|
| Status |
Public on Dec 10, 2021 |
| Title |
Epcam_hi_LPS_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bronchiolar epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 6 to 12 weeks
Sex: Male
tissue: Lung
cell type: bronchiolar epithelial
|
| Treatment protocol |
LPS inhalation (5ml of 2mg/ml). The primary lung ECs were freshly isolated using Liberase and DNase-I digestion. The cells were sorted directly into Trizol (Ambion, #15596018)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from polyA-enriched mRNA using the KAPA Stranded mRNA-Seq Kit and were further amplified for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
KAPA RNA Stranded PolyA
|
| Data processing |
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Ensembl version 98
Expression values were also computed using RSEM version 1.2.28 based on Ensembl version 98 transcript annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)
|
| |
|
| Submission date |
Jun 06, 2021 |
| Last update date |
Dec 10, 2021 |
| Contact name |
Claude Perreault |
| E-mail(s) |
claude.perreault@umontreal.ca
|
| Organization name |
Institute for Research in Immunology and Cancer
|
| Street address |
2950, Chemin de Polytechnique
|
| City |
Montréal |
| State/province |
Québec |
| ZIP/Postal code |
H3C 3J7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE176228 |
Transcriptomic analysis of lung epithelial cells after LPS inhalation |
|
| Relations |
| BioSample |
SAMN19587829 |
| SRA |
SRX11078050 |
