|
| Status |
Public on Oct 01, 2022 |
| Title |
consi1 |
| Sample type |
SRA |
| |
|
| Source name |
control-siRNA HBE-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human bronchial epithelial (HBE) cell line
sirna: control
|
| Treatment protocol |
The siRNA transfection was performed with the transfection reagent (GenMute™ siRNA Transfection Reagent, SignaGen Laboratories) following the manufacturer’s protocol. Briefly, 5×10^4 cells were placed in each well of 6-well plates for 18 h prior to transfection. The siRNA in 1 ml growth medium were incubated with HBE cells for 5 h. The transfection medium was removed and replaced with 2ml fresh growth medium.
|
| Growth protocol |
HBE cells were purchased from American Type Culture Collection (CRL-2741), and were cultured in RPMI 1640 (Gibco, C11875500BT) with 10% FBS (Gibco, 10082147) and 1% penicillin-streptomycin (Beyotime Biotechnology) in 5% CO2 at 37 ̊C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HBE cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80℃ under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MGISEQ-2000RS |
| |
|
| Description |
control-siRNA HBE-rep-1
|
| Data processing |
The sequencing data was filtered with SOAPnuke (v1.5.2) by removing reads containing sequencing adapter;
removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%
removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to reference genome (GRCh38) using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_exp.csv: Expression level of gene was calculated by RSEM (v1.2.12).
|
| |
|
| Submission date |
Oct 07, 2021 |
| Last update date |
Oct 02, 2022 |
| Contact name |
Wenqi Diao |
| E-mail(s) |
wdiao@zju.edu.cn
|
| Organization name |
Second Affiliated Hospital of Zhejiang University School of Medicine
|
| Department |
Department of Respiratory and Critical Care Medicine
|
| Lab |
Key Laboratory of Respiratory Disease of Zhejiang Province
|
| Street address |
88 JieFang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310009 |
| Country |
China |
| |
|
| Platform ID |
GPL30209 |
| Series (1) |
| GSE185523 |
RNASeq of human bronchial epithelial (HBE) cells with cGAS-siRNA transfected |
|
| Relations |
| BioSample |
SAMN22134355 |
| SRA |
SRX12521762 |
