|
| Status |
Public on Aug 04, 2022 |
| Title |
shDKC1 total RNA replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
transfection: siRNAs targeting DKC1
genotype: DKC1 silencing
|
| Treatment protocol |
Cells were transfected with siRNAs targeting DKC1 (Invitrogen, catalog number HSS102781: 5’-AACACCUGGAAGCAUAAUCUUGGCC-3’, HSS102782: 5’-UAAACAACCAGUCACCUUGGGAUCC-3’, HSS102785: 5’-GAAGUCACAACAGAGUGCAGGCAAA-3’) and an appropriate control (Cat. N° 12935300 - Invitrogen xy) using Lipofectamine RNAiMAX reagent (Invitrogen) in OptiMEM medium (Invitrogen) according to the manufacturer’s instructions
|
| Growth protocol |
MCF-7 (female, estrogen-positive invasive breast ductal carcinoma derived) cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin, 1 mg/ml streptomycin, and 2 mM L-glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Polysomal separation was performed as follows: samples were loaded in 10-50% linear sucrose gradients, ultra-centrifuged and fractionated with an automated fraction collector. All the fractions containing subpolysomal or polysomal RNA were identified and pooled in two separate tubes. RNA was purified by extraction with 1 volume of phenol-chloroform and precipitated with isopropanol.
RNA libraries were prepared for sequencing using standard Illumina protocols: Illumina TruSeq RNA Sample Prep Kit was used with 1.5 ug of total RNA as input.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rawcounts_genes.tsv
rawcounts_transcripts.tsv
|
| Data processing |
Illumina Casava 1.8 software was used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence and low-quality nucleotides, then quantified against the Gencode v28 transcriptome using STAR (genes) and Salmon(transcripts) with default parameters
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample
|
| |
|
| Submission date |
Nov 13, 2020 |
| Last update date |
Aug 04, 2022 |
| Contact name |
Erik Dassi |
| E-mail(s) |
erik.dassi@unitn.it
|
| Organization name |
University of Trento
|
| Department |
CIBIO
|
| Street address |
Via Sommarive, 9
|
| City |
Trento |
| State/province |
TN |
| ZIP/Postal code |
38123 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE161480 |
The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence [RNA-seq] |
| GSE161481 |
The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence |
|
| Relations |
| BioSample |
SAMN16794959 |
| SRA |
SRX9507763 |
