|
| Status |
Public on Jun 03, 2024 |
| Title |
Scramble-2 |
| Sample type |
SRA |
| |
|
| Source name |
Cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cell line
cell line: GT1-7
cell type: Mouse hypothalamic GnRH neuronal cells
genotype: Scramble control
treatment: Scramble
|
| Treatment protocol |
GT1-7 cells were transfected with Klf4 siRNA or siRNA scramble in Opti-MEM I and lipofectamine 2000 for 24 hours, vehicle cells were serum starved for 6 hours prior to treatment and then placed in Ca2+ free DMEM with 1% penicillin strepomycin for 1 hour prior to collection
|
| Growth protocol |
GT1-7 hypothamic neuronal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin streptomycin with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol and chloroform extraction, aqueous phase saved and RNA precipitated into a pellet with sodium acetate, glycogen, and ispropanol
RNA libraries were prepared using Takara SMART-Seq Ultra Low Input v4
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
MAP-RSeq.v3.0
Pipeline included STAR.V2.5.2b, STAR-Fusion, featurCounts(Subread)v1.5.1, FastQC, RSeQC.v3.0.0
Downstream analyses included several R packages: EdgeR and WGCNA
Applied two different methods in EdgeR for Differential Expression Analysis (Pairwise and GLM).
Assembly: mm10
Supplementary files format and content: xlsx files contain RPKM values for each sample
|
| |
|
| Submission date |
Feb 07, 2023 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Justin L Grobe |
| E-mail(s) |
jgrobe@mcw.edu
|
| Organization name |
Medical College of Wisconsin
|
| Street address |
8701 W Watertown Plank Road
|
| City |
Milwaukee |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE224716 |
Effects of Klf4 knockdown in GT1-7 cells |
|
| Relations |
| BioSample |
SAMN33187989 |
| SRA |
SRX19302707 |
