Experiment Overview
| Repository ID: | FR-FCM-ZYEF | Experiment name: | Aberrant cell signaling in peripheral blood mononuclear cells upon interferon alpha stimulation in patients with primary Sjögren?s syndrome associates with type I interferon signature | MIFlowCyt score: | 86.00% |
| Primary researcher: | Richard Davies | PI/manager: | Richard Davies | Uploaded by: | Richard Davies |
| Experiment dates: | 2015-06-23 - 2015-10-22 | Dataset uploaded: | Nov 2017 | Last updated: | Apr 2018 |
| Keywords: | [Sjögren’s syndrome] [extraglandular manifestations] [autoantibodies] [phosphoflow] [type I interferon] | Manuscripts: | |||
| Organizations: |
University of Bergen, Clinical Institute 2, Bergen, (Norway)
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| Purpose: | To gain insights into potential dysfunctional intracellular signalling profiles of pSS patients we conducted an exploratory analysis of MAPK/ERK and JAK/STAT signalling networks in peripheral blood mononuclear cells (PBMC) from 25 female pSS patients and 25 female age-matched healthy donors using phospho-specific flow cytometry. We analyzed unstimulated samples, and samples during a 4 hour time period following activation by interferon alpha. | ||||
| Conclusion: | The phosphorylation profiles following stimulation with IFNα2b differed significantly between pSS patients and healthy donors, especially regarding STAT1 Y701. PCA further grouped patients according to clinical characteristics such as presence of autoantibodies and extraglandular manifestations. | ||||
| Comments: | Stimulation with interferon alpha was conducted using a 4 hour reverse time course. Barcoded samples included a PBMC sample from a single donor (IC) to assess assay variation. Key 9x barcoding stimulus are as follows- POlow + PB low= Unstimulated, POlow + PBmid= IC (unstimulated), POlow + PBhigh= 3 hours, POmid + PBlow= 15 minutes, POmid + PBmid= 60 minutes, POmid + PBhigh = 4 hours, POhigh + PBlow = 30 minutes, POhigh + PBmid = 2 hours, and POhigh + PBhigh= IC (stimulated). | ||||
| Funding: | The authors’ research is supported by the EU H2020 contract HarmonicSS (H2020-SC1-2016-RTD/731944), the Broegelmann Foundation, the Western Norway Regional Health Authorities (grant nr. 912065) and the University of Bergen. | ||||
| Quality control: | An optimized multiplex flow cytometry protocol for the analysis of intracellular signaling in peripheral blood mononuclear cells | The cytometer was routinely calibrated with BD cytometer setup and tracking beads (BD Biosciences). Stimulated and unstimulated PBMC from a single donor was included in each FC barcoded assay to monitor assay variation. | |||
Experiment variables
