|
| Status |
Public on Jun 26, 2018 |
| Title |
MRE_KO2_3T9_sample1 |
| Sample type |
SRA |
| |
|
| Source name |
3T9 FIBROBLAST
|
| Organism |
Mus musculus |
| Characteristics |
"serpine1_3utr": miR-30_MRE_deleted_clone2
tissue: 3T9 FIBROBLAST
|
| Growth protocol |
cells were grown in complete medium (10% FBS)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare RNA libraries following the Illumina TruSeq Library Preparation Kit instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA sequencing Illumina
|
| Data processing |
FASTQ data of the total RNA sequencing experiment were aligned using TopHat 2.0.6 with default parameters
Differentially expressed genes (DEGs) were identified using the Bioconductor package DESeq2 based on read counts, considering genes whose q value relative to the control is lower than 0.05 and whose maximum expression is higher than RPKM of 1
Genome_build: mm9
Supplementary_files_format_and_content: Excel Spreadsheet containing FPKM counts each gene and the output of the analysis with DESeq2 package to identify regulated genes
|
| |
|
| Submission date |
Oct 05, 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) |
| GSE104648 |
Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism [RNA-Seq] |
| GSE104650 |
Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism |
|
| Relations |
| BioSample |
SAMN07741497 |
| SRA |
SRX3245643 |
