DOI: 10.5061/dryad.tqjq2bw8w
title: UL12.5 mice brain and UL12.5 neurons were differentiated from 90D iPSCs rna-seq

description: Mitochondrial DNA (mtDNA) mutations and/or depletion are implicated in
 epilepsy and many neurodegenerative diseases. However, systematic
 investigation into how mtDNA alterations relate to epilepsy and
 neural degeneration is needed. Here, we established a mouse model in which
 mtDNA depletion is induced by the Herpes Simplex Virus Type 1 (HSV-1)
 protein UL12.5 in the brain led to an epileptic phenotype
 characterized by abnormal electroencephalography (EEG) patterns
 and increased neural excitability in hippocampus. We
 also found that UL12.5 mediated mtDNA depletion in neurons
 in vitro (rho-) causes epilepsy–like abnormal EEG.
 Caloric restriction (CR) or glucose restriction (GR) is a
 strategy proven to reduce epileptic activity, however GR
 mimetic 2-deoxy-D-glucose (2-DG),
 induced degeneration in mtDNA depleted neurons.
 Mechanistically, mtDNA depletion increased
 mitochondria-endoplasmic reticulum (ER) contacts,
 facilitating GR-induced mitochondrial calcium overload.
 Rho- neurons did not show changes in mitochondrial motility or
 membrane potential. Our study revealed an unexpected axis of mtDNA
 depletion, ER-mitochondrial contacts, and calcium overload in the rho-
 neuron model. Fasting-induced GR causes early motor dysfunction,
 accelerates epilepsy progression, and worsens neurodegeneration in UL12.5
 mice. Importantly, the IP3R inhibitor 2-APB blocks the neurodegeneration
 induced by fasting. This is the first description of animal and neuronal
 models of mitochondrial epilepsy. Our findings with these models
 suggest that GR may not be a viable clinical intervention in
 patients with mtDNA depletion.
description: <strong>RNA-seq analysis</strong>
 Total RNA was extracted with TRIzol. Libraries were prepared
 using an Illumina TruSeq RNA Sample Prep kit (Illumina, 20020594)
 following the manufacturer’s instruction. The RNA-seq experiment was
 performed at Annoroad Gene Technology Co. Ltd. (Beijing, China). The raw
 reads of RNA-seq were trimmed from 3′ to 5′ ends for each read, and the
 reads shorter than 50 bp were discarded. The reads that passed the quality
 control were mapped to mouse genome (mm10) with STAR (version 2.7).
 Stringtie (version 2.1.4) were then used to estimate transcript abundance
 in fragments per kilobase per million (FPKM). Genes were annotated as
 differentially expressed using DESeq2 (version 1.44). The GO analysis and
 KEGG pathway analysis were performed using R packages.
description: # UL12.5 mice brain and UL12.5 neurons were differentiated from 90D iPSCs
 rna-seq
 [https://doi.org/10.5061/dryad.tqjq2bw8w](https://doi.org/10.5061/dryad.tqjq2bw8w) We have submitted our raw data and clean data. three UL12.5 mouse brain tissue samples, numbered ul125-164, ul125-167, and ul125-172 respectively. three FLAG mouse brain tissue samples, numbered FLAG\_ nao-1, FLAG\_ nao-2, and FLAG\_ nao-3 respectively. three FLAG neurons samples, numbered neuronflag-1, neuronflag-2, and neuronflag-3 respectively and UL12.5 neurons samples, numbered neuronul125-1,neuronul125-2,neuronul125-3 respectively. Total RNA was extracted with TRIzol. Libraries were prepared using an Illumina TruSeq RNA Sample Prep kit (Illumina, 20020594) following the manufacturer’s instruction. The RNA-seq experiment was performed