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| Status |
Public on Sep 06, 2023 |
| Title |
Ctrl3 |
| Sample type |
SRA |
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| Source name |
Ovary
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| Organism |
Cricetulus griseus |
| Characteristics |
tissue: Ovary
cell line: stably expressing Cdh13
cell type: CHO cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells with a miRNeasy kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequencing was performed on NovaSeq 6000 platform in a 101 base single mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were mapped to the chinese hamster reference genome (GCF_003668045.1) using Hisat2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: NCBI chinese hamster reference genome (GCF_003668045.1_CriGri-PICR_genomic.fna)
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
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| Submission date |
Dec 19, 2022 |
| Last update date |
Jun 06, 2024 |
| Contact name |
Daisuke Motooka |
| E-mail(s) |
[email protected]
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| Organization name |
NGS core facility, Research Institute for Microbial Diseases, Osaka University
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| Street address |
3-1, Yamadaoka
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| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
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| Platform ID |
GPL27425 |
| Series (1) |
| GSE221308 |
Xbp1 knockdown in CHO cells stably expressing Cdh13 (RNA-Seq) |
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| Relations |
| BioSample |
SAMN32309276 |
| SRA |
SRX18769905 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6858194_siCtrl-3_FPKM.txt.gz |
140.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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