|
| Status |
Public on Jul 08, 2024 |
| Title |
7_SS111 |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Retina
cell line: hTERT RPE1
cell type: epithelial cell
genotype: +chr 8; +chr 9; +chr18
|
| Growth protocol |
Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the miRNeasy mini kit (Qiagen).
Small RNA sequencing libraries were constructed using the TruSeq Small RNA Library Prep Kit (Illumina) according to manufacturer protocol.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
7_SS111
|
| Data processing |
FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Assembly: custom genome, containing all human microRNAs (canonical and Isoforms)
Supplementary files format and content: raw_counts.txt: raw reads for all miRNAs in all samples
|
| |
|
| Submission date |
Nov 08, 2023 |
| Last update date |
Jul 08, 2024 |
| Contact name |
Francesco Nicassio |
| E-mail(s) |
francesco.nicassio@iit.it
|
| Organization name |
Istituto Italiano di Tecnologia
|
| Department |
Center for genomic science
|
| Street address |
Via Adamello 16
|
| City |
Milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE247267 |
Increased RNA and protein degradation is required for counteracting transcriptional burden and proteotoxic stress in human aneuploid cells |
|
| Relations |
| BioSample |
SAMN38155318 |
| SRA |
SRX22416412 |
