|
| Status |
Public on Sep 13, 2017 |
| Title |
H3_Hsv |
| Sample type |
SRA |
| |
|
| Source name |
HSV1-infected human fibroblast KMB17 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KMB17
cell type: Human fetal lung tissue-derived fibroblast cells
passages: 20-28
infection: HSV-1 strain 17 (GenBank: NC_001806.2)
|
| Treatment protocol |
KMB17 cells were mock- infected or infected with HSV-1 at a multiplicity of infection (m.o.i) of 1.
|
| Growth protocol |
Human fibroblast KMB17 strain (Institute of Medical Biology, CAMS), a normal diploid cell line that was originated from fetal lung tissue, was cultured in Minimum Essential Medium (MEM) supplemented with 10% bovine serum (Minhai Biotech, Beijing, China) at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 48 h postinfection, total RNA from HSV-1 infected and uninfected KMB17 cells was isolated with Trizol regeant (Invitrogen) followed by digestion with DNase I (Epicentre) for 15 min at 37°C.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
circRNAs of human 6 samples _rRNA_HSV1_CIRCexplorer.fa
Candidate_lncRNAs of human 6 samples_rRNA_HSV1.fa
isoforms.fpkm_expression
circRNA.fpkm_expression
Genes.fpkm_expression
lncRNA_Prediction.fpkm_expression
|
| Data processing |
Raw reads of FASTQ files were obtained and assessed for quality using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/). The reads containing adapter, ploy-N and low quality reads were removed using Cutadapt (https://pypi.python.org/pypi/cutadapt/1.4.2) [2] to obtain clean reads with high quality.
For circRNA analysis, clean paired-end RNA-seq reads with 150 bp in length of were aligned to the human reference genome hg38 (GRCh38.p7) using Tophat (v2.1.0) (Tophat2, -N 2 -r 50 --library-type fr-firststrand --mate-std-dev20 -a 4 -i 70 -I 40000 --read-edit-dist 2 --min-segment-intron 70 --max-segment-intron 40000 -p 26 ) for linear transcripts. For the mapped reads, they were assembled into know and novel linear transcripts using Cufflinks (v2.1.1) (Cufflinks2, -I 40000 --max-bundle-frags 1000000 -p 26 -u -L CUFF). All transcripts were pooled and merged to generate final transcriptome using Cuffmerge (v 2.1.1) (Cuffmerge2, -p 26). In contrast, the unmapped reads were aligned to the AGM reference genome for fusion transcripts using Tophat-Fusion (v2.1.0) (Tophat-Fusion2, -N 2 --library-type fr-firststrand -a 4 -i 70 -I 40000 --read-edit-dist 2 --min-segment-intron 70 --max-segment-intron 40000 -p 26 --fusion-search --no-coverage-search --bowtie1). Fusion transcripts from TopHat-Fusion and the transcripts from the assembled linear RNAs were analyzed with circExplorer to identify candidate circRNAs.
For mRNA analysis, the human reference genome hg38 (GRCh38.p7) was served as mRNA annotation reference.
For lncRNA analysis, transcripts that met the following criteria were further analyzed: (1) RNA length ≥200 bp; (2) transcript reads ≥3; (3) exon number ≥1. Subsequently, transcripts were subjected to protein coding potential evaluation by CNCI (v2) [7] and CPC (0.9-r2) [8] with default parameters. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts predicted without coding potential were considered as lncRNAs.
Genome_build: human reference genome hg38 (GRCh38.p7)
Supplementary_files_format_and_content: fasta files and fpkm expression value of circRNAs, lncRNAs and genes
|
| |
|
| Submission date |
Sep 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiandong Shi |
| E-mail(s) |
dongdong9286@yeah.net
|
| Organization name |
Institute of Medical Biology
|
| Department |
Department of Vaccine Research
|
| Street address |
935# Jiaoling Road
|
| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650118 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE103763 |
Genome-wide analysis of herpes simplex virus type 1 (HSV-1) infected cells |
|
| Relations |
| BioSample |
SAMN07634610 |
| SRA |
SRX3179970 |
