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Sample GSM4292486 Query DataSets for GSM4292486
Status Public on Mar 19, 2020
Title WT-Rituximab-Day4_rep1
Sample type SRA
 
Source name Ovary
Organism Cricetulus griseus
Characteristics strain: CHO-S
tissue: Ovary
time point: Day 4
Treatment protocol N/A
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).
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
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
 
Submission date Jan 31, 2020
Last update date Mar 19, 2020
Contact name Nathan E. Lewis
E-mail(s) n4lewis@ucsd.edu
Organization name University of California, San Diego
Department Pediatrics
Street address 9500 Gilman Dr.
City San Diego
State/province CA
ZIP/Postal code 92123
Country USA
 
Platform ID GPL22327
Series (1)
GSE144624 Multiplex secretome engineering enhances recombinant protein production and purity
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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