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| Status |
Public on Jun 10, 2021 |
| Title |
HSAEC-Never1 |
| Sample type |
SRA |
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| Source name |
Primary Human small airway epithelial cells
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| Organism |
Homo sapiens |
| Characteristics |
sample type: never smoked
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| Growth protocol |
Freshly isolated HSAECs were plated onto rat tail collagen type I-coated dishes in Small Airway Epithelial Growth Medium (SAGM, Lonza) with a 1% antibiotic–antimycotic solution (AA, Invitrogen) at 37 °C in 5% CO2. HSAECs were used until passage 2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
cDNA libraries for RNA sequencing were established from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) for selecting poly-A mRNA followed by strand-specific library preparation using MGIEasy RNA Directional Library Prep Set V2.0 (MGI tech). The resulting double-stranded library fragments were further processed into single-stranded circular DNA (sscDNA), which is the final form of MGI library. The sscDNA libraries were quantified by Qubit ssDNA Assay Kit and used for generating DNA nanoballs (DNBs) by rolling circle replication reaction. DNBs were then loaded into a flow cell for sequencing on DNBSEQ-G400 platform (MGI tech), according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Data processing |
Single-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R
Genome_build: hg19
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| Submission date |
Nov 25, 2020 |
| Last update date |
Jun 10, 2021 |
| Contact name |
Yusuke Yamamoto |
| E-mail(s) |
yuyamamo@ncc.go.jp
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| Phone |
+81-335422511
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| Organization name |
National cancer center research institute
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| Lab |
Cellular signaling
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| Street address |
5-1-1, Tsukiji, Chuo-ku
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| City |
Chuo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
104-0045 |
| Country |
Japan |
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| Platform ID |
GPL28038 |
| Series (1) |
| GSE162154 |
RNA-seq of human small airawy epithelial cells in patients with COPD and Never-smoker |
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| Relations |
| BioSample |
SAMN16913213 |
| SRA |
SRX9582694 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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