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Sample GSM7918643 Query DataSets for GSM7918643
Status Public on Mar 04, 2024
Title WT mouse with 0 day IMQ treatment ,repeat2
Sample type SRA
 
Source name spleen
Organism Mus musculus
Characteristics tissue: spleen
Sex: Male
strain: C57BL/6
genotype: WT
treatment: IMQ Day0
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_D0_rep2
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 SAMN38452842
SRA SRX22654379

Supplementary file Size Download File type/resource
GSM7918643_WT_D0_rep2.FPKM.txt.gz 4.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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