| Individuals | |
|---|---|
| · C#28 | C#28_C28- Barcode_004.fcs · C#28_C28- Panel 1_001.fcs · C#28_C28- Panel 2_002.fcs · C#28_C28- Panel 3_003.fcs |
| · C001 | C001_C001- Barcode_004.fcs · C001_C001- Panel 1_001.fcs · C001_C001- Panel 2_002.fcs · C001_C001- Panel 3_003.fcs |
| · C11 | C11_C11- Barcode_009.fcs · C11_C11- Panel 1_006.fcs · C11_C11- Panel 2_007.fcs · C11_C11- Panel 3_008.fcs |
| · C12 | C12_C12- Barcode_013.fcs · C12_C12- Panel 1_010.fcs · C12_C12- Panel 2_011.fcs · C12_C12- Panel 3_012.fcs |
| · C16 | C16_Barcode_018.fcs · C16_Panel 1_015.fcs · C16_Panel 2_016.fcs · C16_Panel 3_017.fcs |
| · C19 | C19_C19- Barcode_031.fcs · C19_C19- Panel 1_028.fcs · C19_C19- Panel 2_029.fcs · C19_C19- Panel 3_030.fcs |
| · C22(2) | C22(2)_C22(2)- Barcode_004.fcs · C22(2)_C22(2)- Panel 1_001.fcs · C22(2)_C22(2)- Panel 2_002.fcs · C22(2)_C22(2)- Panel 3_003.fcs |
| · C23 | C23_C23- Barcode_008.fcs · C23_C23- Panel 1_005.fcs · C23_C23- Panel 2_006.fcs · C23_C23- Panel 3_007.fcs |
| · C25 | C25_C25- Barcode_004.fcs · C25_C25- Panel 1_001.fcs · C25_C25- Panel 2_002.fcs · C25_C25- Panel 3_003.fcs |
| · C26 | C26_C26- Barcode_031.fcs · C26_C26- Panel 1_028.fcs · C26_C26- Panel 2_029.fcs · C26_C26- Panel 3_030.fcs |
| · C41 | C41_C41- Barcode_012.fcs · C41_C41- Panel 1_009.fcs · C41_C41- Panel 2_010.fcs · C41_C41- Panel 3_011.fcs |
| · C43 | C43_C43- Barcode_012.fcs · C43_C43- Panel 1_009.fcs · C43_C43- Panel 2_010.fcs · C43_C43- Panel 3_011.fcs |
| · C46 | C46_C46- Barcode_012.fcs · C46_C46- Panel 1_009.fcs · C46_C46- Panel 2_010.fcs · C46_C46- Panel 3_011.fcs |
| · C5 | C5_C5- Barcode_005.fcs · C5_C5- Panel 1_002.fcs · C5_C5- Panel 2_003.fcs · C5_C5- Panel 3_004.fcs |
| · C6 | C6_Barcode_008.fcs · C6_Panel 1_005.fcs · C6_Panel 2_006.fcs · C6_Panel 3_007.fcs |
| · DC743 | DC743_DC743- Barcode_008.fcs · DC743_DC743- Panel 1_005.fcs · DC743_DC743- Panel 2_006.fcs · DC743_DC743- Panel 3_007.fcs |
| · DC744 | DC744_DC744- Barcode_004.fcs · DC744_DC744- Panel 1_001.fcs · DC744_DC744- Panel 2_002.fcs · DC744_DC744- Panel 3_003.fcs |
| · DC751 | DC751_DC751- Barcode_008.fcs · DC751_DC751- Panel 1_005.fcs · DC751_DC751- Panel 2_006.fcs · DC751_DC751- Panel 3_007.fcs |
| · DC752 | DC752_DC752- Barcode_012.fcs · DC752_DC752- Panel 1_009.fcs · DC752_DC752- Panel 2_010.fcs · DC752_DC752- Panel 3_011.fcs |
| · DC756 | DC756_DC756- Barcode_004.fcs · DC756_DC756- Panel 1_001.fcs · DC756_DC756- Panel 2_002.fcs · DC756_DC756- Panel 3_003.fcs |
| · DC758 | DC758_DC758- Barcode_008.fcs · DC758_DC758- Panel 1_005.fcs · DC758_DC758- Panel 2_006.fcs · DC758_DC758- Panel 3_007.fcs |
| · DC759 | DC759_DC759- Barcode_008.fcs · DC759_DC759- Panel 1_005.fcs · DC759_DC759- Panel 2_006.fcs · DC759_DC759- Panel 3_007.fcs |
