 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 13, 2011 |
| Title |
Shotgun sequencing of polyA+ RNA isolated from the iPS cell line clone 6.9; mRNA-Seq_ff_ips_6_9_r1 |
| Sample type |
SRA |
| |
|
| Source name |
iPS cell line clone 6.9 derived from reprogramming of foreskin fibroblasts, biological replicate 1 (r1); mRNA-Seq_ff_ips_6_9_r1
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: ff_ips_6_9_r1
sample common name: iPS DF 6.9 Cell Line
molecule: genomic DNA
disease: None
biomaterial_provider: Thomson Laboratory
biomaterial_type: Cell Line
line: iPS DF 6.9
lineage: NA
differentiation_stage: induced pluripotent stem cell
differentiation_method: NA
passage: 33
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)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library construction protocol: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
sample_term_id: NTR_0001172
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 6.9 derived from reprogramming of foreskin fibroblasts
Library name: mRNA-Seq_ff_ips_6_9_r1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6935
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6923
****************
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: GSM706052_UCSD.iPS_DF_6.9.mRNA-Seq.mRNA-Seq_ff_ips_6_9_r1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_ff_ips_6_9_r1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD reads produced by mRNA-Seq on the iPS DF 6.9 Cell Line, Library mRNA-Seq_ff_ips_6_9_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.9492
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: 15,319,378
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.84
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM706052_UCSD.iPS_DF_6.9.mRNA-Seq.mRNA-Seq_ff_ips_6_9_r1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_ff_ips_6_9_r1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD mRNA-Seq read mappings from the iPS DF 6.9 Cell Line, Library mRNA-Seq_ff_ips_6_9_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.9500
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: iD6.9 mRNA r1
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line mRNA-Seq Library mRNA-Seq_ff_ips_6_9_r1 EA Release 4
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,319,378
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.84
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
| |
|
| Submission date |
Apr 08, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
UCSD AND SALK |
| Organization name |
University of California, San Diego
|
| Street address |
Health Sciences Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92092 |
| Country |
USA |
| |
|
| Platform ID |
GPL13393 |
| Series (1) |
| GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
| Relations |
| Reanalyzed by |
GSE99453 |
| SRA |
SRX056686 |
| BioSample |
SAMN00255370 |
| Named Annotation |
GSM706052_UCSD.iPS_DF_6.9.mRNA-Seq.mRNA-Seq_ff_ips_6_9_r1.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM706052_UCSD.iPS_DF_6.9.mRNA-Seq.mRNA-Seq_ff_ips_6_9_r1.bed.gz |
198.0 Mb |
(ftp)(http) |
BED |
| GSM706052_UCSD.iPS_DF_6.9.mRNA-Seq.mRNA-Seq_ff_ips_6_9_r1.wig.gz |
14.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