at Annoroad Gene Technology Co. Ltd. (Beijing, China). The raw reads of RNA-seq were trimmed from 3′ to 5′ ends for each read, and the reads shorter than 50 bp were discarded. The reads that passed the quality control were mapped to mouse genome (mm10) with STAR (version 2.7). Stringtie (version 2.1.4) (https://doi.org/10.5061/dryad.tqjq2bw8w) ## Description of the data and file structure **Cleandata of three UL12.5 mouse brain tissue samples, numbered ul125-164, ul125-167, and ul125-172 respectively:** 09d9c3b17ca61ac188721cbcd814ac1d Cleandata/ul125-164/ul125-164.base.png 111338b8e376394c4dd2c09e585975c2 Cleandata/ul125-164/ul125-164.quality.pdf 1aacf0f02d305e8807dac9dade06306f Cleandata/ul125-164/ul125-164.quality.png 2d595633909a02c997a58c7de789f792 Cleandata/ul125-164/ul125-164_R2.fq.gz 3f872b69438b517d0b60111ce62343b5 Cleandata/ul125-164/ul125-164_R1.fq.gz b4e26f52b91e7d28fd44da56ef5536f1 Cleandata/ul125-164/ul125-164.base.pdf 243c70079b736c73e673a64660937604 Cleandata/ul125-167/ul125-167.quality.pdf 26e1bab99e6a8afb86f28acf81356362 Cleandata/ul125-167/ul125-167.base.png 92721705f9ef3d024c94283710a55943 Cleandata/ul125-167/ul125-167_R1.fq.gz bc8896a26170d6dcc4b3b30d18e8d26a Cleandata/ul125-167/ul125-167_R2.fq.gz c3d18f135640e69124282e2a00582c50 Cleandata/ul125-167/ul125-167.quality.png da90f73d41bb17fa3d0ad01395a46b45 Cleandata/ul125-167/ul125-167.base.pdf 26de3914112064c084520332a1d1f742 Cleandata/ul125-172/ul125-172.quality.pdf 3e37ec8f984041e3f9c7308f94a6680e Cleandata/ul125-172/ul125-172.base.png aca73aac9efc19a6a654de79af076752 Cleandata/ul125-172/ul125-172_R1.fq.gz dc5b20ef52a2cf6c95fdeeb1bccb798b Cleandata/ul125-172/ul125-172_R2.fq.gz e12ad808aaacfbf84925398734c5b466 Cleandata/ul125-172/ul125-172.base.pdf f38ccd17a02b0ff8fb02c78de00be96c Cleandata/ul125-172/ul125-172.quality.png **Rawdata of three UL12.5 mouse brain tissue samples, numbered ul125-164, ul125-167, and ul125-172 respectively:** 3a5675eb597017964fd18091679d5c37 Rawdata/ul125-164/ul125-164_R1.fq.gz 491339a1728034bdf0fce0b2caeb42ef Rawdata/ul125-164/ul125-164.base.pdf 6e3ec251a2e3005b8ebf7f58132a8fa2 Rawdata/ul125-164/ul125-164.quality.pdf 7cd83f5b5a7b45d02594b2828119a493 Rawdata/ul125-164/ul125-164_R2.fq.gz f6a63e117ea305d60b83cf4eafd5bd9a Rawdata/ul125-164/ul125-164.quality.png fa37704a3f673c5e5cbbd4311aafad58 Rawdata/ul125-164/ul125-164.base.png 09cf7a5b1dfba21ecf6dad4f7433831b Rawdata/ul125-167/ul125-167.base.png 0e03d79ea8e5638b204e502136f9d0f9 Rawdata/ul125-167/ul125-167.quality.png 48dc408fad171e1d75dd727fa77c08c5 Rawdata/ul125-167/ul125-167.base.pdf 9d107f078bab541f2ebef9748b1fff8c Rawdata/ul125-167/ul125-167_R1.fq.gz f74b6f52fe728655af02ac608d5db75b Rawdata/ul125-167/ul125-167_R2.fq.gz fa267d646174d31d6f1392c307d33962 Rawdata/ul125-167/ul125-167.quality.pdf 023d19ebcfaa9f6707675df448965327 Rawdata/ul125-172/ul125-172.base.png 10c7be12f60043f1aafcd0e05f8c6d51 Rawdata/ul125-172/ul125-172.quality.png 431ad3af04cde823b95b779d774bc70b Rawdata/ul125-172/ul125-172_R1.fq.gz 50de7e118ac6518749a3ac0d674e1d3c Rawdata/ul125-172/ul125-172.base.pdf 55039a174a52171b7ce4da43f40b0d88 Rawdata/ul125-172/ul125-172.quality.pdf f7fb5e155aaee545b97d7d2f55f9b6a9 Rawdata/ul125-172/ul125-172_R2.fq.gz **Cleandata of three FLAG mouse brain tissue samples, numbered FLAG\_ nao-1, FLAG\_ nao-2, and FLAG\_ nao-3 respectively:** 20d27673a7880636a3ad9a9ec5d6c441 Cleandata/FLAG_nao_-1/FLAG_nao_-1_R1.fq.gz 