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Experiment Overview

Repository ID: FR-FCM-Z4VP Experiment name: Flow cytometry data for determination of the Ki-67 proliferation index for diagnosis of myelodysplastic syndromes MIFlowCyt score: 82.61%
Primary researcher: Stefan Mestrum PI/manager: Mathie Leers Uploaded by: Stefan Mestrum
Experiment dates: 2016-01-01 - 2021-01-01 Dataset uploaded: Feb 2022 Last updated: Feb 2022
Keywords: [flow cytometry] [proliferation] [Ki-67] [data] [gating procedure] [MDS] [Ogata score] Manuscripts:
Organizations: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Department of Molecular Cell Biology, Maastricht, (Nederland)
Zuyderland Medical Center, Department of Clinical Chemistry & Hematology, Sittard-Geleen, (Nederland)
Purpose: Gating the Ki-67-FITC positive fractions is a critical step in the determination of the Ki-67 proliferation index of the different bone marrow cell populations of non-clonal cytopenic patients, MDS patients and other patients with myeloid malignancies. Therefore, we investigated whether using manually placed rectangular gates and predefined gating thresholds based on fluorescence intensities produced similar results as compared to placing polygonal gates.
Conclusion: Placement of rectangular gates decreases the likelihood of including Ki-67 negative cells, as the gating threshold does not differ for the individual populations. Therefore, placing rectangular gates results in less inter-observer variability and more sensitively detection of differences between non-clonal cytopenic patients and MDS patients. Differences diminished by the use of predefined gating thresholds based on the fluorescent intensity of the Ki-67 staining. By using predefined gating thresholds, the intensity of the Ki-67 staining becomes a confounder in analyzing the Ki-67 proliferation indices and is influenced by a variety of factors. These factors include among others inter-operator variations, antibody batch variations and differences in staining intensities between the non-clonal cytopenic patient group and MDS patient group. These data enable reproduction of the staining and gating procedure for flow cytometric analysis of the Ki-67 proliferation index in non-clonal cytopenic and MDS patients.
Comments: None
Funding: Not disclosed
Quality control: To correct for background staining by the conjugated primary antibodies, a negative control using FITC-directly conjugated to non-relevant, isotype immunoglobulins was used. To prevent staining abnormalities caused by ageing of the sample, flow cytometry was performed within 24 hours of receival of the femoral heads. To ensure sufficient cells for flow cytometric analyses, a white blood cell count of approximately 20 x 109 cells/L (quantified with Sysmex XN-9000) was used preferentially. The instrument setup was performed according to standard procedures. Verification of the optical alignment and fluidics system of the Navios™ Flow Cytometer was performed using Flow-Check™ Pro Fluorospheres (Beckman Coulter). The compensation for each fluorochrome was established using Flow-Set™ Pro Fluorospheres (Beckman Coulter) and was performed weekly.


