|
| Status |
Public on Jun 26, 2018 |
| Title |
MRE_KO2_3T9_12h |
| Sample type |
SRA |
| |
|
| Source name |
3T9 fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
"serpine1_3utr": miR-30_MRE_deleted_clone2
cell line: 3T9 fibroblast
time: 12h
treatment: Serum-Stimulated MRE-KO2 cells at 12 hours
|
| Growth protocol |
cells were kept in absence of serum for 72 hours to induce quiescence (0h samples). Then, cells were stimulated with serum at collected at different time-points (8hrs and 12hrs)
|
| 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 NovaSeq 6000 |
| |
|
| Description |
GEO_fghini_3T9_serum_RNAseq_TPM.xls
|
| Data processing |
FASTQ data of the total RNA sequencing experiment were aligned using TopHat 2.0.6 with default parameters
Read Counts were obtained for each gene using FeatureCounts
Raw Read Counts were normalized to TPM (transcript per million)
Genome_build: mm9
Supplementary_files_format_and_content: Excel Spreadsheet containing TPM for each gene
|
| |
|
| Submission date |
Apr 01, 2018 |
| Last update date |
Jun 26, 2018 |
| Contact name |
Francesco Nicassio |
| E-mail(s) |
[email protected]
|
| 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 |
GPL24247 |
| Series (2) |
| GSE104650 |
Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism |
| GSE112578 |
Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism [RNA-Seq_2] |
|
| Relations |
| BioSample |
SAMN08828584 |
| SRA |
SRX3870959 |