| · DC763 | DC763_DC763- Barcode_012.fcs · DC763_DC763- Panel 1_009.fcs · DC763_DC763- Panel 2_010.fcs · DC763_DC763- Panel 3_011.fcs |
| · DC765 | DC765_DC765- Barcode_016.fcs · DC765_DC765- Panel 1_013.fcs · DC765_DC765- Panel 2_014.fcs · DC765_DC765- Panel 3_015.fcs |
| · DC769 | DC769_DC769- Barcode_012.fcs · DC769_DC769- Panel 1_009.fcs · DC769_DC769- Panel 2_010.fcs · DC769_DC769- Panel 3_011.fcs |
| · DC775 | DC775_DC775- Barcode_031.fcs · DC775_DC775- Panel 1_028.fcs · DC775_DC775- Panel 2.fcs · DC775_DC775- Panel 3_030.fcs |
| · DC801 | DC801_DC801- Barcode_004.fcs · DC801_DC801- Panel 1_001.fcs · DC801_DC801- Panel 2_002.fcs · DC801_DC801- Panel 3_003.fcs |
| · DC807 | DC807_DC807- Barcode_008.fcs · DC807_DC807- Panel 1_005.fcs · DC807_DC807- Panel 2_006.fcs · DC807_DC807- Panel 3_007.fcs |
| · DC809 | DC809_DC809- Barcode_027.fcs · DC809_DC809- Panel 1_024.fcs · DC809_DC809- Panel 2_025.fcs · DC809_DC809- Panel 3_026.fcs |
| · DC811 | DC811_DC811- Barcode_031.fcs · DC811_DC811- Panel 1_028.fcs · DC811_DC811- Panel 2_029.fcs · DC811_DC811- Panel 3_030.fcs |
| · DC818 | DC818_Barcode_004.fcs · DC818_Panel 1_001.fcs · DC818_Panel 2_002.fcs · DC818_Panel 3_003.fcs |
| · DC820 | DC820_Barcode_012.fcs · DC820_Panel 1_009.fcs · DC820_Panel 2_010.fcs · DC820_Panel 3_011.fcs |
| · DC828 | DC828_DC828- Barcode_012.fcs · DC828_DC828- Panel 1_009.fcs · DC828_DC828- Panel 2_010.fcs · DC828_DC828- Panel 3_011.fcs |
| · DC829 | DC829_DC829- Barcode_031.fcs · DC829_DC829- Panel 1_028.fcs · DC829_DC829- Panel 2_029.fcs · DC829_DC829- Panel 3_030.fcs |
| · DC833 | DC833_DC833- Barcode_017.fcs · DC833_DC833- Panel 1_014.fcs · DC833_DC833- Panel 2_015.fcs · DC833_DC833- Panel 3_016.fcs |
| · DC840 | DC840_Barcode_004.fcs · DC840_Panel 1_001.fcs · DC840_Panel 2_002.fcs · DC840_Panel 3_003.fcs |
| · DC841 | DC841_Barcode_012.fcs · DC841_Panel 1_009.fcs · DC841_Panel 2_010.fcs · DC841_Panel 3_011.fcs |
| · DC846 | DC846_Barcode_018.fcs · DC846_Panel 1_015.fcs · DC846_Panel 2_016.fcs · DC846_Panel 3_017.fcs |
| · M015 | M015_M015- Barcode_012.fcs · M015_M015- Panel 1_009.fcs · M015_M015- Panel 2_010.fcs · M015_M015- Panel 3_011.fcs |
| · M019 | M019_M019- Barcode_031.fcs · M019_M019- Panel 1_028.fcs · M019_M019- Panel 2_029.fcs · M019_M019- Panel 3_030.fcs |
| · M023 | M023_M023- Barcode_004.fcs · M023_M023- Panel 1_001.fcs · M023_M023- Panel 2_002.fcs · M023_M023- Panel 3_003.fcs |
| · M024 | M024_M024- Barcode_008.fcs · M024_M024- Panel 1_005.fcs · M024_M024- Panel 2_006.fcs · M024_M024- Panel 3_007.fcs |
| · DC855 | DC855_Barcode_008.fcs · DC855_Panel 1_005.fcs · DC855_Panel 2_006.fcs · DC855_Panel 3_007.fcs |
