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| Status |
Public on Nov 20, 2019 |
| Title |
3936 Day 4 rep1 (dataset 2) |
| Sample type |
SRA |
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| Source name |
CHO suspension culture
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| Organism |
Cricetulus griseus |
| Characteristics |
cell line: 3936
day: 4
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted and lysate with TRI-Reagent, followed by Direct-zol RNA kit for RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
3936 Day 4 rep1
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| Data processing |
Sequenced reads were trimmed for adaptor and low-quality sequence with Trim_Galore!, then mapped to GCF_000419365.1 with STAR with parameters cut -c 36
Gene counts in exonic regions were calculated using featureCounts, then expressed in Reads Per Kilobase of exon per Megabase of library size (RPKM) with an R script
Genome_build: GCF_000419365.1
Supplementary_files_format_and_content: CSV text files include RPKM values for each sample
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| Submission date |
Nov 19, 2019 |
| Last update date |
Nov 21, 2019 |
| Contact name |
Davide Vito |
| E-mail(s) |
davide.vito91@gmail.com
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| Organization name |
University of Kent
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| Street address |
Ingram Building, University of Kent
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| City |
Canterbury |
| State/province |
Kent |
| ZIP/Postal code |
CT2 7NH |
| Country |
United Kingdom |
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| Platform ID |
GPL26969 |
| Series (2) |
| GSE140669 |
Defining lncRNAs Associated with CHO Cell Growth and IgG Productivity by RNA-Seq II |
| GSE140671 |
Defining lncRNAs Associated with CHO Cell Growth and IgG Productivity by RNA-Seq |
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| Relations |
| BioSample |
SAMN13327581 |
| SRA |
SRX7182952 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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