TeSR Sex: Male batch: Replicate 1 experiment_type: mRNA-Seq extraction_protocol: RNeasy Blood and Tissue Kit (Qiagen) extraction_protocol_mrna_enrichment: Poly(A)Purist MAG Kit (Ambion) extraction_protocol_fragmentation: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) mrna_preparation_initial_mrna_qnty: 20-100 ng mrna_preparation_fragment_size_range: 200 nt rna_preparation_5'_rna_adapter_sequence: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) rna_preparation_3'_rna_adapter_sequence: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) rna_preparation_reverse_transcription_primer_sequence: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) rna_preparation_5'_dephosphorylation: NA rna_preparation_5'_phosphorylation: NA rna_preparation_3'_rna adapter_ligation_protocol: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) rna_preparation_5'_rna_adapter_ligation_protocol: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) rna_preparation_reverse_transcription_protocol: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) library_generation_pcr_template: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) library_generation_pcr_polymerase_type: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) library_generation_pcr_thermocycling_program: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) library_generation_pcr_number_cycles: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) library_generation_pcr_f_primer_sequence: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) library_generation_pcr_r_primer_sequence: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) library_generation_pcr_primer_conc: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies) library_generation_pcr_product_isolation_protocol: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)
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Extracted molecule |
total RNA |
Extraction protocol |
Library construction protocol: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
AB SOLiD 4 System |
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Description |
sample_term_id: NTR_0001173 assay_term_id: OBI_0001271 nucleic_acid_term_id: SO_0000871 Design description: Shotgun sequencing of polyA+ RNA isolated from the iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts Library name: mRNA-Seq_ff_ips_19_11_r1 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6933 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6900 **************** 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: GSM706050_UCSD.iPS_DF_19.11.mRNA-Seq.mRNA-Seq_ff_ips_19_11_r1.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: mRNA-Seq_ff_ips_19_11_r1.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line mRNA-Seq Data ANALYSIS DESCRIPTION: SOLiD reads produced by mRNA-Seq on the iPS DF 19.11 Cell Line, Library mRNA-Seq_ff_ips_19_11_r1 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.9490 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: 13,133,143 NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8 PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.69 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 25 MAXIMUM_REPLICATE_CORRELATION: 0.94
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ANALYSIS FILE NAME: GSM706050_UCSD.iPS_DF_19.11.mRNA-Seq.mRNA-Seq_ff_ips_19_11_r1.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: mRNA-Seq_ff_ips_19_11_r1.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line mRNA-Seq Data ANALYSIS DESCRIPTION: SOLiD mRNA-Seq read mappings from the iPS DF 19.11 Cell Line, Library mRNA-Seq_ff_ips_19_11_r1 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.9498 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: iD19.11 mRNA r1 BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line mRNA-Seq Library mRNA-Seq_ff_ips_19_11_r1 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 13,133,143 NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 8 PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.69 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 25 MAXIMUM_REPLICATE_CORRELATION: 0.94
**********************************************************************
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Submission date |
Apr 08, 2011 |
Last update date |
May 15, 2019 |
Contact name |
UCSD AND SALK |
Organization name |
University of California, San Diego
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Street address |
Health Sciences Drive
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92092 |
Country |
USA |
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Platform ID |
GPL13393 |
Series (1) |
GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
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Relations |
Reanalyzed by |
GSE99453 |
SRA |
SRX056684 |
BioSample |
SAMN00255367 |
Named Annotation |
GSM706050_UCSD.iPS_DF_19.11.mRNA-Seq.mRNA-Seq_ff_ips_19_11_r1.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM706050_UCSD.iPS_DF_19.11.mRNA-Seq.mRNA-Seq_ff_ips_19_11_r1.bed.gz |
170.8 Mb |
(ftp)(http) |
BED |
GSM706050_UCSD.iPS_DF_19.11.mRNA-Seq.mRNA-Seq_ff_ips_19_11_r1.wig.gz |
13.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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