|
| Status |
Public on Aug 10, 2017 |
| Title |
Ctrl_3 |
| Sample type |
SRA |
| |
|
| Source name |
human fibroblast KMB17 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KMB17
cell type: Human fetal lung tissue-derived fibroblast cells
infected with: nothing (mock)
passages: 20-28
virus strain: none
|
| 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 |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
small RNA
|
| Data processing |
Briefly, the sequences were blasted to human reference genome hg38 (GRCh38.p7), the RFam and Repbase to identify possible mRNA, rRNA, tRNA, snRNA, snoRNA and other ncRNAs.
To identify the known miRNAs, the remaining sequences were aligned to the miRBase (release 21.0) by using Bowtie. Matched sequences with no more than one mismatch were considered as known miRNAs.
Besides, the unmatched sequences were used to predict candidate novel miRNAs using miRDeep2. The hairpin RNA structures containing the unmatched sequences were predicated complying with criteria of the pre-miRNAs to identify potentially novel miRNAs.
Expression level of miRNAs was determined by normalizing reads to tags per million (TPM) counts. The TPM was calculated as follows: normalized expression, TPM = (actual miRNA count/number of total clean read) × 106.
Genome_build: human reference genome hg38 (GRCh38.p7)
Supplementary_files_format_and_content: sequence, count and TPM expression value of novel and known miRNAs
|
| |
|
| Submission date |
Aug 09, 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 |
GPL16791 |
| Series (1) |
| GSE102470 |
Genome-wide small RNAs analysis of herpes simplex virus type 1 (HSV-1) infected cells |
|
| Relations |
| BioSample |
SAMN07488090 |
| SRA |
SRX3083333 |
