|
| Status |
Public on Apr 23, 2024 |
| Title |
GBS_BEC_I_R1_total_RNA |
| Sample type |
SRA |
| |
|
| Source name |
Brain-like endothelial cells generated from induced pluripotent stem cells (iPSC-BECs) AND Group B Streptococcus (GBS)
|
| Organisms |
Streptococcus sp. 'group B'; Homo sapiens |
| Characteristics |
disease state: infected
|
| Treatment protocol |
iPSC-BECs were differentiated and infected with GBS at an MOI of 10 for 5 hours
|
| Growth protocol |
Human: Growth of hCMEC/D3 cell line: hCMEC/D3 cells were maintained on tissue culture flasks coated with 1% rat tail collagen in EndoGRO MV medium (Millipore-Sigma). Cells were split onto 24-well tissue culture plastic dishes for experiments and allowed to grow to confluency (4 days) before infection experiments were conducted. Streptococcus: Wild-type GBS strains were cultivated in Todd-Hewitt broth (THB) at 37C in static culture/
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using the MirVana RNA (Thermo Scientific) isolation kit
Sequencing was performed on a NextSeq500 platform (Illumina) in single-end mode for 75 cycles
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
GBS infecting IPSC-BECs replicate 1
|
| Data processing |
Adapter filtering: Illumina’s TruSeq “Read 1” adapter sequence using cutadapt version: 1.15
Trimming of reads with a Phred score below 20 using cutadapt version 1.15
Poly(A) clipping reads using READemption 0.4.3
Discarding of reads with a length below 20 using READemption version 0.4.3
Aligning of reads to both genomes using segemehl version 0.2.0
Gene quantification using READemption version 0.4.3
Differential gene expression analysis using DESeq2 version: 1.18.1, R version: 3.4.4
Genome_build: Human: GENCODE version: 26, NCBI assembly name: GRCh38.p10 / Streptococcus: accession number: HG939456.1, Genbank assembly accession number: GCA_000689235.1
Supplementary_files_format_and_content: csv files containing DESeq2 results
|
| |
|
| Submission date |
Feb 25, 2022 |
| Last update date |
Apr 23, 2024 |
| Contact name |
Till David Sauerwein |
| Organization name |
ZB MED - Information Centre for Life Sciences
|
| Department |
Data Science and Services
|
| Street address |
Gleueler Str. 60
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL31999 |
| Series (1) |
| GSE197489 |
Group B Streptococcal transcriptome when interacting with brain endothelial cells |
|
| Relations |
| BioSample |
SAMN26264349 |
| SRA |
SRX14295141 |
