|
| Status |
Public on Mar 04, 2024 |
| Title |
WT mouse with 2 days IMQ treatment ,repeat1 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
Sex: Male
strain: C57BL/6
genotype: WT
treatment: IMQ Day2
|
| Treatment protocol |
Spleen samples were minced through a 70-μm mesh to obtain single-cell suspensions, treated with Red cell lysis buffer (TIANGEN) and washed with PBS for following experiments.
|
| Growth protocol |
Wildtype C57BL/6 and PKR KO mice received a daily topical dose of 62.5 mg IMQ cream (5%; Aldara; 3M Pharmaceuticals) on the shaved dorsal skin for 1-5 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from spleens of mice were extracted with TRIzol (Life technologies) according to the manufacturer’s protocol.
For total RNA Ribo– RNA-seq libraries were prepared with TruSeq® Stranded Total RNA Library Prep Gold Kit. Deep sequencing was performed on Illumina NovaSeq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT_D2_rep1
|
| Data processing |
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Remove low quality bases and adaptor sequences via Trimmomatic.
Align trimmed data to rRNA sequene to remove reads from ribosomal RNAs.
Align clean data to mm10 genome by HISAT2 then calculate FPKM of linear RNAs.
The unmapped reads were realignment to mm10 mouse genome by TopHat-Fusion and identify circRNAs via CIRCexplorer3.
Assembly: mm10
Supplementary files format and content: FPKM
|
| |
|
| Submission date |
Nov 27, 2023 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Li Yang |
| E-mail(s) |
liyang_fudan@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Institutes of Biological Sciences
|
| Street address |
131 Dong-An Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE248678 |
Ribo– RNA-seq of psoriasis mouse model |
| GSE248680 |
Therapeutic application of circular RNA aptamers in a mouse model of psoriasis |
|
| Relations |
| BioSample |
SAMN38452839 |
| SRA |
SRX22654382 |
