|
| Status |
Public on Oct 13, 2021 |
| Title |
Lib_1B_CD127p |
| Sample type |
SRA |
| |
|
| Source name |
Cells isolated from frozen tumor samples
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: TRM CD103+ CD127+
|
| Treatment protocol |
Cells from frozen TILs were harvested in R10 culture medium, washed with PBS 1x and immediately proccesed for surface staining for FACS sorting (FACS Aria cell sorter).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted in 10 µL PBS 1X (Sigma-Aldrich), spun down immediately and stored frozen at -80°C in a maximum volume of 7 µL PBS 1X (Sigma-Aldrich).
Library preparation was performed by starting directly from ̴500 cells per sample using the SMART-Seq Stranded Kit (Clontech-Takara) and following the manufacturer’s protocol. Libraries were qualitatively assessed by using TapeStation 4200, quantified by Qubit Fluorimeter, then multiplexed in equimolar pools and sequenced on a NextSeq-550 Illumina Platform, generating on average 32.9 million 75bp-PE reads per sample .
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Basecalls performed using RTA v2 version 2.4.11
RNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.5.1b
Differential Gene Expression analysis was performed using EdgeR 3.20.9
Genome_build: GRCh38
|
| |
|
| Submission date |
Jul 21, 2020 |
| Last update date |
Oct 13, 2021 |
| Contact name |
Emilia Maria Cristina Mazza |
| E-mail(s) |
[email protected]
|
| Organization name |
Humanitas Clinical and Research Center
|
| Street address |
Via Alessandro Manzoni, 56
|
| City |
Rozzano, Milan |
| ZIP/Postal code |
20089 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE154842 |
Tumor-reactive tissue resident memory T cells, regulatory T cells and prognosis in early luminal-like breast cancer |
|
| Relations |
| BioSample |
SAMN15591551 |
| SRA |
SRX8785425 |
