|
Status |
Public on Mar 29, 2020 |
Title |
Donor.A 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: PEneg
|
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
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|
|
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.
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|
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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 |
SAMN10477377 |
SRA |
SRX5062505 |