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| Status |
Public on Nov 23, 2016 |
| Title |
132h-2 |
| Sample type |
SRA |
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| Source name |
CHO-S
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| Organism |
Cricetulus griseus |
| Characteristics |
cell line: CHO-S
time after seeding (h): 132
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| Growth protocol |
CHO-S (Life Technologies # A11557-01) cells were cultured in CD CHO medium (Life Technologies # 10743-029) supplemented with 8 mM L-glutamine (Life Technologies # 25030-024), Anti-clumping agent 1:500 (Life Technologies # 0010057 AE), and Pen-Strep 1:100 (Life Technologies # 15140-122) in 2 L Corning shake flasks (Sigma # 431255) with 400 mL medium. All cultures were maintained in an incubator kept at 37°C, 5% CO2, 70% humidity and 25 mm throw, shaking at 120 rpm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
5 x 10^6 cells were harvested for transcriptomic analysis via RNA-Seq. Cells were centrifuged and the pellet resuspended in 2%/98% DTT/RLT buffer and stored at -80°C. RNA was extracted with Qiagen's RNeasy mini kit (Qiagen #74104) according to manufacturer's protocol with on-column DNase digestion.
RNA libraries for sequencing were prepared using TruSeq Stranded mRNA Sample prep kit with 96 dual indexes (Illumina, CA, USA) according to the manufacturer’s instructions with the following changes. The protocols were automated using an Agilent NGS workstation (Agilent, CA, USA) using purification steps as previously described (Borgström et al., 2011; Lundin et al., 2010). Libraries were clustered using cBot and sequenced on HiSeq2500 (HiSeq Control Software 2.2.38/RTA 1.18.61) with a 2x126 setup in RapidHighOutput mode.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample taken at t=132, replicate #2
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| Data processing |
FastQC (Andrews, 2010) was used to assess read quality.
Trimmomatic v0.32 (Bolger et al., 2014) was used to trim reads with adapters or low quality scores.
STAR2.4.0a (Dobin et al., 2013) was used to align trimmed reads to the CHO-K1 genome (Xu et al., 2011).
Mapping results were stored using SAMtools 1.0(Li et al., 2009).
Cufflinks 2.2.1 (Trapnell et al., 2010) was used to assemble mapped reads and quantify expression levels.
Genome_build: CHOK1 reference genome from ncbi ftp site: ftp://ftp.ncbi.nlm.nih.gov/genomes/Cricetulus_griseus/CHR_Un/cgr_ref_CriGri_1.0_chrUn.fa.gz
Supplementary_files_format_and_content: Tab delimited file containing FPKM measurements for genes.
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| Submission date |
Feb 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Nathan Lewis |
| E-mail(s) |
n4lewis@ucsd.edu
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| Organization name |
UCSD
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| Street address |
9500 Gilman Dr. MC 0760
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0760 |
| Country |
USA |
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| Platform ID |
GPL20904 |
| Series (1) |
| GSE77800 |
CHO-S transcriptome in batch culture |
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| Relations |
| SRA |
SRX1570981 |
| BioSample |
SAMN04501048 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2059647_T132_2.txt.gz |
154.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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