|
Status |
Public on Jun 11, 2024 |
Title |
WT_RNA_Rep1 |
Sample type |
SRA |
|
|
Source name |
MEF
|
Organism |
Mus musculus |
Characteristics |
cell line: MEF cell type: mouse embryonic fibroblasts genotype: WT
|
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 |
SAMN33902980 |
SRA |
SRX19765382 |