|
| Status |
Public on Oct 13, 2017 |
| Title |
69F,MAB at MOI of 1000:1,at 1 day after infection |
| Sample type |
SRA |
| |
|
| Source name |
normal primary human bronchial epithelial (NHBE) cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: differentiated respiratory epithelial cells
age: 69 years old
gender: Female
|
| Treatment protocol |
The mycobacteria were added to the Transwell at MOI of either 100 or 1000, reflecting 5x10^6 or 5x10^7 mycobacteria in PBS respectively, in a total volume of 100 μL.
|
| Growth protocol |
After expansion of NHBE cells (Lonza, Walkersville, MD) in T-75 flasks, cells were detached using trypsin and seeded at a density of 5X104 cells per well on a Transwell insert (6.5-mm diameter, 0.4-μm pore size, Costar Transwell) coated with type I rat tail collagen (Sigma), and then cultured in Lonza ALI differentiation medium (LONZA, Walkersville, MD). After their surfaces were exposed to air for at least 3 weeks (ALI phase), the differentiated epithelium was infected with either MAC or MAB.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Infected and uninfected control respiratory epithelial cells were washed 3 times with PBS and total RNA was extracted using RNeasy Mini kit and treated with DNase I. Illumina TruSeq Stranded mRNA Sample Preparation Kit with 750ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Truseq Stranded mRNA LT kit)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
sample demultiplexing: bcl2fastq 2.17.1.14
pseudo-alignment and quantification: salmon0.6.1, extra flags: --useVBOpt --biasCorrect
Differential expression analysis: R 3.3.2, DEseq2 1.12.3, tximport 1.0.3
Genome_build: Ensembl Hg38
Supplementary_files_format_and_content: salmon quantification output, tab delimited file
Supplementary_files_format_and_content: DESeq2 results, comma seperated values
|
| |
|
| Submission date |
Jan 11, 2017 |
| Last update date |
Sep 05, 2023 |
| Contact name |
Andrew Martins |
| E-mail(s) |
andrew.martins@yale.edu
|
| Organization name |
Yale School of Medicine
|
| Department |
Immunobiology
|
| Street address |
100 College Street Rm 1155
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE93526 |
Gene signature profiles in respiratory epithelium infected with nontuberculous mycobacteria |
|
| Relations |
| BioSample |
SAMN06218178 |
| SRA |
SRX2485381 |
