|
| Status |
Public on Feb 07, 2024 |
| Title |
21_Ca_C2_12_II_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
IECs (C2BBe1)
|
| Organisms |
Candida albicans; Homo sapiens |
| Characteristics |
strain: SC5314
cell line: IECs (C2BBe1)
treatment: individual C.alb. and C2BBe1 samples combined for dual-RNAseq
time: 12 h
oxygen condition: normoxic
|
| Treatment protocol |
Differentiated intestinal epithelial cells (IECs) were infected with 2×10^6 Candida cells/well and incubated at 37°C and 5% CO2 in DMEM medium for 0.75, 3, 6, 12, or 24 h. In parallel, C2BBe1 and C. albicans cells were cultured individually in 6-well plates in DMEM medium. Prior to infection, individual C. albicans and C2BBe1 samples were harvested (0h).
|
| Growth protocol |
The intestinal epithelial Caco-2 brush border expressing 1 cell line (C2BBe1; ATCC, CRL2102) was cultivated and differentiated in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum , 10µg/ml Holotransferrin , and 1% non-essential amino acids at 37°C with 5% CO2 for 12 d in collagen-coated 6-well plates (5×10^5 cells/well). Candida albicans overnight cultures were cultured for 16 h in YPD broth (1% yeast extract, 2% peptone, 2% ᴅ-glucose) at 30°C with shaking at 180 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At each respective time point, the medium was removed, unadhered Candida cells were washed away, and 650 µl of RLT buffer (RNeasy Minikit; Qiagen) was added to each well. The plates were frozen with liquid nitrogen and thawed at room temperature (RT). Each well was scraped and the suspensions were centrifuged for 8 min (20,000×g) to pellet the Candida cells. The supernatant was removed and the host RNA was isolated using the RNeasy Minikit (Qiagen) according to the manufacturer’s instructions.
After poly(A) enrichment, mRNA was fragmented and random-primed cDNA synthesis was performed followed by adaptor ligation and adaptor-specific PCR amplification. Single sequence reads of 50 bp were produced.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Dual-RNAseq
CcCa_Calbicans_counts.xls
CcCa_Calbicans_counts_mrn.xls
CcC2_Hsapiens_counts.xls
CcC2_Hsapiens_counts_mrn.xls
|
| Data processing |
quality control using multiQC (v1.7)
quality trimming of raw data using trimmomatic (v0.36)
mapping using HiSat2 (v2.1.0)
read counts using featureCounts (v1.28.0)
Assembly: Homo sapiens: Ensembl_GRCh38; C_albicans_SC5314_version_A22
Supplementary files format and content: *counts.xls
|
| |
|
| Submission date |
Jul 17, 2023 |
| Last update date |
Feb 07, 2024 |
| Contact name |
Sascha Schäuble |
| E-mail(s) |
sascha.schaeuble@leibniz-hki.de
|
| Organization name |
Leibniz Institute for Natural Product Research and Infection Biology
|
| Street address |
Beutenbergstraße 11a
|
| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18448 |
| Series (1) |
| GSE237496 |
Candida albicans interaction with intestinal epithelial cells |
|
| Relations |
| BioSample |
SAMN36503626 |
| SRA |
SRX21049011 |
