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Sample GSM3511836 Query DataSets for GSM3511836
Status Public on Jun 05, 2019
Title T44negILC3 donor: 11
Sample type RNA
 
Source name Tonsil NKp44- ILC3
Organism Homo sapiens
Characteristics donor: 3
cell type: NKp44- ILC3
tissue: Tonsil
Extracted molecule total RNA
Extraction protocol Buffy coats were provided by the blood bank (Sanquin, Amsterdam). Tonsils were obtained from routine tonsillectomies and tissue collection was done at the Academic Medical Center (AMC), Onze Lieve Vrouwe Gasthuis (OLVG) hospital (Amsterdam, The Netherlands). Inflamed nasal polyps were obtained from chronic rhinosinusitis patients during surgery and umbilical cord blood was collected at the AMC. The collection and use of all human samples was approved by the Medical Ethical Committee of the AMC and with informed consent. Peripheral blood and umbilical cord blood mononuclear cells were isolated by Ficoll-Hypaque density gradient (Lymphoprep; Axis-Shield). Tonsil tissue was cut in fine pieces and mechanically disrupted using the Stomacher 80 Biomaster. Cell suspensions were filtered through a 70- µm cell strainer. Nasal tissues were manually cut into fine pieces and digested for 45 min at 37°C with Liberase TM (125 µg/mL) and DNase I (50 U/mL). Cell suspensions were filtered through a 70 µm cell strainer. Mononuclear cells were then isolated by Ficoll-Hypaque density gradient. Subsequently, ILCs were isolated as described previously .
Label biotin
Label protocol Briefly, PB and cord blood was enriched for ILCs by immunomagnetic cell sorting, using a negative selection of CD3, CD14, CD16 and CD19 with Mojosort magnetic cell separation system (BioLegend, San Diego, CA, USA) Tonsillar mononuclear cells were depleted of CD3 and CD19 cells by MACS depletion. The cells suspensions were stained with antibodies against Lineage (CD1a, CD3, CD4, CD5, CD14, CD19, CD16, CD34, CD94, CD123, BDCA2, TCRαβ, TCRγδ, FcER1α), CD45, CD161, CD127, CD117, CRTH2, KLRG1, NKp44, NKp46, CD56 and IL-1R1. Cells were sorted on a FACSAria, purity of the sorted cells in all experiments was >99%.
 
Hybridization protocol Affymetrix protocol
Scan protocol Affymetrix protocol
Data processing R/Bioconductor, limma rma
 
Submission date Dec 13, 2018
Last update date Jun 05, 2019
Contact name Balthasar Adrianus Heesters
Organization name Utrecht University
Department Pharmaceutical Sciences
Lab Heesters
Street address Universiteitsweg 99
City Utrecht
State/province Utrecht
ZIP/Postal code 3584 CG
Country Netherlands
 
Platform ID GPL24324
Series (1)
GSE123817 KLRG1 and NKp46 discriminate subpopulations of human CD117+ CRTH2- ILCs biased toward ILC2 or ILC3

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
TC0100006437.hg.1 4.231206025
TC0100006476.hg.1 4.931347571
TC0100006479.hg.1 6.534008709
TC0100006480.hg.1 6.038797318
TC0100006483.hg.1 7.889915013
TC0100006486.hg.1 5.989963833
TC0100006490.hg.1 4.151337493
TC0100006492.hg.1 7.184465056
TC0100006494.hg.1 5.175946749
TC0100006497.hg.1 4.877632793
TC0100006499.hg.1 5.114281411
TC0100006501.hg.1 4.9724313
TC0100006502.hg.1 5.036670295
TC0100006514.hg.1 5.29429826
TC0100006516.hg.1 5.536101387
TC0100006517.hg.1 3.74284103
TC0100006524.hg.1 7.556709971
TC0100006540.hg.1 3.72446734
TC0100006548.hg.1 3.819229553
TC0100006550.hg.1 6.607135342

Total number of rows: 19367

Table truncated, full table size 565 Kbytes.




Supplementary file Size Download File type/resource
GSM3511836_03_H05.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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