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| Status |
Public on Mar 19, 2020 |
| Title |
WT-Rituximab-Day4_rep1 |
| Sample type |
SRA |
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| Source name |
Ovary
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| Organism |
Cricetulus griseus |
| Characteristics |
strain: CHO-S
tissue: Ovary
time point: Day 4
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| Treatment protocol |
N/A
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| Growth protocol |
Batch cultivation was performed in 250 mL shake flasks containing 60-80 mL CD-CHO medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 8 mM L-glutamine (Life Technologies) and 0.2% anti-clumping reagent (Life Technologies). Prior to inoculation into fed-batch bioreactors, cells were adapted from CD-CHO medium to FortiCHO (Gibco, Carlsbad, CA, USA), OptiCHO (Gibco), or ActiPro (GE Healthcare, Chicago, IL, USA) medium during three passages. All media were supplemented with 1% Anti-Anti (Life Technologies), 0.1% anti-clumping agent (Life Technologies) and 8 mM L-glutamine (Lonza, Basel, Switzerland).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cell cultures were resuspended in RLT buffer (Qiagen) and kept at -80°C until RNA was extracted using the RNeasy kit (Qiagen) and on-column DNAse digestion. RNA was eluted in 40µl of nuclease free water (RNAse/DNAse free); concentration was measured on Qubit and the purity was checked on Fragment Analyzer. Complementary DNA synthesis was obtained from 1 μg of RNA using the High capacity cDNA RT kit (Thermo Fisher scientific) as per manufacturer’s instructions.
Samples were diluted to 60ng/µL in 50µL and library preparation was performed with Illumina’s TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: 20020595), according to manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
RNA-Seq quality was assessed using FastQC. Adapter sequences and low-quality bases were trimmed using Trimmomatic (Bolger et al. 2014).
Sequence alignment was accomplished using STAR (Dobin et al. 2013) against the CHO genome (GCF_000419365.1_C_griseus_v1.0) with default parameters.
HTSeq (Anders et al. 2015) was used to quantify the expression of each gene. We performed differential gene expression analysis using DESeq2 (Anders and Huber 2010).
Genome_build: C_griseus_v1.0 (GCF_000419365.1)
Supplementary_files_format_and_content: tab-delimited text file includes count values for each Sample
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| Submission date |
Jan 31, 2020 |
| Last update date |
Mar 19, 2020 |
| Contact name |
Nathan E. Lewis |
| E-mail(s) |
n4lewis@ucsd.edu
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| Organization name |
University of California, San Diego
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| Department |
Pediatrics
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| Street address |
9500 Gilman Dr.
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| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92123 |
| Country |
USA |
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| Platform ID |
GPL22327 |
| Series (1) |
| GSE144624 |
Multiplex secretome engineering enhances recombinant protein production and purity |
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| Relations |
| BioSample |
SAMN13957915 |
| SRA |
SRX7656770 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4292486_Bio301-WT-Rituximab-Day4.quant.gene.txt.gz |
349.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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