|
| Status |
Public on Jul 06, 2023 |
| Title |
HBEC3 cells, RKO3, batch2 |
| Sample type |
SRA |
| |
|
| Source name |
HBEC3-KT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HBEC3-KT
cell type: Human Bronchial cells
genotype: RYBP knockout
|
| Growth protocol |
keratinocyte SFM medium , Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with PureLink RNA Mini Kit (Invitrogen).
Total RNA integrity was verified with an Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified with a NanoDrop 8000 instrument (Thermo Fisher). RNA-seq libraries were prepared from total RNA with the KAPA RNA HyperPrep kit with RiboErase (KAPA Biosystems)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing was performed with an Illumina NextSeq 500 machine and 75 bp paired-end runs were performed.
paired-end RNAseq reads were trimmed using TrimGalore with defaut parameters.
Trimmed reads were aligned to the mouse genome mm9 with STAR (v2.5.1) , and gene count were performed using a STAR (v2.5.1)
The limma (v3.38.2) statistical package19 was used to call the differential expressed gene. Statistical significance for differentially expressed genes was q<0.05 with FC > 2.
Assembly: hg19
Supplementary files format and content: bigWig, counts coverage
|
| |
|
| Submission date |
Jul 20, 2022 |
| Last update date |
Jul 06, 2023 |
| Contact name |
Gerd Pfeifer |
| E-mail(s) |
gerd.pfeifer@vai.org
|
| Organization name |
Van Andel Research Institute
|
| Street address |
333 Bostwick Ave. NE
|
| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE208686 |
Dysfunction of 5-methylcytosine oxidases and the Polycomb protein RYBP leads to widespread DNA hypermethylation and cell transformation [RNA-seq] |
| GSE208689 |
Dysfunction of 5-methylcytosine oxidases and the Polycomb protein RYBP leads to widespread DNA hypermethylation and cell transformation |
|
| Relations |
| BioSample |
SAMN29855237 |
| SRA |
SRX16367649 |
