|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Mar 14, 2023 |
Title |
S34C |
Sample type |
SRA |
|
|
Source name |
F10411_ALI_day_28
|
Organism |
Papio anubis |
Characteristics |
cell tyep: tracheal epithelial cells
|
Treatment protocol |
No treatments to report. The cells were harvested at ALI day 28.
|
Growth protocol |
Primary fetal baboon tracheal epithelial cells (FBTECs) were cultured on air-liquid interface (ALI) to generate a pseudostratified mucociliary epithelium . Briefly, 1 x 105 cells in 100 µl of BronchiaLifeTM epithelial airway medium (BLEAM) (Cat# LL-0023, Lifeline® Cell Technology, Oceanside, CA, USA) were seeded in the apical chamber of a 0.4 µm pore-sized Transwell® insert (Cat# 3470, Corning®, Corning, NY, USA) pre-coated with human type IV collagen (Cat# C7521, Sigma Aldrich, St. Louis, MO, USA) with 1 ml of BLEAM in the basolateral chamber (ALI day -2). The following day, fresh BLEAM media was replaced in the apical and basolateral chambers (100 µl and 1 ml, respectively). Following two days of submerged culture, media from the apical chamber was removed to expose the cells to air (ALI day 0), and 1 ml of HBTEC ALI differentiation medium (Cat# LM-0050, Lifeline® Cell Technology) supplemented with Penicillin (100 I.U./ml) - Streptomycin (100 µg/ml) was added to the basolateral chamber. The media was replaced every other day and the cells allowed to differentiate for up to 28 days.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted via direct lysis of cells in the ALI well using the PureLinkTM RNA mini kit (Cat# 12183018A, Thermo Scientific, Waltham, MA, USA) and included DNase treatment (Cat# 12185-010, Thermo Scientific) on the column to remove contaminating genomic DNA. RNA concentrations were measured with a NanoPhotometer® N60 (Implen, Westlake Village, CA, USA) RNA-sequencing was performed on a NextSeq 2000 P2 Flowcell, (Illumina, San Diego, CA, USA) following library preparation using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria). The library preparation and sequencing were performed by the Genomics Core at the University of Oklahoma Health Sciences Center (OUHSC)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 2000 |
|
|
Data processing |
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC. Reads were aligned to the Olive baboon (Papio anubis) genome Panu_3.0 (Ensembl release 104) using STAR and per transcript reads were counted with featureCounts/Subread v2.0.4. Differentiall expression analyses was performed using edgeR package in the context of limma/voom workflow Assembly: Panu_3.0 Supplementary files format and content: tab-delimited text file includes ENSEMBL id and raw read counts for each transcript, in each sample
|
|
|
Submission date |
Mar 07, 2023 |
Last update date |
Mar 14, 2023 |
Contact name |
Jonathan Daniel Wren |
E-mail(s) |
jdwren@gmail.com
|
Phone |
4052716989
|
Organization name |
OMRF
|
Department |
GHD
|
Lab |
MC103
|
Street address |
825 NE 13th St
|
City |
Oklahoma City |
State/province |
OK |
ZIP/Postal code |
73105 |
Country |
USA |
|
|
Platform ID |
GPL33218 |
Series (1) |
GSE226820 |
The Isolation and In vitro Differentiation of Primary Fetal Baboon Tracheal Epithelial Cells for the Study of SARS-CoV-2 Host-Virus Interactions |
|
Relations |
BioSample |
SAMN33611752 |
SRA |
SRX19585125 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|