|
| Status |
Public on Dec 01, 2023 |
| Title |
DJ1_KO_OVA_263 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
Sex: female
mouse strain_(background): C57BL/6J
cell type: lung cells
treatment: Total lung cells from DJ-1 KO mice after OVA challenge
time: 7 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol® Reagent kit . 1 ug of total RNA was used for the construction of sequencing libraries.
Genomic RNA libraries have been prepared according to Illumina’s protocols using the Illumina TruseqTM RNA sample prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina NovaSeq6000 sequencing
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36)
Then clean reads were separatelyaligned to reference genome with orientation mode using hisat2 software. This software was used to map with default parameters
Use htseq to count each gene reads with default parameters
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jul 04, 2022 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Kuan Li |
| E-mail(s) |
linen_temp1995@sohu.com
|
| Organization name |
Department of Basic Medicine, Haihe Hospital, Tianjin University
|
| Street address |
Jingu road 890
|
| City |
Tianjin |
| ZIP/Postal code |
300350 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE207415 |
DJ-1 governs airway progenitor cell/eosinophil interactions to promote allergic inflammation |
|
| Relations |
| BioSample |
SAMN28179641 |
| SRA |
SRX15226196 |
