|
| Status |
Public on May 03, 2024 |
| Title |
01_FEB |
| Sample type |
SRA |
| |
|
| Source name |
Brain microvascular endothelium
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain microvascular endothelium
cell line: HBEC-5i (ATCC CRL-3245)
cell type: cell line
treatment: Control-40C
|
| Treatment protocol |
Co-incubation of iRBCs was performed for 7 h in T-25 flasks at either 37°C or 40°C (iRBC-IT4var04-37C or iRBC-IT4var04-40C). HBEC-5i cells cultured at 37°C or 40°C +/- niRBCs (hematocrit 1%) served as controls (Control-37C or niRBCs-37C or Control-40C)
|
| Growth protocol |
The HBEC-5i cell line (ATCC CRL-3245) was cultured in DMEM/F12 medium supplemented with L-glutamine and sodium bicarbonate (2.438 g/l) at 37°C in 5% CO2. . falciparum isolate IT4 (FCR3S1.2) was cultured in human 0+ erythrocytes at a hematocrit of 5% in 154 the presence of 10% human A+ serum according to standard procedures (Trager and Jensen, 2005). 155 Parasites were synchronized once a week with 5% sorbitol (Lambros and Vanderberg, 1979).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were collected in TRIzol (Thermo Fisher Scientific) and isoated using the PureLink RNA Mini Kit (Thermo Fisher Scientific). Removal of possible contamination with gDNA with TURBO DNA-free 194 kit (Fisher Scientific, Thermo Fisher).
Library preparation and subsequent RNA sequencing was performed on an Illumina HiSeq 4000 PE100 platform from BGI (BGI Group).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The RNAseq data were mapped to the human reference genome (GRCh38.109) using CLC Genomics 202 Workbench 21.0 (QIAGEN)
Assembly: GRCh38.109
Supplementary files format and content: ExpressionBroweser as MS-excel file contains gene and transcript expression level counts, normalized expression counts and statistics and differential gene expression between multiple treatment variables.
|
| |
|
| Submission date |
May 01, 2024 |
| Last update date |
May 03, 2024 |
| Contact name |
Johannes Allweier |
| E-mail(s) |
johannes.allweier@bnitm.de
|
| Organization name |
Bernhard Nocht Institute for Tropical Medicine
|
| Street address |
Bernhard-Nocht-Straße 74
|
| City |
Hamburg |
| ZIP/Postal code |
20359 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE266399 |
Cytoadhesion of Plasmodium falciparum-infected red blood cells changes the expression of cytokine-, histone- and antiviral protein-encoding genes in brain endothelial cells |
|
| Relations |
| BioSample |
SAMN41153729 |
| SRA |
SRX24427244 |
