|
| Status |
Public on Jun 26, 2018 |
| Title |
SCA+-1 |
| Sample type |
SRA |
| |
|
| Source name |
FACS sorted Stem Cell antigen-1 (Sca-1) positive cells, representing undifferentiated/basal cells with properties of mammary stem/progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: normal mammary epithelial cells
cell type: FACS sorted Stem Cell antigen-1 (Sca-1) positive cells
|
| 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 |
CommaDb
|
| 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 the raw counts of each gene and the output of the analysis with DESeq2 package to identify regulated genes
|
| |
|
| Submission date |
May 30, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL13112 |
| Series (1) |
| GSE99401 |
MiR-34a controls proliferation and plasticity of early-progenitors in the normal mammary gland and in breast cancer |
|
| Relations |
| BioSample |
SAMN07176216 |
| SRA |
SRX2867643 |
