|
| Status |
Public on Dec 01, 2023 |
| Title |
BER-DSRCT, Sphere Culture, Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
BER-DSRCT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BER-DSRCT
genotype: WT
treatment: Sphere
|
| Treatment protocol |
N/A
|
| Growth protocol |
Cells were grown for 4 days in sphere or adherent culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were prepared with RNeasy Plus kit (Qiagen, Hilden, Germany)
libraries were created from 500ng of total RNA using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero (San Diego, CA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BER_Sphere_vs_Adherent_rsem_DGE_results.xlsx
|
| Data processing |
Gene counts were generated by alignment to human transcriptome GRCh38 using STAR in RSEM.
Differential gene expression analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: Excel file of differential gene expression analysis from DESeq2 within each cell line including base expression, log2FC, and FDR
|
| |
|
| Submission date |
Nov 27, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Sean Bong Lee |
| E-mail(s) |
slee30@tulane.edu
|
| Organization name |
Tulane University School of Medicine
|
| Department |
Pathology
|
| Lab |
Lee Lab
|
| Street address |
1700 Tulane Ave
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE248761 |
Transcriptomic Analysis Identifies B-Lymphocyte Kinase as a Therapeutic Target for Desmoplastic Small Round Cell Tumor Cancer Stem Cell-Like Cells [RNA-seq] |
| GSE248857 |
Transcriptomic Analysis Identifies B-Lymphocyte Kinase as a Therapeutic Target for Desmoplastic Small Round Cell Tumor Cancer Stem Cell-Like Cells |
|
| Relations |
| BioSample |
SAMN38454002 |
| SRA |
SRX22655649 |