| · M012 | M012_M012- Barcode_004.fcs · M012_M012- Panel 1_001.fcs · M012_M012- Panel 2_002.fcs · M012_M012- Panel 3_003.fcs |
| · M014 | M014_M014- Barcode_008.fcs · M014_M014- Panel 1_005.fcs · M014_M014- Panel 2_006.fcs · M014_M014- Panel 3_007.fcs |
| Sample Type | |
|---|---|
| · pSS | DC743_DC743- Barcode_008.fcs · DC744_DC744- Barcode_004.fcs · DC751_DC751- Barcode_008.fcs · DC752_DC752- Barcode_012.fcs · DC756_DC756- Barcode_004.fcs · DC758_DC758- Barcode_008.fcs · DC759_DC759- Barcode_008.fcs · DC763_DC763- Barcode_012.fcs · DC765_DC765- Barcode_016.fcs · DC769_DC769- Barcode_012.fcs · DC775_DC775- Barcode_031.fcs · DC801_DC801- Barcode_004.fcs · DC807_DC807- Barcode_008.fcs · DC809_DC809- Barcode_027.fcs · DC811_DC811- Barcode_031.fcs · DC818_Barcode_004.fcs · DC820_Barcode_012.fcs · DC828_DC828- Barcode_012.fcs · DC829_DC829- Barcode_031.fcs · DC833_DC833- Barcode_017.fcs · DC840_Barcode_004.fcs · DC841_Barcode_012.fcs · DC846_Barcode_018.fcs · DC855_Barcode_008.fcs · DC743_DC743- Panel 1_005.fcs · DC744_DC744- Panel 1_001.fcs · DC751_DC751- Panel 1_005.fcs · DC752_DC752- Panel 1_009.fcs · DC756_DC756- Panel 1_001.fcs · DC758_DC758- Panel 1_005.fcs · DC759_DC759- Panel 1_005.fcs · DC763_DC763- Panel 1_009.fcs · DC765_DC765- Panel 1_013.fcs · DC769_DC769- Panel 1_009.fcs · DC775_DC775- Panel 1_028.fcs · DC801_DC801- Panel 1_001.fcs · DC807_DC807- Panel 1_005.fcs · DC809_DC809- Panel 1_024.fcs · DC811_DC811- Panel 1_028.fcs · DC818_Panel 1_001.fcs · DC820_Panel 1_009.fcs · DC828_DC828- Panel 1_009.fcs · DC829_DC829- Panel 1_028.fcs · DC833_DC833- Panel 1_014.fcs · DC840_Panel 1_001.fcs · DC841_Panel 1_009.fcs · DC846_Panel 1_015.fcs · DC855_Panel 1_005.fcs · DC743_DC743- Panel 2_006.fcs · DC744_DC744- Panel 2_002.fcs · DC751_DC751- Panel 2_006.fcs · DC752_DC752- Panel 2_010.fcs · DC756_DC756- Panel 2_002.fcs · DC758_DC758- Panel 2_006.fcs · DC759_DC759- Panel 2_006.fcs · DC763_DC763- Panel 2_010.fcs · DC765_DC765- Panel 2_014.fcs · DC769_DC769- Panel 2_010.fcs · DC775_DC775- Panel 2.fcs · DC801_DC801- Panel 2_002.fcs · DC807_DC807- Panel 2_006.fcs · DC809_DC809- Panel 2_025.fcs · DC811_DC811- Panel 2_029.fcs · DC818_Panel 2_002.fcs · DC820_Panel 2_010.fcs · DC828_DC828- Panel 2_010.fcs · DC829_DC829- Panel 2_029.fcs · DC833_DC833- Panel 2_015.fcs · DC840_Panel 2_002.fcs · DC841_Panel 2_010.fcs · DC846_Panel 2_016.fcs · DC855_Panel 2_006.fcs · DC743_DC743- Panel 3_007.fcs · DC744_DC744- Panel 3_003.fcs · DC751_DC751- Panel 3_007.fcs · DC752_DC752- Panel 3_011.fcs · DC756_DC756- Panel 3_003.fcs · DC758_DC758- Panel 3_007.fcs · DC759_DC759- Panel 3_007.fcs · DC763_DC763- Panel 3_011.fcs · DC765_DC765- Panel 3_015.fcs · DC769_DC769- Panel 3_011.fcs · DC775_DC775- Panel 3_030.fcs · DC801_DC801- Panel 3_003.fcs · DC807_DC807- Panel 3_007.fcs · DC809_DC809- Panel 3_026.fcs · DC811_DC811- Panel 3_030.fcs · DC818_Panel 3_003.fcs · DC820_Panel 3_011.fcs · DC828_DC828- Panel 3_011.fcs · DC829_DC829- Panel 3_030.fcs · DC833_DC833- Panel 3_016.fcs · DC840_Panel 3_003.fcs · DC841_Panel 3_011.fcs · DC846_Panel 3_017.fcs · DC855_Panel 3_007.fcs |