Experiment variables

Individuals
· MDS patients MDS Ki67-103 00011210 001.fcs · MDS Ki67-103 00011211 002.fcs · MDS Ki67-104 00009622 001.fcs · MDS Ki67-104 00009623 002.fcs · MDS Ki67-105 00009839 001.fcs · MDS Ki67-105 00009840 002.fcs · MDS Ki67-106 00009546 001.fcs · MDS Ki67-106 00009547 002.fcs · MDS Ki67-107 00010954 001.fcs · MDS Ki67-107 00010955 002.fcs · MDS Ki67-108 00009814 001.fcs · MDS Ki67-108 00009815 002.fcs · MDS Ki67-109 00009510 001.fcs · MDS Ki67-109 00009511 002.fcs · MDS Ki67-110 00010926 001.fcs · MDS Ki67-110 00010927 002.fcs · MDS Ki67-111 00009721 001.fcs · MDS Ki67-111 00009722 002.fcs · MDS Ki67-112 00011028 001.fcs · MDS Ki67-112 00011029 002.fcs · MDS Ki67-113 00010141 001.fcs · MDS Ki67-113 00010142 002.fcs · MDS Ki67-186 00011745 001.fcs · MDS Ki67-186 00011746 002.fcs · MDS Ki67-187 00011752 001.fcs · MDS Ki67-187 00011753 002.fcs · MDS Ki67-188 00012659 002.fcs · MDS Ki67-188 0012658 001.fcs · MDS Ki67-189 00012641 001.fcs · MDS Ki67-189 00012642 002.fcs · MDS Ki67-195 00012764 001.fcs · MDS Ki67-195 00012765 002.fcs · MDS Ki67-200 00011929 001.fcs · MDS Ki67-200 00011930 002.fcs · MDS Ki67-202 00012820 001.fcs · MDS Ki67-202 00012821 002.fcs · MDS Ki67-203 00012424 001.fcs · MDS Ki67-203 00012425 002.fcs · MDS Ki67-204 00013034 001.fcs · MDS Ki67-204 00013035 002.fcs · MDS Ki67-205 00013615 001.fcs · MDS Ki67-205 00013616 002.fcs · MDS Ki67-206 00013704 001.fcs · MDS Ki67-206 00013705 002.fcs · MDS Ki67-070 00006303 001.fcs · MDS Ki67-070 00006304 002.fcs · MDS Ki67-072 00006270 001.fcs · MDS Ki67-072 00006271 002.fcs · MDS Ki67-073 00006493 001.fcs · MDS Ki67-073 00006494 002.fcs · MDS Ki67-074 00006566 001.fcs · MDS Ki67-074 00006567 002.fcs · MDS Ki67-075 00006918 001.fcs · MDS Ki67-075 00006919 002.fcs · MDS Ki67-076 00007212 001.fcs · MDS Ki67-076 00007213 002.fcs · MDS Ki67-077 00007276 001.fcs · MDS Ki67-077 00007277 002.fcs · MDS Ki67-078 00007323 001.fcs · MDS Ki67-078 00007324 002.fcs · MDS Ki67-079 00007451 001.fcs · MDS Ki67-079 00007452 002.fcs · MDS Ki67-080 00007495 001.fcs · MDS Ki67-080 00007496 002.fcs · MDS Ki67-081 00007577 001.fcs · MDS Ki67-081 00007578 002.fcs · MDS Ki67-082 00007696 001.fcs · MDS Ki67-082 00007697 002.fcs · MDS Ki67-083 00007910 001.fcs · MDS Ki67-083 00007911 002.fcs · MDS Ki67-084 00007931 001.fcs · MDS Ki67-084 00007932 002.fcs · MDS Ki67-085 00007970 001.fcs · MDS Ki67-085 00007971 002.fcs · MDS Ki67-086 00007999 001.fcs · MDS Ki67-086 00008000 002.fcs · MDS Ki67-087 00008006 001.fcs · MDS Ki67-087 00008007 002.fcs · MDS Ki67-088 00008117 001.fcs · MDS Ki67-088 00008118 002.fcs · MDS Ki67-089 00008161 001.fcs · MDS Ki67-089 00008162 002.fcs · MDS Ki67-090 00008266 001.fcs · MDS Ki67-090 00008267 002.fcs · MDS Ki67-091 00008472 001.fcs · MDS Ki67-091 00008473 