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| Status |
Public on Oct 01, 2019 |
| Title |
CHO cells, A1-1_STA |
| Sample type |
SRA |
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| Source name |
Chinese hamster ovary (CHO) cells
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| Organism |
Cricetulus griseus |
| Characteristics |
cell line: amplified progeny of cell line of antibody-producing CHO DG44
growth phase: Stationary phase
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cell cultures were re-suspended in RLT buffer (Qiagen) and kept at −80 °C until RNA was extracted using the RNeasy kit (Qiagen) and on-column DNAse digestion.
Library preparation was performed with Illumina’s TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: RS-122-2103), according to manufacturer’s protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Description |
CHO-Core-16
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| Data processing |
The RNA libraries were mapped to the CHO genome (C_griseus_v1.0) using STAR aligner (v. 2.5.4b )
Alignments were processed to quantify gene expression counts with HTSeq-count (v. 0.7.2)
Genes with very low expression (with a cutoff of one count in at least two samples) were excluded from further downstream analysis
To comply with intellectual property requirements, the sequencing data were processed to exclude unmapped reads. This results in less than 5% reduction in available reads.
Genome_build: C_griseus_v1.0
Supplementary_files_format_and_content: comma-separated values (CSV) file of raw counts in matrix format, with sample names denoted by columns and genes by row
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| Submission date |
Jun 28, 2019 |
| Last update date |
Oct 01, 2019 |
| Contact name |
Nathan E Lewis |
| Organization name |
UCSD
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| Street address |
9500 Gilman Dr
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92122 |
| Country |
USA |
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| Platform ID |
GPL21152 |
| Series (1) |
| GSE133511 |
Transcriptome profiles of antibody-producing CHO cells across different amplification strategies |
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| Relations |
| BioSample |
SAMN12162708 |
| SRA |
SRX6384018 |
| 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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