|
| Status |
Public on Apr 24, 2020 |
| Title |
TLC_S84 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mammary gland
cell type: Tomato luminal cells (TLC)
treatment: Luminal cell ablation
|
| Treatment protocol |
Single cell suspension from mammary gland was stained with different primary antibodies for the markers of interest.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mammary gland cells were isolated by FACS and collected into kit lysis buffer. RNA was extracted with Qiagen RNeasy Micro Kit.
The multiplexed libraries (18 pM) were loaded on flow cells and sequences were produced using a NovaSeq 6000 S2 Reagent Kit (200 cycles) from a NovaSeq 6000 System (Illumina).
Indexed cDNA libraries were obtained using the Ovation Solo RNA-Seq System (NuGen) following manufacturer recommendation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Approximately 19 million of paired-end reads per sample were mapped against the mouse reference genome (GRCm38/mm10) using STAR software to generate read alignments for each sample.
Annotations Mus_musculus.GRCm38.87.gtf were obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTSeq. These counts were normalized for 20 millions of mapped reads.
The fold changes of mean gene expression for the duplicates were used to calculate the level of differential gene expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include raw counts.
|
| |
|
| Submission date |
Mar 06, 2019 |
| Last update date |
Apr 24, 2020 |
| Contact name |
Alessia Centonze |
| E-mail(s) |
alessia.centonze@ulb.ac.be
|
| Organization name |
Université libre de Bruxelles
|
| Lab |
Laboratory of Stem cell and Cancer
|
| Street address |
Route de Lennik 808
|
| City |
Bruxelles |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE127975 |
Heterotypic cell-cell communication regulates multipotency in glandular epithelial stem cells |
|
| Relations |
| BioSample |
SAMN11080255 |
| SRA |
SRX5488142 |
