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| Status |
Public on Apr 13, 2011 |
| Title |
Shotgun sequencing of polyA+ RNA isolated from the H9 cell line; mRNA-Seq_h9_r1 |
| Sample type |
SRA |
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| Source name |
H9 cell line, biological replicate 1 (r1); mRNA-Seq_h9_r1
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: H9_r1
sample common name: H9 Cell Line
disease: None
biomaterial_provider: Thomson Laboratory
biomaterial_type: Cell Line
line: H9
lineage: NA
differentiation_stage: embryonic stem cell
differentiation_method: NA
passage: 42
medium: TeSR
Sex: Female
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_0000838
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: Shotgun sequencing of polyA+ RNA isolated from the H9 cell line
Library name: mRNA-Seq_h9_r1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6927
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6860
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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 |
Various levels of processed data files will be made available as this project proceeds.
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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 |
| SRA |
SRX056678 |
| BioSample |
SAMN00255371 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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