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Can I upload data from human subjects?

Regulations in different countries are different; however, most countries have some sort of a law that will prohibit you from uploading and sharing patient's health related data if the makes the individual person identifiable. Typically, privacy rule requirements do not apply to information that has been de-identified, and therefore, de-identified data may usually be shared for research purposes. Please review the rules and regulations applicable to you, such as the Health Insurance Portability and Accountability Act (HIPAA) information on De-identification of Protected Health Information or to relevant information from an appropriate regulatory authority as applicable based on your residence. So typically, in order to upload and share your data with FlowRepository, you will need to "de-identify" your data, i.e., remove any sort of patient identification from your data before uploading your files.

In order to de-identify your data, first, make sure that inappropriate patient identifiers are not part of any of the file names. If a patient name, date of birth, etc. are part of the file names, then you will need to rename those files manually before doing anything else.

Next, please note that FCS data files contain a segment with keyword/value pairs. Most of these keep basic information essential for the interpretation of the raw data matrix of fluorescence expression levels and other values. These include the number of acquired parameters, their names, acquisition voltage settings, the total number of events (particles), and many other keywords as specified in the FCS data file standard. In clinical environments, some of these keywords may include identifiers that could be used to identify an individual and shall therefore be removed. Generally, there are several approaches to de-identify the FCS files.

Probably most conveniently, you may use FlowRepository's fully automated FCS de-identification utility by checking the De-identify all FCS files before uploading check-box that is included in the upload Applet as shown above. This de-identification is integrated in the data upload process and is performed on your computer locally so that sensitive information does not leave your computer.

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Automated de-identification means the removal of all keyword values of FCS keywords that are not in the list of safe essential keywords. This list has been created based on the FCS data file standard as well as careful examination of a few hundred FCS data files produced by dozens of instruments from several vendors. Currently, the list contains these safe essential keywords:

$BEGINANALYSIS, $BEGINDATA, $BEGINSTEXT, $BYTEORD, $DATATYPE, $ENDANALYSIS, $ENDDATA, $ENDSTEXT, $MODE, $NEXTDATA, $PAR, $TOT, $DATE, $BTIM, $ETIM, $TIMESTEP, $TR, $SPILLOVER, SPILLOVER, SPILL, $SPILL, $VOL, $COMP, $PnB, $PnE, $PnN, $PnR, $PnV, $PnS, $PnG, $PnF, $PnL, $PnO, $PnP, $PnT, $PnD, $PnCALIBRATION, $DFCiTOj, $CYT, $CYTSN, APPLICATION, LASERnDELAY, LASERnNAME, LASERnPOWER, LASERnWAVELENGTH, $SYS, FIRMWAREVERSION, NOZZLEDIAMETER, NUMSORTWAYS, SHEATHPRESSURE, UTOPEXBUILD, VOLTAGECHANGED, CREATOR, PnCHANNELTYPE, PnLASER, PnBS, PnMS, PnDISPLAY, APPLY COMPENSATION, THRESHOLD, AUTOBS, FSC ASF, WINDOW EXTENSION, CYTNUM, #CFLOWDECADESn, #PnVirtualGain, #CFLOWCAPTUREDDATE, #LASERCONFIGURATION, #CFLOWnCOLORCOMP, #ATIM, #ACQUISITIONTIMEMILLI, #SPACERS, #PnMaxUsefulDataChannel, TEMPELECTRONICS, $PnDISPLAY, Manufacturer, Acq. Software, FJ_FCS_VERSION, FJ_$TIMESTEP, FJ$ACQSTATE, FJ_$PnR, $PROJ, CST BASELINE DATE, CST SETUP DATE, CYTOMETER CONFIG CREATE DATE, CYTOMETER CONFIG NAME, CST BEADS LOT ID, CST SETUP STATUS, $PKn, $PKNn, TUBE NAME, WIDTHPARAMUPSHIFT, SOFTWAREREVISION, P$SPEED, P$SPEEDIS, P$ACQTIMES, P$COUNTVOLUME, P$CNTSENO, P$CELLCONC, P$PMODEn, P$PLLn, P$PULn, TEMPOPTICS, $LOST, LasernDelay, @CYTOMETERID, @CAROUSEL, @Y2KDATE, @Acquisition Protocol Offset, @STOPREASON, @ABSCALFACTOR, ACQTIME, @BUILDNUMBER, @RATIONUMERATORMUX, @RATIODENOMINATORMUX, @BASELINEOFFSET, @COMPENSATIONMODE, @RESAVEDFILE, $RUNNUMBER, @PnADDRESS, @PnU, @PnC, @PnZ, @PnQ, @TUBENO, @PnX, @DISCRIMINATOR, $WELLID, $ETIME, @PANEL, VSH_APP, VSH_APP_VERSION, ANALOG_COMP, @CRS20BITFORMAT, @BLUETARGETPOWER, @REDLASERSHUTTER, @VIOLETLASERPOWER_START, @AUX_SIGNAL, @BLUELASERPOWER_START, @REDLASERPOWER_START, @BLUELASERPOWER_END, @VIOLETLASERPOWER_END, @BLUELASERSHUTTER, @REDLASERPOWER_END, @VIOLETTARGETPOWER, @REDTARGETPOWER, @VIOLETLASERSHUTTER, PnLo, PnHi, PnDetectorName, PnType, QnS, QnI, QnU, GTI$BEGINLOG, GTI$PLOTxxx, GTI$PARAMxxx, GTI$Rxxx, GTI$CHANxxx, GTI$DILUTIONFACTOR, GTI$QUANTITY, $RnI, GTI$WIDTHSCALE, GTI$TERMINATIONCOUNT, GTI$Gxxx, GTI$ANALYSISDATE, GTI$AREASCALE, GTI$ENDLOG, GTI$REFRESHRATE, GTI$ANALYSISTIME, GTI$COMPENSATIONxxx, GTI$NGATES, GTI$SUBREGIONLIST, GTI$PMTxxx, GTI$HIGHCONCTRIGGER, GTI$NUMPLOTS, GTI$ERRORCOUNT, GTI$ANALYSISSETUPEND, GTI$ASSAYTYPE, GTI$TIMESCALE, GTI$TOTALNUMREADINGS, GTI$INSTRUMENTTYPE, GTI$FLOWRATECAL, GTI$NREGIONS, GTI$PUMPSAMPLESPEED, GTI$ANALYSISSETUPBEGIN, GTI$ORIGINALVOLUME, GTI$WELL, GTI$SPILLOVERUUID, DET_SPILL, APPLY_COMPENSATION, TUBE_NAME, SOFTWARE, $ENDANYLYSIS, #PnMaxUsefulChannelDNA, WELL ID, PLATE ID, PLATE NAME, WORKSTATION, PANEL NAME, PANEL_NAME, START BATCH, END BATCH, BD$AcqLibVersion, BD$NPAR, BD$PnN, BD$WORDn, BD$LASERMODE, CalibFile, PnTHRESVOL, $TEMPELECTRONICS, $TEMPOPTICS, flowCore_$PnRmax, flowCore_$PnRmin, flowCore_$PnR, transformation, FCSversion, TIMETICKS, CYTOF_DATA_SHIFT, @PnGAIN, @RATIO_DENOMINATOR, @RATIO_NUMERATOR, @PnDIVIDER