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| Status |
Public on Aug 23, 2023 |
| Title |
NH_III_4_n |
| Sample type |
SRA |
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| Source name |
tumor tissue
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| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: tumor tissue
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor tissues and skin of the leg and flank were surgically collected and subsequently crushed using a bead crusher (MS-100R, TOMY) with 6 mm diameter beads. The beads and samples were placed in a tube together and crushed five times (3000 rpm, 1 min, 2°C). RNA was then purified using the ReliaPrep RNA Cell Miniprep System (Promega).
RNA libraries for RNA-seq were performed at Novogene, the analysis contractor.
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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 |
Sequences were aligned by HISAT2.
Samtools was used to convert SAM files to indexed, sorted, and merged BAM files.
Transcripts were assembled and quantified using StringTie.
Assembly: X. tropicalis v10.0 genome assembly
Supplementary files format and content: tab-delimited text files include gene counts for each Sample
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| Submission date |
May 24, 2023 |
| Last update date |
Aug 23, 2023 |
| Contact name |
Tatsuo Michiue |
| E-mail(s) |
tmichiue@g.ecc.u-tokyo.ac.jp
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| Organization name |
The University of Tokyo
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| Street address |
3-8-1, Komaba
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| City |
Meguro-ku |
| ZIP/Postal code |
153-8902 |
| Country |
Japan |
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| Platform ID |
GPL30018 |
| Series (1) |
| GSE233287 |
Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis |
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| Relations |
| BioSample |
SAMN35346100 |
| SRA |
SRX20502919 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7421600_NH_III_4_n.csv.gz |
115.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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