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Sample GSM7446511 Query DataSets for GSM7446511
Status Public on Jun 07, 2023
Title HTR8_NF3
Sample type SRA
Source name Placenta
Organism Homo sapiens
Characteristics tissue: Placenta
cell line: HTR-8/SVneo
cell type: trophoblast
treatment: PBS
Treatment protocol Cells were infected with ZIKV GZ01 with a multiplicity of infection (MOI) of 1 plaque-forming unit per cell and incubated for 1h at 37 °C. Next, the inoculum was removed and the cells were washed twice with phosphate-buffered saline (PBS) to eliminate the unbound virus. Complete culture medium was added to each well, and cells were incubated at 37 °C and 5% CO2.
Growth protocol HTR8 cells and U251 cells were seeded in 24-well plates at 5 × 10^4 cells per well one day prior to infection.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard llumina protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description FPKM.HTR8_NF3
Data processing Cutadapt software (,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown( were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Assembly: Homo sapiens, Ensembl v96
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
Submission date Jun 05, 2023
Last update date Jun 07, 2023
Contact name Qiqi Chen
Phone 15591822232
Organization name Sun Yat-sen University
Department School of Public Health (Shenzhen)
Street address Guangming District, Shenzhen City, Guangdong Province
City Shenzhen
State/province Guangdong Province
ZIP/Postal code 518107
Country China
Platform ID GPL24676
Series (1)
GSE234128 Transcriptional Profile of ZIKV Infection in HTR8 cells and U251 cells
SRA SRX17720039
BioSample SAMN30961487

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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