|
| Status |
Public on Dec 20, 2023 |
| Title |
Cells 24hpi 1, uninfected cells [C-1A] |
| Sample type |
SRA |
| |
|
| Source name |
Cells 24hpi 1, uninfected cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT-8
treatment: Uninfected
sample/time point: Cells 24hpi
|
| Treatment protocol |
Infection with bovine coronavirus, cryptosporidium parvum or both. Uninfected controls
|
| Growth protocol |
HCT-8 cells were grown in RPMI 1640 plus 10% FBS and split twice a week
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN RNAeasy plus
Strand specific TruSeq mRNA-seq library prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
low quality read trimming - Trimmomatic V 0.36
rRNA removal - sortmerna V 1.7
sequence alignment - TopHat V 2.1.1
transcriptome assembly - Cufflinks V 2.1.1
expression normalization - Cufflinks V 2.1.1
differential expression - Cufflinks V 2.1.1
Assembly: GRCh37
|
| |
|
| Submission date |
Jan 23, 2023 |
| Last update date |
Dec 20, 2023 |
| Contact name |
Alejandro Jimenez Melendez |
| E-mail(s) |
alejandro.jimenez.melendez@nmbu.no
|
| Organization name |
NMBU
|
| Department |
PARAFAG
|
| Lab |
Parasitology
|
| Street address |
Elizabeth Stephansens vei 15
|
| City |
Ås |
| ZIP/Postal code |
1430 |
| Country |
Norway |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE223548 |
RNA-Seq analysis of HCT-8 cells infected with BCoV and/or Cparvum |
|
| Relations |
| BioSample |
SAMN32881905 |
| SRA |
SRX19144937 |
