 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 20, 2019 |
| Title |
3080 Seed train rep1 (dataset 2) |
| Sample type |
SRA |
| |
|
| Source name |
CHO suspension culture
|
| Organism |
Cricetulus griseus |
| Characteristics |
cell line: 3080
day: 0
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
3080 Seed train rep1
|
| 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
|
| |
|
| Submission date |
Nov 19, 2019 |
| Last update date |
Nov 21, 2019 |
| Contact name |
Davide Vito |
| E-mail(s) |
davide.vito91@gmail.com
|
| Organization name |
University of Kent
|
| Street address |
Ingram Building, University of Kent
|
| City |
Canterbury |
| State/province |
Kent |
| ZIP/Postal code |
CT2 7NH |
| Country |
United Kingdom |
| |
|
| 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 |
|
| Relations |
| BioSample |
SAMN13327584 |
| SRA |
SRX7182949 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
