|
| Status |
Public on Feb 02, 2024 |
| Title |
tIMEC_RNA_1 |
| Sample type |
SRA |
| |
|
| Source name |
tIMEC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: tIMEC
cell type: mammary epthelial cell-derived cell line
genotype: WT
treatment: none
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Cells were seeded at maintenance density four days before collection. Three biological replicates per condition were collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were directly lysed on plates, and tissue collected from primary lung tumours (PT) was lysed with TRIzol (Thermo Fisher cat. #15596026), and total RNAs were extracted according to the manufacturer’s instructions. ontaminating genomic DNA was removed by DNase (Qiagen cat. #79254) digestion. RNA quality and concentration were assessed using the 2100 Bioanalyzer (Agilent cat. #G2939BA) and the Qubit fluorometer (Thermo Fisher cat. #Q33226), respectively.
RNA-seq libraries were prepared by using the TruSeq® Stranded Total RNA (Illumina #20020596) supplemented with Illumina Ribo-Zero plus rRNA Depletion Kit (Illumina #20037135) starting from 500 ng of total RNA.Libraries were sequenced on an Illumina HiSeq 2500 with SE 50 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Quality of the reads was checked using FastQC and trimmed using Trimmomatic v0.39
Reads were aligned to the human genome hg19 using Tophat2
Further analysis was performed using HOMER. Tag Directories were created for each of the three replicates per cell type and genes were annotated using analyzeRepeats.pl rna hg19 –rpkm
For differential expression analysis, analyzeRepeats.pl rna hg19 –raw was run to get the raw counts needed as an input for edgeR. Differential expression analyses were undertaken using the edgeR v3.20.9 and limma v3.34.9 software packages
Lowly expressed genes were filtered with the filterByExpr function from edgeR. Compositional differences between libraries were normalized using the trimmed mean of log expression ratios method (TMM), counts were transformed to log2-CPM and differential expression was assessed
Assembly: hg19
Supplementary files format and content: table containing normalized gene expression values for differential analysis
Supplementary files format and content: table containing rpkm-normalized gene expression values used as input for IMAGE
|
| |
|
| Submission date |
Aug 19, 2022 |
| Last update date |
Feb 02, 2024 |
| Contact name |
CIBIO Zippo |
| E-mail(s) |
alessio.zippo@unitn.it
|
| Organization name |
University of Trento
|
| Department |
Cellular, Computation and Integrative Biology (CIBIO)
|
| Lab |
Chromatin Biology & Epigenetics
|
| Street address |
via sommarive 9
|
| City |
Trento |
| State/province |
Not Applicable |
| ZIP/Postal code |
38123 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE211608 |
Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting a transcriptional memory [total RNA-seq] |
| GSE211610 |
Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting a transcriptional memory |
|
| Relations |
| BioSample |
SAMN30409844 |
| SRA |
SRX17147588 |
