|
| Status |
Public on Sep 28, 2022 |
| Title |
WT ILC1-2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver ILC1 cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: liver
cell type: ILC1 cells (CD45.2+CD3-CD19-NKp46+NK1.1+CD49a+CD49b-)
genotype: WT
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
ILC1 cells were lysed in TRIZOL, followed by total mRNA extraction using Direct-zol RNA Miniprep kit (Zymo Research)
Sequencing libraries were generated using NEBNext® UltraTM 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 1500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling. 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
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Differential expression analysis of two groups (three biological replicates per condition) was performed using the edgeR R package (3.34.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression txt file
|
| |
|
| Submission date |
Oct 20, 2021 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Zhigang Tian |
| E-mail(s) |
tzg@ustc.edu.cn
|
| Phone |
+8615665425083
|
| Organization name |
Univerity of Science and Technology of China
|
| Street address |
Huangshan Road，number 443
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230000 |
| Country |
China |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN22420366 |
| SRA |
SRX12698806 |
