|
Status |
Public on Dec 20, 2023 |
Title |
Virus 24hpi 18, cells infected with bovine coronavirus [V18A] |
Sample type |
SRA |
|
|
Source name |
Virus 24hpi 18, cells infected with bovine coronavirus
|
Organism |
Homo sapiens |
Characteristics |
cell line: HCT-8 treatment: Infected with Bovine coronavirus sample/time point: Virus 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 |
SAMN32881888 |
SRA |
SRX19144954 |