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| Status |
Public on May 03, 2024 |
| Title |
CON rep1 |
| Sample type |
SRA |
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| Source name |
wild type
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| Organism |
Mus musculus |
| Characteristics |
tissue: skin
treatment: Control
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen, Carlsbard, CA, USA) and genomic DNA was removed using DNase I (TaKara, Shiga, Japan)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
CON1
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| Data processing |
The raw paired-end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean data from K. obovata samples was used to do denovo assembly with Trinity (http://trinityrnaseq.sourceforge.net/)
All the assembled transcripts were searched against the (National Center for Biotechnology Information) NCBI protein non-redundant (NR), Clusters of Orthologous Genes (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases using BLASTX to identify the proteins that had the highest sequence similarity with the given transcripts to retrieve their function annotations and a typical cut-off E-values less than 1.0×10−5 was set. Blast2GO software
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
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| Submission date |
Apr 28, 2024 |
| Last update date |
May 03, 2024 |
| Contact name |
Yishan Lv |
| E-mail(s) |
shaowen.liu@majorbio.com
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| Organization name |
Zhejiang Chinese Medical University
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| Street address |
548 Binwen Road
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| City |
hanzhou |
| ZIP/Postal code |
310053 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE266043 |
Tetrastigma hemsleyanum Polysaccharides Alleviate Imiquimod-Induced Psoriasis-Like Skin Lesions in Mice by Modulating the JAK/STAT3 Signaling Pathway |
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| Relations |
| BioSample |
SAMN41105591 |
| SRA |
SRX24386980 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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