|
| Status |
Public on Jun 11, 2024 |
| Title |
KO_USP44_RNA_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
MEF
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MEF
cell type: mouse embryonic fibroblasts
genotype: USP44 Rescue
|
| Growth protocol |
MEFs were derived from mixed 129xC57BL/6-strain of ES cells that were immortalized with SV40 large T antigen. USP44 null cells were generated from exon 1 removal. Lentiviral transduction with USP44 cDNA was used to generate resuce cell line. Cells were cultured in DMEM with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from MEF cells was isolated using QIAzol reagent and processed with RNeasy Plus Mini Kit (Qiagen).
mRNA-seq libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
All steps were performed with default settings unless otherwise denoted
Sequence reads were trimmed with fastx_trimmer (fastx/0.0.14)
Trimmed sequence reads were mapped to mm10 using star/2.7.9a
Read count extraction was performed using htseq/0.9.1 reverse strand option
Assembly: mm10
Supplementary files format and content: tab-deliminted text files include htseq-count values for each sample
|
| |
|
| Submission date |
Mar 24, 2023 |
| Last update date |
Jun 11, 2024 |
| Contact name |
Steven A Johnsen |
| E-mail(s) |
Steven.Johnsen@bosch-health-campus.com
|
| Organization name |
Robert Bosch Center for Tumor Diseases
|
| Street address |
Auerbachstrasse 112
|
| City |
Stuttgart |
| ZIP/Postal code |
70376 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE228130 |
USP44 overexpression drives a MYC-like gene expression program in neuroblastoma through epigenetic reprogramming |
| GSE228132 |
USP44 overexpression drives a MYC-like gene expression program in neuroblastoma through epigenetic reprogramming |
|
| Relations |
| BioSample |
SAMN33902972 |
| SRA |
SRX19765390 |
