|
| Status |
Public on Mar 29, 2020 |
| Title |
Donor.B CSF2+ |
| Sample type |
SRA |
| |
|
| Source name |
primary T lymphocytes derived from human peripheral blood mononuclear cells (PBMC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Effector memory T lymphocytes
label: PEpos
|
| Treatment protocol |
TEM were stimulated for 3h with PMA/ionomycin and labelled for GM-CSF secretion with a GM-CSF cytokine secretion kit (Miltenyi Biotec) before sorting for PE+/- cells with a BD Sorter Aria II
|
| Growth protocol |
TEM were isolated by magnetic enrichment for CD4 (Miltentyi Biotec) and sorted for CD4+CD25-CD45RA-CCR7- and incubated overnight in complete media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PE+/- cells were resuspended in Trizol. Samples of 3 donors were combined and total RNA was extracted with Direct-Zol RNA mini Prep (Zymo Research)
PolyA RNA libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from 400ng of total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Human peripheral blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec). Effector Memory T cell subsets were then sorted based on the expression of the following surface markers: CD4+CD25–CD45RA-CCR7-.
|
| Data processing |
Reads were quality filtered according to the Illumina pipeline, then were aligned to human genome build GRCh38/hg38 using using TopHat v2.1.0 with the option “--b2-very-sensitive”. Only uniquely mapped reads were retained
Gene expression counts were estimated using HTSeq v0.6.1, summarized across all exons as annotated in the GENCODE v25, with option “union” and “no strand-specific assay”.
Differentially expressed genes were identified using EdgeR R-package v3.2.2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.gene.counts.txt files contain raw read counts for each samples. *.edgeR_results.txt files contain differentially expressed genes for each comparison.
|
| |
|
| Submission date |
Nov 26, 2018 |
| Last update date |
Mar 29, 2020 |
| Contact name |
Chiara Balestrieri |
| E-mail(s) |
balestrieri.c@gmail.com
|
| Organization name |
IRCCS San Raffaele Scientific Institute
|
| Department |
Center for Omics Sciences
|
| Street address |
Via Olgettina 58
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE122941 |
A molecular network regulating the pro-inflammatory phenotype of human memory T lymphocytes (RNA-Seq) |
| GSE122946 |
A molecular network regulating the proinflammatory phenotype of human memory T lymphocytes |
|
| Relations |
| BioSample |
SAMN10477379 |
| SRA |
SRX5062503 |
