|
| Status |
Public on Sep 23, 2021 |
| Title |
mLN cDC1s - Vps33B KO - HDM-treated - rep3 |
| Sample type |
SRA |
| |
|
| Source name |
mLN cDC1s
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Vps33BdeltaDC
treatment: HDM-sensitized
|
| Treatment protocol |
mice were intranally immunized with 50 μg HDM, mLN cDC1s were sorted 24 h later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mLNs were isolated and digested, then cDC1s were sorted by FACS, RNA was harvested using Trizol reagent.RNA-seq was performed by Illumina NovaSeq 6000 with 150-base paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
R20076009_S15
|
| Data processing |
Raw data (raw reads) of fastq format were firstly trimmed and filtered. 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. All the downstream analyses were based on the clean data with high quality.
Sequenced reads were aligned to mm10 whole genome using hisat2 v2.0.5 with parameters -q -p 50 --qc-filter, where reference genome and gene splice sites files were downloaded from genome website directly.
HTSeq 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts for each gene of each sample
|
| |
|
| Submission date |
Sep 21, 2021 |
| Last update date |
Sep 23, 2021 |
| Contact name |
Gonghua Huang |
| E-mail(s) |
[email protected]
|
| Organization name |
Guangdong Medical University
|
| Street address |
1 Xincheng Avenue
|
| City |
Dongguan |
| ZIP/Postal code |
523808 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE184505 |
Vacuolar protein sorting 33B deficiency effect on conventional dendritic cell type 1 subpopulation |
|
| Relations |
| BioSample |
SAMN21530266 |
| SRA |
SRX12279476 |
