|
| Status |
Public on Aug 30, 2019 |
| Title |
ZNFX1-overexpressed in Rig-I-/- cells |
| Sample type |
SRA |
| |
|
| Source name |
ZNFX1-overexpressed in Rig-I-/- cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: epithelial
genotype/variation: ZNFX1-overexpressed in Rig-I-/- cells
|
| Growth protocol |
The A549 cells were purchased from ATCC and cultured in endotoxin-free DMEM (GIBCO), supplemented with 10% FBS (GIBCO) and 1% penicillin-streptomycin (GIBCO).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was harvested using Trizol reagent. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (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 NovaSeq 6000 |
| |
|
| Description |
Human_Q497-01-T04_good
|
| 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, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. HISAT2 tools software were used to map to reference genome.
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped(FPKM).
Genome_build: GRCh38_release95
Supplementary_files_format_and_content: files include RPKM values for each Sample
|
| |
|
| Submission date |
Jun 18, 2019 |
| Last update date |
Aug 30, 2019 |
| Contact name |
Xin Jia |
| E-mail(s) |
[email protected]
|
| Phone |
15802019293
|
| Organization name |
Sun Yat-sen University
|
| Department |
College of Life Sciences
|
| Lab |
State Key Laboratory of Biocontrol
|
| Street address |
135 XinGangXi Road
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510275 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE132892 |
Next Generation Sequencing Facilitates Quantitative Analysis of Genes expression profiles in ZNFX1 overexpression in Rig-I-/- cells with or without poly I:C stimulation |
| GSE132979 |
Mitochondria-localized ZNFX1 functions as a dsRNA sensor to initiate antiviral responses via MAVS |
|
| Relations |
| BioSample |
SAMN12084400 |
| SRA |
SRX6085407 |
