|
| Status |
Public on Jul 10, 2020 |
| Title |
Treated48_2 |
| Sample type |
SRA |
| |
|
| Source name |
Choroid Plexus Epithelia
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary choroid plexus epithelial cells
treatment: B. burgdorferi infected - 48 hours
|
| Treatment protocol |
Cell cultures were grown to approximately 80% confluency, washed, and medium replaced. B. burgdorferi was added to each flask at a 10:1 multiplicity of infection (10 bacteria: 1 cell) for 48 hours.
|
| Growth protocol |
Primary human choroid plexus epithelial cells were obtained from ScienCell (Catalog #1310). Cells were maintained in tissue-treated T-75 flasks in epithelial cell medium (ScienCell, catalog #4101), supplemented with 2% FBS and EpiCGS (ScienCell, catalog #4125).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell cultures were thoroughly washed, and RNA was harvested by phenol-chloroform extraction via Trizol. The Rneasy Mini kit from Qiagen (catalog #74106) was used for isolation following manufacterer's instructions.
RNA libraries were prepared using the NEBNext Ultra II RNA-seq library kit (catalog #7775S) for Illumina sequencing following manufacterer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw data was provided in Fastq format
Reads were trimmed for adaptor and poor quality using Trimmomatic and quality assessed by FASTQC before and after trimming.
Reads were aligned to the human (hg19) assembly using Hisat2 version 2.1.0 and indexed by Samtools version 1.9
Differential gene expression was performed using DESeq2 version 1.24.0. Differential genes were considered statistically significant if FDR < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files. A single file that includes counts, FDR values, fold change, and gene annotation for all samples. Individual files for each sample that contain counts and annotations.
|
| |
|
| Submission date |
Jun 25, 2020 |
| Last update date |
Jul 11, 2020 |
| Contact name |
Derick Thompson |
| E-mail(s) |
[email protected]
|
| Organization name |
University of North Dakota
|
| Department |
Biomedical Sciences
|
| Street address |
504 Hamline Street
|
| City |
Grand Forks |
| State/province |
ND |
| ZIP/Postal code |
58203 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE153261 |
The Lyme disease bacterium, Borrelia burgdorferi, stimulates an inflammatory response in human choroid plexus epithelial cells |
|
| Relations |
| BioSample |
SAMN15369434 |
| SRA |
SRX8617532 |
