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Sample GSM8019042 Query DataSets for GSM8019042
Status Public on Mar 04, 2024
Title IMQ mouse deliveried EPIC repeat1
Sample type SRA
Source name spleen
Organism Mus musculus
Characteristics tissue: spleen
Sex: Male
strain: C57BL/6
genotype: WT
treatment: IMQ (imiquimod) treatment at day 0 and day 1, and delivered (i.v.) EPIC by LNP at 1.5 day
Treatment protocol Spleen samples were minced through a 70-μm mesh to obtain single-cell suspensions. Then obtained single-cell suspensions were treated with Red cell lysis buffer (TIANGEN) and washed with PBS for following experiments.
Growth protocol Wild-type C57BL/6 mice received a daily topical dose of 62.5 mg IMQ cream (5%; Aldara; 3M Pharmaceuticals) on the shaved dorsal skin for 2 days, then EPIC-LNP was delivered (i.v.) at D1.5.
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 OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
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: Text file cotains FPKM.
Submission date Jan 16, 2024
Last update date Mar 06, 2024
Contact name Li Yang
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)
GSE248680 Therapeutic application of circular RNA aptamers in a mouse model of psoriasis
GSE253346 Ribo– RNA-seq of psoriasis mouse model delivered (i.v.) EPIC by LNP at D1.5
BioSample SAMN39459305
SRA SRX23231244

Supplementary file Size Download File type/resource
GSM8019042_LNP_rep1.FPKM.xls.gz 4.0 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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