|
| Status |
Public on Jul 31, 2023 |
| Title |
DKO Fast #3 |
| Sample type |
SRA |
| |
|
| Source name |
INS-1E_TFEB/TFE3 DKO_Fast
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: INS-1E
cell type: rat insulinoma derived cell line
genotype/variation: TFEB/TFE3 DKO
treatment: Fasting conditions (Fast)
|
| Treatment protocol |
Cells were plated on 12-well plates and treated with full medium (GC) or Minimum Essential Medium (Fast) for 16h (overnight)
|
| Growth protocol |
Cells were grown in 10cm dishes using RPMI 1640; 10%FBS; 10mM Hepes; 1mM PyrNa; 2mM Glutamine; 0,05 mM beta-mercaptoethanol, PenStrep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific). For RNA-seq analysis, library preparation was performed with a total of 100ng of RNA from each sample using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen) according to manufacturer's instructions. Amplified fragmented cDNA of 300bp in size was sequenced in single-end mode by NovaSeq 6000 (Illumina) with a read length of 100bp
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the Novaseq6000 (Illumina) with a read length of 100 bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
S257_20190409115059_15
DKO_Fast_3_unique
Transcriptome profile of knockout, Fast biological rep3
|
| Data processing |
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq. Sequence reads were trimmed BBDuk (sourceforge.net/projects/bbmap/) to remove adapter sequences and low-quality end bases (Q < 20). Alignment was performed with STAR 2.6.0a(1) on the Hg38 reference provided by UCSC Genome Browser (2). Alignment to mm10, and rn6 reference genome assembly (1), and counting by gene (3) using Ensembl assembly (release 93). Gene expression levels were determined with HTseq-count 0.9.1(3). Differential expression analyses were performed using edgeR (4) a statistical package based on generalized linear models, suitable for multifactorial experiments. The threshold for statistical significance chosen was False Discovery Rate (FDR)<0,05.
|
| |
|
| Submission date |
Jul 02, 2020 |
| Last update date |
Jul 31, 2023 |
| Contact name |
Rossella De Cegli |
| E-mail(s) |
decegli@tigem.it
|
| Phone |
08119230692
|
| Organization name |
Tigem
|
| Street address |
Via Campi Flegrei 34
|
| City |
Pozzuoli |
| ZIP/Postal code |
80078 |
| Country |
Italy |
| |
|
| Platform ID |
GPL25947 |
| Series (2) |
| GSE153709 |
Transcriptome profile of INS-1E Ctrl and DKO cells |
| GSE154063 |
Transcriptome profile of ENDOC-BH1 cells and isolated murine islets modulating TFEB expression |
|
| Relations |
| BioSample |
SAMN15425263 |
| SRA |
SRX8657102 |