002.fcs · MDS Ki67-092 00008596 001.fcs · MDS Ki67-092 00008597 002.fcs · MDS Ki67-093 00008609 001.fcs · MDS Ki67-093 00008610 002.fcs · MDS Ki67-094 00008674 001.fcs · MDS Ki67-094 00008675 002.fcs · MDS Ki67-095 00008787 001.fcs · MDS Ki67-095 00008788 002.fcs · MDS Ki67-096 00009123 001.fcs · MDS Ki67-096 00009124 002.fcs · MDS Ki67-097 00009287 001.fcs · MDS Ki67-097 00009288 002.fcs · MDS Ki67-098 00007673 001.fcs · MDS Ki67-098 00007674 002.fcs
· Non-clonal cytopenia patients Ki67-159 00009821 001.fcs · Ki67-159 00009822 002.fcs · Ki67-161 00009315 001.fcs · Ki67-161 00009316 002.fcs · Ki67-162 00009774 001.fcs · Ki67-162 00009775 002.fcs · Ki67-163 00008778 001.fcs · Ki67-163 00008779 002.fcs · Ki67-164 00008761 001.fcs · Ki67-164 00008762 002.fcs · Ki67-168 00010148 001.fcs · Ki67-168 00010149 002.fcs · Ki67-169 00010431 001.fcs · Ki67-169 00010432 002.fcs · Ki67-170 00010418 001.fcs · Ki67-170 00010419 002.fcs · Ki67-171 00010919 002.fcs · Ki67-171 00010918 001.fcs · Ki67-172 00010873 001.fcs · Ki67-172 00010874 002.fcs · Ki67-173 00010859 001.fcs · Ki67-173 00010860 002.fcs · Ki67-174 00010899 001.fcs · Ki67-174 00010900 002.fcs · Ki67-177 00008605 001.fcs · Ki67-177 00008606 002.fcs · Ki67-178 00008749 001.fcs · Ki67-178 00008750 002.fcs · Ki67-180 00010942 001.fcs · Ki67-180 00010943 002.fcs · Ki67-181 00011224 001.fcs · Ki67-181 00011225 002.fcs · Ki67-183 001.fcs · Ki67-183 002.fcs · Ki67-184 00011901 001.fcs · Ki67-184 00011902 002.fcs · Ki67-185 00011936 001.fcs · Ki67-185 00011937 002.fcs · Ki67-208 00013024 001.fcs · Ki67-208 00013025 002.fcs

Sample Type
· Bone marrow aspirates MDS Ki67-103 00011210 001.fcs · MDS Ki67-103 00011211 002.fcs · MDS Ki67-104 00009622 001.fcs · MDS Ki67-104 00009623 002.fcs · MDS Ki67-105 00009839 001.fcs · MDS Ki67-105 00009840 002.fcs · MDS Ki67-106 00009546 001.fcs · MDS Ki67-106 00009547 002.fcs · MDS Ki67-107 00010954 001.fcs · MDS Ki67-107 00010955 002.fcs · MDS Ki67-108 00009814 001.fcs · MDS Ki67-108 00009815 002.fcs · MDS Ki67-109 00009510 001.fcs · MDS Ki67-109 00009511 002.fcs · MDS Ki67-110 00010926 001.fcs · MDS Ki67-110 00010927 002.fcs · MDS Ki67-111 00009721 001.fcs · MDS Ki67-111 00009722 002.fcs · MDS Ki67-112 00011028 001.fcs · MDS Ki67-112 00011029 002.fcs · MDS Ki67-113 00010141 001.fcs · MDS Ki67-113 00010142 002.fcs · MDS Ki67-186 00011745 001.fcs · MDS Ki67-186 00011746 002.fcs · MDS Ki67-187 00011752 001.fcs · MDS Ki67-187 00011753 002.fcs · MDS Ki67-188 00012659 002.fcs · MDS Ki67-188 0012658 001.fcs · MDS Ki67-189 00012641 001.fcs · MDS Ki67-189 00012642 002.fcs · MDS Ki67-195 00012764 001.fcs · MDS Ki67-195 00012765 002.fcs · MDS Ki67-200 00011929 001.fcs · MDS Ki67-200 00011930 002.fcs · MDS Ki67-202 00012820 001.fcs · MDS Ki67-202 00012821 002.fcs · MDS Ki67-203 00012424 001.fcs · MDS Ki67-203 00012425 002.fcs · MDS Ki67-204 00013034 001.fcs · MDS Ki67-204 00013035 002.fcs · MDS Ki67-205 00013615 001.fcs · MDS Ki67-205 00013616 002.fcs · MDS Ki67-206 00013704 