| · Healthy donor | C#28_C28- Barcode_004.fcs · C001_C001- Barcode_004.fcs · C11_C11- Barcode_009.fcs · C12_C12- Barcode_013.fcs · C16_Barcode_018.fcs · C19_C19- Barcode_031.fcs · C22(2)_C22(2)- Barcode_004.fcs · C23_C23- Barcode_008.fcs · C25_C25- Barcode_004.fcs · C26_C26- Barcode_031.fcs · C41_C41- Barcode_012.fcs · C43_C43- Barcode_012.fcs · C46_C46- Barcode_012.fcs · C5_C5- Barcode_005.fcs · C6_Barcode_008.fcs · M012_M012- Barcode_004.fcs · M014_M014- Barcode_008.fcs · M015_M015- Barcode_012.fcs · M019_M019- Barcode_031.fcs · M023_M023- Barcode_004.fcs · M024_M024- Barcode_008.fcs · C#28_C28- Panel 1_001.fcs · C001_C001- Panel 1_001.fcs · C11_C11- Panel 1_006.fcs · C12_C12- Panel 1_010.fcs · C16_Panel 1_015.fcs · C19_C19- Panel 1_028.fcs · C22(2)_C22(2)- Panel 1_001.fcs · C23_C23- Panel 1_005.fcs · C25_C25- Panel 1_001.fcs · C26_C26- Panel 1_028.fcs · C41_C41- Panel 1_009.fcs · C43_C43- Panel 1_009.fcs · C46_C46- Panel 1_009.fcs · C5_C5- Panel 1_002.fcs · C6_Panel 1_005.fcs · M012_M012- Panel 1_001.fcs · M014_M014- Panel 1_005.fcs · M015_M015- Panel 1_009.fcs · M019_M019- Panel 1_028.fcs · M023_M023- Panel 1_001.fcs · M024_M024- Panel 1_005.fcs · C#28_C28- Panel 2_002.fcs · C001_C001- Panel 2_002.fcs · C11_C11- Panel 2_007.fcs · C12_C12- Panel 2_011.fcs · C16_Panel 2_016.fcs · C19_C19- Panel 2_029.fcs · C22(2)_C22(2)- Panel 2_002.fcs · C23_C23- Panel 2_006.fcs · C25_C25- Panel 2_002.fcs · C26_C26- Panel 2_029.fcs · C41_C41- Panel 2_010.fcs · C43_C43- Panel 2_010.fcs · C46_C46- Panel 2_010.fcs · C5_C5- Panel 2_003.fcs · C6_Panel 2_006.fcs · M012_M012- Panel 2_002.fcs · M014_M014- Panel 2_006.fcs · M015_M015- Panel 2_010.fcs · M019_M019- Panel 2_029.fcs · M023_M023- Panel 2_002.fcs · M024_M024- Panel 2_006.fcs · C#28_C28- Panel 3_003.fcs · C001_C001- Panel 3_003.fcs · C11_C11- Panel 3_008.fcs · C12_C12- Panel 3_012.fcs · C16_Panel 3_017.fcs · C19_C19- Panel 3_030.fcs · C22(2)_C22(2)- Panel 3_003.fcs · C23_C23- Panel 3_007.fcs · C25_C25- Panel 3_003.fcs · C26_C26- Panel 3_030.fcs · C41_C41- Panel 3_011.fcs · C43_C43- Panel 3_011.fcs · C46_C46- Panel 3_011.fcs · C5_C5- Panel 3_004.fcs · C6_Panel 3_007.fcs · M012_M012- Panel 3_003.fcs · M014_M014- Panel 3_007.fcs · M015_M015- Panel 3_011.fcs · M019_M019- Panel 3_030.fcs · M023_M023- Panel 3_003.fcs · M024_M024- Panel 3_007.fcs |
