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| Status |
Public on Apr 13, 2011 |
| Title |
Shotgun sequencing of polyA+ RNA from the H1 cell line differentiated into neural progenitor cells; mRNA-Seq_h1-npc_r2 |
| Sample type |
SRA |
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| Source name |
H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); mRNA-Seq_h1-npc_r2
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: H1-NPC_r2
sample common name: H1 Derived Neuronal Progenitor Cultured Cells
disease: None
biomaterial_provider: Thomson Laboratory
biomaterial_type: Cell Line
line: H1
lineage: NA
differentiation_stage: embryonic stem cell differentiated into neural progenitor cells
differentiation_method: H1 cells were differentiated by culturing in insulin, SB, Noggin
passage: 27
medium: TeSR
Sex: Male
batch: Replicate 2
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: CL_0000047
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: Shotgun sequencing of polyA+ RNA isolated from the H1 cell line differentiated into neural progenitor cells
Library name: mRNA-Seq_h1-npc_r2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6932
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
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: GSM706049_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_h1-npc_r2.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD reads produced by mRNA-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Donor mRNA-Seq_h1-npc_r2 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.9496
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: 14,860,811
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.03
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.12
**********************************************************************
ANALYSIS FILE NAME: GSM706049_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_h1-npc_r2.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD mRNA-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells, Donor mRNA-Seq_h1-npc_r2 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.9504
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: HDNP mRNA r2
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Donor mRNA-Seq_h1-npc_r2 Library mRNA-Seq_h1-npc_r2 EA Release 4
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,860,811
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.03
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.12
**********************************************************************
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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
|
| Street address |
Health Sciences Drive
|
| 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 |
SRX056683 |
| BioSample |
SAMN00215950 |
| Named Annotation |
GSM706049_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r2.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM706049_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r2.bed.gz |
194.1 Mb |
(ftp)(http) |
BED |
| GSM706049_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r2.wig.gz |
12.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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