|
| Status |
Public on Jun 26, 2018 |
| Title |
MRE_KO2_1 |
| Sample type |
SRA |
| |
|
| Source name |
3T9 FIBROBLAST
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: miR-30_MRE_deleted_clone2
cell line: 3T9
cell type: fibroblast
|
| Growth protocol |
cells were grown in complete medium (10% FBS)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA, including small species, was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
small RNA sequecing Illumina
|
| 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
Raw counts were finally normalized using CPM (copies-per-million)
Genome_build: mm9
Supplementary_files_format_and_content: Excel Spreadsheet containing the raw counts of miRNA, including miRNA isoforms
|
| |
|
| Submission date |
Oct 04, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL13112 |
| Series (2) |
| GSE104598 |
Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism [miRNA-Seq] |
| GSE104650 |
Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism |
|
| Relations |
| BioSample |
SAMN07737771 |
| SRA |
SRX3243595 |
