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Data released on March 17, 2014

Workflow, Neuroscience

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Supporting material for "A data repository and analysis framework for spontaneous neural activity recordings in developing retina".

Eglen, SJ; Weeks, M; Jessop, M; Simonotto, J; Jackson, T; Sernagor, E. (2014): Supporting material for "A data repository and analysis framework for spontaneous neural activity recordings in developing retina". GigaScience Database. http://dx.doi.org/10.5524/100089 RIS BibTeX Text

We present a curated repository of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5. The associated GigaScience paper describes the structure of the data, along with examples of reproducible research using these data files.

Citing the data
We are grateful to our colleagues for sharing their recordings. If you use any of these data sets, we request that you acknowledge the relevant authors by citing the corresponding papers:

Blankenship 2011
Blankenship, A.G., Hamby, A.M., Firl, A., Vyas, S., Maxeiner, S., Willecke, K., Feller, M.B.: The role of neuronal connexins 36 and 45 in shaping spontaneous firing patterns in the developing retina. J. Neurosci. 31, 9998–10008 (2011). doi:10.1523/jneurosci.5640-10.2011

Demas 2003
Demas, J., Eglen, S.J., Wong, R.O.L.: Developmental loss of synchronous spontaneous activity in the mouse retina is independent of visual experience.J. Neurosci. 23, 2851–2860 (2003)

Demas 2006
Demas, J., Sagdullaev, B.T., Green, E., Jaubert-Miazza, L., McCall, M.A., Gregg, R.G., Wong, R.O.L., Guido, W.: Failure to maintain eye-specific segregation in nob, a mutant with abnormally patterned retinal activity. Neuron 50, 247–259 (2006). doi:10.1016/j.neuron.2006.03.033

Hennig 2011
Hennig, M.H., Grady, J., van Coppenhagen, J., Sernagor, E.: Age-dependent homeostatic plasticity of GABAergic signaling in developing retinal networks. J. Neurosci. 31, 12159–12164 (2011). doi:10.1523/jneurosci.3112-11.2011

Kirkby 2013
Kirkby, L.A., Feller, M.B.: Intrinsically photosensitive ganglion cells contribute to plasticity in retinal wave circuits. Proc. Natl. Acad. Sci. U. S. A. 110, 12090–12095 (2013). doi:10.1073/pnas.1222150110

Maccione 2014
Maccione, A., Hennig, M.H., Gandolfo, M., Muthmann, O., van Coppenhagen, J., Eglen, S.J., Berdondini, L., Sernagor, E.: Following the ontogeny of retinal waves: Pan-Retinal recordings of population dynamics in the neonatal mouse. J. Physiol., (2014). doi:10.1113/jphysiol.2013.262840

Stacy 2005
Stacy, R.C., Demas, J., Burgess, R.W., Sanes, J.R., Wong, R.O.L.: Disruption and recovery of patterned retinal activity in the absence of acetylcholine. J. Neurosci. 25, 9347–9357 (2005). doi:10.1523/jneurosci.1800-05.2005

Stafford 2009
Stafford, B.K., Sher, A., Litke, A.M., Feldheim, D.A.: Spatial-temporal patterns of retinal waves underlying activity-dependent refinement of retinofugal projections. Neuron 64, 200–212 (2009). doi:10.1016/j.neuron.2009.09.021

Sun 2008
Sun, C., Warland, D.K., Ballesteros, J.M., van der List, D., Chalupa, L.M.: Retinal waves in mice lacking the beta2 subunit of the nicotinic acetylcholine receptor. Proc. Natl. Acad. Sci. U. S. A. 105, 13638–13643 (2008). doi:10.1073/pnas.0807178105

Torborg 2004
Torborg, C., Wang, C.-T., Muir-Robinson, G., Feller, M.B.: L-type calcium channel agonist induces correlated depolarizations in mice lacking the beta2 subunit nAChRs. Vision Res. 44, 3347–3355 (2004). doi:10.1016/j.visres.2004.08.015

Wong 1993
Wong, R.O., Meister, M., Shatz, C.J.: Transient period of correlated bursting activity during development of the mammalian retina. Neuron 11, 923–938 (1993). doi:10.1016/0896-6273(93)90122-8

Xu 2011
Xu, H.-P., Furman, M., Mineur, Y.S., Chen, H., King, S.L., Zenisek, D., Jimmy Zhou, Z., Butts, D.A., Tian, N., Picciotto, M.R., Crair, M.C.: An instructive role for patterned spontaneous retinal activity in mouse visual map development. Neuron 70, 1115–1127 (2011). doi:10.1016/j.neuron.2011.04.028

Related manuscripts:

doi:doi:10.1186/2047-217X-3-3

Additional information:

https://portal.carmen.org.uk

Projects:


Files (FTP site) (Aspera):Aspera user name: gigadb , password: gigadb Table Settings
Items per page:

File Name Sample ID File Type File Format Size Release Date

readme.txt

Readme TEXT 1 4 14151.38 KB 2014-03-17

bmcart-biblio.sty

Article UNKNOWN 1 5 1196711.69 KB 2014-03-17

bmcart.cls

Article UNKNOWN 1 5 5739056.04 KB 2014-03-17

bmc-mathphys.bst

Article UNKNOWN 1 5 5564154.34 KB 2014-03-17

Makefile

Code UNKNOWN 1 4 26202.56 KB 2014-03-17

waverepo.bib

Article UNKNOWN 1 6 10054098.18 KB 2014-03-17

sjemea_0.40.tar.gz

Code TAR 2 7 32658223.11 MB 2014-03-17

waverepo_paper.Rnw

Article UNKNOWN 1 5 4969848.53 KB 2014-03-17

waverepo_installs.R

Code UNKNOWN 1 3 5290.52 KB 2014-03-17

carmen-workflow-crop.pdf

Article PDF 1 4 95939.37 KB 2014-03-17