|
| Status |
Public on Mar 03, 2023 |
| Title |
IMQ-3 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Mus musculus |
| Characteristics |
tissue: skin
strain: BALB/c
Sex: Male
condition: imiquimod-induced psoriasis-like mouse model
genotype: BALB/c mouse
treatment: imiquimod
|
| Treatment protocol |
The mice were subjected to adaptive feeding for 7 days prior to the initiation of the experiments. The backs of all the mice were shaved and depilated using depilatory cream to expose the back skin.Three groups except the control group received the application of 62.5 mg IMQ cream (5% w/w) daily on their back skins for five consecutive days. On day 13, back skin tissues were collected.
|
| Growth protocol |
Male BALB/c mice (22 ± 2 g) aged 6-8 weeks and were offered free access to food and water within a specific pathogen-free environment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited txt file includes Count and FPKM values for each sample
|
| |
|
| Submission date |
Mar 02, 2023 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Congcong Zhu |
| E-mail(s) |
ccongzhu@126.com
|
| Phone |
19921544312
|
| Organization name |
Shanghai Skin Disease Hospital
|
| Street address |
1278 Baode Road
|
| City |
Shanghai |
| ZIP/Postal code |
200443 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE226452 |
Transcriptome analysis of the potential mechanism of Longkui Yinxiao soup in the treatment of imiquimod-induced psoriasis-like mice |
|
| Relations |
| BioSample |
SAMN33574805 |
| SRA |
SRX19554646 |
