|
| Status |
Public on Jun 27, 2019 |
| Title |
5’Tag-seq Mut_3 |
| Sample type |
SRA |
| |
|
| Source name |
Lung alveolar epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: LNGFR positive alveolar epithelial cells
tissue: lung
transfection: mutant surfactant protein C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cultured alveolar epithelial cells were first stained with APC conjucated anti-human LNGFR antibody. Cells were next stained with anti-APC microbeads (Miltenyi). Labeled cells were magnetically sorted twice.
Whole transcript amplification for cultured alveolar epithelial type II cells was performed using 5’Tag-seq method according to a previous report with modifications (Shichino et al., 2019). 5’ regions of amplified cDNA were enriched using NEBNext UltraII FS library prep kit (New England Biolabs) according to the manufacturer’s protocol except using CS1 adapter, trP1 primer, and IonA-BC[N]-CS1-primer for adding sequencing adapters and barcodes. Library concentration was quantified by using the KAPA Library Quantification Kit for Ion Torrent (KAPA Biosystems) according to the manufacture’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
| |
|
| Data processing |
Adapter trimming and quality filtering of fastq files were performed by using Cutadapt-v1.18. Trimmed reads were mapped to the Refseq hg38 RNA by using Bowtie2-2.2.5 with the following parameters: -t -p 16 -N 1 -D 200 -R 20 -L 20 -i S,1,0.50 --nofw.
Total tag number was normalized using R-3.4.0 and TCC package.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw tag-count values for each sample
|
| |
|
| Submission date |
Mar 14, 2019 |
| Last update date |
Jun 29, 2019 |
| Contact name |
Kazushige Shiraishi |
| Organization name |
Tokyo University of Science
|
| Street address |
Yamasaki 2669
|
| City |
Noda, Chiba |
| ZIP/Postal code |
278-0022 |
| Country |
Japan |
| |
|
| Platform ID |
GPL23934 |
| Series (1) |
| GSE128291 |
Transcriptome analysis of cultured human alveolar epithelial type 2 cells |
|
| Relations |
| BioSample |
SAMN11125810 |
| SRA |
SRX5521483 |
