|
| Status |
Public on Jan 16, 2019 |
| Title |
Sample 3_HBoV1 infected HAE-3 |
| Sample type |
SRA |
| |
|
| Source name |
HAE-ALI_HBoV1 infected
|
| Organisms |
Homo sapiens; Human bocavirus |
| Characteristics |
cell type: Primary human airway epithelial (HAE) cells
infected with: Human Bocavirus 1 (HBoV1)
time point: 7 days post-infection
|
| Treatment protocol |
The differentiated HAE cells were infected by HBoV1 at a MOI of 1000 viral genome copies (vgc)/cell
|
| Growth protocol |
Primary human airway epithelial cells were cultured on collagen-coated, semipermeable membrane inserts of 0.33 cm2, and then were polarized/differentiated at an ALI for 3-4 weeks. Briefly, in the first 2 to 3 days after 2 ×104 airway epithelial cells were seeded onto the Transwell insert, SAGM-H media were fed in both the apical and basolateral chambers of the insert to start the culture, then the SAGM-H media were aspirated from both chambers, and the cells were fed with 500 µl of PneumaCultTM-ALI medium (StemCell, Vancouver, BC, Canada) in the basolateral chamber. The medium was changed every 3-4 days. The ALI-cultured HAE took 3-4 weeks for full differentiation. We chose the cultures with a transepithelial electrical resistance (TEER) of over 1,000 Ω∙cm2, as determined with an epithelial Ohm-voltmeter (Millicell-ERS; EMD-Millipore, Billerica, MA), for subsequent HBoV1 infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 7 days post-infection, HBoV1 infected-cell were collected and RNA samples were extracted using the miRNeasy Mini Kit by following the manufacturer’s instruction
TailorMix miRNA V2 library preparation kit was used to prepare the small RNA library with the special RNA length between 100-200 nucleotides.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
3_S4_L001
|
| Data processing |
Illumina bcl2fastq software was used for basecalling.
Cutadapt was used to trim reads adaptor at 3’-end
Bowtie 2 was used to align smRNA-seq reads to HBoV1 genome for identification of all small RNAs. The count of HBoV1 mapping reads was extracted using an in-house-developed script from alignment file.
Genome_build: HBoV1 genome
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Dec 03, 2018 |
| Last update date |
Jan 16, 2019 |
| Contact name |
Jianming Qiu |
| E-mail(s) |
jqiu@kumc.edu
|
| Phone |
9135884413
|
| Organization name |
University of Kansas Medical Center
|
| Department |
Microbiology
|
| Lab |
Qiu lab
|
| Street address |
3901 rainbow blvd
|
| City |
Kansas City |
| State/province |
KS |
| ZIP/Postal code |
66160 |
| Country |
USA |
| |
|
| Platform ID |
GPL25879 |
| Series (1) |
| GSE123253 |
Small RNA-seq analysis of human airway epithelium infected by Human Bocavirus 1 |
|
| Relations |
| BioSample |
SAMN10517008 |
| SRA |
SRX5088413 |
