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Sample GSM7084205

Query DataSets for GSM7084205

Status

Public on Mar 14, 2023

Title

S39W

Sample type

SRA

Source name

F13514_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