001.fcs · MDS Ki67-206 00013705 002.fcs · Ki67-159 00009821 001.fcs · Ki67-159 00009822 002.fcs · Ki67-161 00009315 001.fcs · Ki67-161 00009316 002.fcs · Ki67-162 00009774 001.fcs · Ki67-162 00009775 002.fcs · Ki67-163 00008778 001.fcs · Ki67-163 00008779 002.fcs · Ki67-164 00008761 001.fcs · Ki67-164 00008762 002.fcs · Ki67-168 00010148 001.fcs · Ki67-168 00010149 002.fcs · Ki67-169 00010431 001.fcs · Ki67-169 00010432 002.fcs · Ki67-170 00010418 001.fcs · Ki67-170 00010419 002.fcs · Ki67-171 00010919 002.fcs · Ki67-171 00010918 001.fcs · Ki67-172 00010873 001.fcs · Ki67-172 00010874 002.fcs · Ki67-173 00010859 001.fcs · Ki67-173 00010860 002.fcs · Ki67-174 00010899 001.fcs · Ki67-174 00010900 002.fcs · Ki67-177 00008605 001.fcs · Ki67-177 00008606 002.fcs · Ki67-178 00008749 001.fcs · Ki67-178 00008750 002.fcs · Ki67-180 00010942 001.fcs · Ki67-180 00010943 002.fcs · Ki67-181 00011224 001.fcs · Ki67-181 00011225 002.fcs · Ki67-183 001.fcs · Ki67-183 002.fcs · Ki67-184 00011901 001.fcs · Ki67-184 00011902 002.fcs · Ki67-185 00011936 001.fcs · Ki67-185 00011937 002.fcs · Ki67-208 00013024 001.fcs · Ki67-208 00013025 002.fcs · MDS Ki67-070 00006303 001.fcs · MDS Ki67-070 00006304 002.fcs · MDS Ki67-072 00006270 001.fcs · MDS Ki67-072 00006271 002.fcs · MDS Ki67-073 00006493 001.fcs · MDS Ki67-073 00006494 002.fcs · MDS Ki67-074 00006566 001.fcs · MDS Ki67-074 00006567 002.fcs · MDS Ki67-075 00006918 001.fcs · MDS Ki67-075 00006919 002.fcs · MDS Ki67-076 00007212 001.fcs · MDS Ki67-076 00007213 002.fcs · MDS Ki67-077 00007276 001.fcs · MDS Ki67-077 00007277 002.fcs · MDS Ki67-078 00007323 001.fcs · MDS Ki67-078 00007324 002.fcs · MDS Ki67-079 00007451 001.fcs · MDS Ki67-079 00007452 002.fcs · MDS Ki67-080 00007495 001.fcs · MDS Ki67-080 00007496 002.fcs · MDS Ki67-081 00007577 001.fcs · MDS Ki67-081 00007578 002.fcs · MDS Ki67-082 00007696 001.fcs · MDS Ki67-082 00007697 002.fcs · MDS Ki67-083 00007910 001.fcs · MDS Ki67-083 00007911 002.fcs · MDS Ki67-084 00007931 001.fcs · MDS Ki67-084 00007932 002.fcs · MDS Ki67-085 00007970 001.fcs · MDS Ki67-085 00007971 002.fcs · MDS Ki67-086 00007999 001.fcs · MDS Ki67-086 00008000 002.fcs · MDS Ki67-087 00008006 001.fcs · MDS Ki67-087 00008007 002.fcs · MDS Ki67-088 00008117 001.fcs · MDS Ki67-088 00008118 002.fcs · MDS Ki67-089 00008161 001.fcs · MDS Ki67-089 00008162 002.fcs · MDS Ki67-090 00008266 001.fcs · MDS Ki67-090 00008267 002.fcs · MDS Ki67-091 00008472 001.fcs · MDS Ki67-091 00008473 002.fcs · MDS Ki67-092 00008596 001.fcs · MDS Ki67-092 00008597 002.fcs · MDS Ki67-093 00008609 001.fcs · MDS Ki67-093 00008610 002.fcs · MDS Ki67-094 00008674 001.fcs · MDS Ki67-094 00008675 002.fcs · MDS Ki67-095 00008787 001.fcs · MDS Ki67-095 00008788 002.fcs · MDS Ki67-096 00009123 001.fcs · MDS Ki67-096 00009124 002.fcs · MDS Ki67-097 00009287 001.fcs · MDS Ki67-097 00009288 002.fcs · MDS Ki67-098 00007673 001.fcs · MDS Ki67-098 00007674 002.fcs

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