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idr0056-stojic-lncrnas's Introduction

A long noncoding RNA regulates microtubule behaviour during mitosis

Authors

Stojic L, Lun ATL, Mascalchi P, Ernst C, Redmond AM, Mangei J, Cooper S, Barr AR, Taylor C, Franklin VNR, Bakal C, Marioni JC, Odom DT, Gergely F

Description

Long noncoding RNAs (lncRNAs) regulate many biological processes and have been implicated in development and disease pathogenesis. The exact function for the large majority of lncRNAs is still unknown. To address whether lncRNAs could play a role in cell division, we combined a microscopy-based high-content RNAi screen with dedicated image analysis workflows to identify lncRNAs that regulate mitotic progression, chromosome segregation and cytokinesis. By targeting over 2000 lncRNAs in HeLa cells, we discovered an assortment of new lncRNAs with unexplored functions in maintenance of genome stability.

idr0056-stojic-lncrnas's People

Contributors

dominikl avatar francesw avatar jburel avatar joshmoore avatar sbesson avatar

Watchers

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Forkers

dominikl francesw snoopycrimecop

idr0056-stojic-lncrnas's Issues

Add support for new variant of Columbus dataset

While working on #1, @dominikl reported failures while applying the rendering settings:

Traceback (most recent call last):
 File "/opt/omero/server/OMERO.server/bin/omero", line 130, in <module>
   rv = omero.cli.argv()
 File "/opt/omero/server/OMERO.server/lib/python/omero/cli.py", line 1626, in argv
   cli.invoke(args[1:])
 File "/opt/omero/server/OMERO.server/lib/python/omero/cli.py", line 1101, in invoke
   stop = self.onecmd(line, previous_args)
 File "/opt/omero/server/OMERO.server/lib/python/omero/cli.py", line 1178, in onecmd
   self.execute(line, previous_args)
 File "/opt/omero/server/OMERO.server/lib/python/omero/cli.py", line 1260, in execute
   args.func(args)
 File "/home/dlindner/omero-cli-render/src/omero_cli_render.py", line 333, in _wrapper
   return func(self, *args, **kwargs)
 File "/home/dlindner/omero-cli-render/src/omero_cli_render.py", line 644, in set
   imgchannels = img.getChannels()
 File "/opt/omero/server/OMERO.server/lib/python/omero/gateway/__init__.py", line 8484, in getChannels
   if not self._prepareRenderingEngine():
 File "/opt/omero/server/OMERO.server/lib/python/omero/gateway/__init__.py", line 7985, in _prepareRenderingEngine
   self._re = self._prepareRE(rdid=rdid)
 File "/opt/omero/server/OMERO.server/lib/python/omero/gateway/__init__.py", line 7959, in _prepareRE
   re.resetDefaultSettings(True, ctx)
 File "/opt/omero/server/OMERO.server/lib/python/omero/gateway/__init__.py", line 4691, in __call__
   return self.handle_exception(e, *args, **kwargs)
 File "/opt/omero/server/OMERO.server/lib/python/omero/gateway/__init__.py", line 4688, in __call__
   return self.f(*args, **kwargs)
 File "/opt/omero/server/OMERO.server/lib/python/omero_api_RenderingEngine_ice.py", line 2326, in resetDefaultSettings
   return _M_omero.api.RenderingEngine._op_resetDefaultSettings.invoke(self, ((save, ), _ctx))
omero.InternalException: exception ::omero::InternalException
{
   serverStackTrace = ome.conditions.InternalException:  Wrapped Exception: (java.lang.RuntimeException):
loci.formats.FormatException: Invalid image number: 4 (series=0, imageCount=4)
	at ome.io.bioformats.BfPixelsWrapper.getPlane(BfPixelsWrapper.java:265)
	at ome.io.bioformats.BfPixelBuffer.getPlane(BfPixelBuffer.java:209)
	at ome.services.RawPixelsBean.findMinMax(RawPixelsBean.java:762)
	at ome.logic.RenderingSettingsImpl.computeLocationStats(RenderingSettingsImpl.java:927)
	at ome.logic.RenderingSettingsImpl.resetChannelBindings(RenderingSettingsImpl.java:856)
	at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:608)
	at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:524)
	at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:1429)
	at ome.services.RenderingBean$11.doWork(RenderingBean.java:2196)
	at sun.reflect.GeneratedMethodAccessor314.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:573)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
	at com.sun.proxy.$Proxy72.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:452)
	at ome.services.util.Executor$Impl.execute(Executor.java:396)
	at ome.services.RenderingBean._resetDefaults(RenderingBean.java:2193)
	at ome.services.RenderingBean.internalReset(RenderingBean.java:713)
	at ome.services.RenderingBean.resetDefaultSettings(RenderingBean.java:677)
	at sun.reflect.GeneratedMethodAccessor1577.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
	at com.sun.proxy.$Proxy97.resetDefaultSettings(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor1577.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
	at com.sun.proxy.$Proxy97.resetDefaultSettings(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor1579.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
	at ome.services.throttling.Callback.run(Callback.java:56)
	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
	at ome.services.blitz.impl.RenderingEngineI.resetDefaultSettings_async(RenderingEngineI.java:380)
	at sun.reflect.GeneratedMethodAccessor1578.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at omero.cmd.CallContext.invoke(CallContext.java:85)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
	at com.sun.proxy.$Proxy99.resetDefaultSettings_async(Unknown Source)
	at omero.api._RenderingEngineTie.resetDefaultSettings_async(_RenderingEngineTie.java:316)
	at omero.api._RenderingEngineDisp.___resetDefaultSettings(_RenderingEngineDisp.java:2017)
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2437)
	at IceInternal.Incoming.invoke(Incoming.java:221)
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
	at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
	at Ice.ConnectionI.message(ConnectionI.java:1056)
	at IceInternal.ThreadPool.run(ThreadPool.java:395)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
	at java.lang.Thread.run(Thread.java:748)

   serverExceptionClass = ome.conditions.InternalException
   message =  Wrapped Exception: (java.lang.RuntimeException):
loci.formats.FormatException: Invalid image number: 4 (series=0, imageCount=4)
}

Looking at the stack trace server-side, the error is thrown while trying to access individual planes:

Caused by: loci.formats.FormatException: Invalid image number: 104 (series=0, imageCount=4)
	at loci.formats.FormatTools.checkPlaneNumber(FormatTools.java:1008) ~[formats-api.jar:0.5.3]
	at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:996) ~[formats-api.jar:0.5.3]
	at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:283) ~[formats-bsd.jar:0.5.3]
	at loci.formats.in.ColumbusReader.openBytes(ColumbusReader.java:198) ~[formats-gpl.jar:0.5.3]
	at loci.formats.ImageReader.openBytes(ImageReader.java:466) ~[formats-api.jar:0.5.3]
...

The reader allowing to read data exported from a PerkinElmer Columbus system was introduced specifically in the context of two IDR studies: id0019 and idr0020. As can be seen from the description or representative samples, the reader currently expects one file containing the pixel data (TIFF) per well samples.

In the case of idr0056, the dataset is structured such that all the well samples within one well are stored within a FLEX file. In order to be able to read the original submitted data, the reader needs to be updated to support this variant of the file format.

Sample plate: /uod/idr/filesets/idr0056-stojic-lncrnas/20190513-ftp/RNAi\ screenA/1921\[652\]/

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