48747f758d1926a540850ecc508fda3b Cleandata/FLAG_nao_-1/FLAG_nao_-1.base.pdf 50605a3861aa16b5d0adb1117e2fc49f Cleandata/FLAG_nao_-1/FLAG_nao_-1.quality.png 672fe5b7365abceebd66a3d96f1e1eeb Cleandata/FLAG_nao_-1/FLAG_nao_-1_R2.fq.gz acb688c9371f6fcad349df5e73da8e48 Cleandata/FLAG_nao_-1/FLAG_nao_-1.quality.pdf c4b300838170f8c5e143936bce3d0d20 Cleandata/FLAG_nao_-1/FLAG_nao_-1.base.png 081c67fa60c786418e68decf2dccf997 Cleandata/FLAG_nao_-2/FLAG_nao_-2.base.pdf 2084086cf47f8590ac255576100e6ac5 Cleandata/FLAG_nao_-2/FLAG_nao_-2.quality.png 38a1a8dc61c4f9c2b25f9825dd95088e Cleandata/FLAG_nao_-2/FLAG_nao_-2_R1.fq.gz a65e235fbdf939cf9e6196835f69cbe5 Cleandata/FLAG_nao_-2/FLAG_nao_-2.base.png beacffc547ea22d42ef22e0cf32029da Cleandata/FLAG_nao_-2/FLAG_nao_-2.quality.pdf fcad0553b28ab490e89f4ecc54bf01e8 Cleandata/FLAG_nao_-2/FLAG_nao_-2_R2.fq.gz 2f8eed1a2219f297097e6614615d684b Cleandata/FLAG_nao_-3/FLAG_nao_-3_R1.fq.gz 5384d15513445ca178e92e75831cc39b Cleandata/FLAG_nao_-3/FLAG_nao_-3.quality.png 64eacdea795b2f4b13c4e5bb64e3c0bb Cleandata/FLAG_nao_-3/FLAG_nao_-3_R2.fq.gz 7552787b117b61b9071258c292b66837 Cleandata/FLAG_nao_-3/FLAG_nao_-3.base.pdf dc91ca52895c681f60018abeca033a5f Cleandata/FLAG_nao_-3/FLAG_nao_-3.base.png df46d3269a641c53d517457393938132 Cleandata/FLAG_nao_-3/FLAG_nao_-3.quality.pdf **Rawdata of three FLAG mouse brain tissue samples, numbered FLAG\_ nao-1, FLAG\_ nao-2, and FLAG\_ nao-3 respectively:** 0ca5ee985aab280dd03d63cab54aa393 Rawdata/FLAG_nao_-1/FLAG_nao_-1.base.png 3be897f3cc5a876fea88ff7549776c6b Rawdata/FLAG_nao_-1/FLAG_nao_-1.base.pdf 9d138187aee3a823bb832a14da920828 Rawdata/FLAG_nao_-1/FLAG_nao_-1_R1.fq.gz d504ed899ba8013219c413896f1b448b Rawdata/FLAG_nao_-1/FLAG_nao_-1_R2.fq.gz d6a4493a99d42f00911eb1cb7d59e7c6 Rawdata/FLAG_nao_-1/FLAG_nao_-1.quality.png fcd966f638270386410a13988011fc45 Rawdata/FLAG_nao_-1/FLAG_nao_-1.quality.pdf b3af4aa28331f2f6f86f931bbff00a10 Rawdata/FLAG_nao_-2/FLAG_nao_-2.base.pdf e28eacaf3799b3ccf645f39a69ea233e Rawdata/FLAG_nao_-2/FLAG_nao_-2_R1.fq.gz f1c1cb016ef8a0e22433c5f534b7088c Rawdata/FLAG_nao_-2/FLAG_nao_-2_R2.fq.gz f2f06a02b8676bbd0e79ca7e69ef4d3f Rawdata/FLAG_nao_-2/FLAG_nao_-2.quality.pdf f8a1dcc1bc5b5e47138b93ce35b68f7f Rawdata/FLAG_nao_-2/FLAG_nao_-2.base.png fd680818786503c3abcf3d921d208106 Rawdata/FLAG_nao_-2/FLAG_nao_-2.quality.png 276d8bb797cedc40edc74656b6a4cb86 Rawdata/FLAG_nao_-3/FLAG_nao_-3.base.pdf 41fa1e27e7696f8d7e026e20737fcfc9 Rawdata/FLAG_nao_-3/FLAG_nao_-3.base.png 6447159dc935d4bfa6fab84346bc90cf Rawdata/FLAG_nao_-3/FLAG_nao_-3_R2.fq.gz 69268d0bb4801c11ce48db6a8b8d2668 Rawdata/FLAG_nao_-3/FLAG_nao_-3.quality.png 914bf3ee97733ea11289680977cc1129 Rawdata/FLAG_nao_-3/FLAG_nao_-3.quality.pdf ef0cb15b51a20b1c8e9d7f99747d1e05 Rawdata/FLAG_nao_-3/FLAG_nao_-3_R1.fq.gz **Rawdata of three FLAG neurons samples, numbered neuronflag-1, neuronflag-2, and neuronflag-3 respectively and UL12.5 neurons samples, numbered neuronul125-1,neuronul125-2,neuronul125-3respectively:** d074c06b9815493842eb7444f1545fbc Rawdata/neuronflag-2/neuronflag-2_R2.fq.gz 33217f01d6a8a532a7c02121bd455969 Rawdata/neuronul125-3/neuronul125-3_R1.fq.gz ff901520fc47d2b0fcabaa100f02e16c Rawdata/neuronflag-3/neuronflag-3_R1.fq.gz 0ce820333c8afb2eac5fdf9dc7d351b0 Rawdata/neuronflag-1/neuronflag-1_R1.fq.gz 16b765390c511f06749512cdcaf564e2 Rawdata/neuronul125-2/neuronul125-2_R2.fq.gz 226aedf18fbed0d2b8a462dbff67daee Rawdata/neuronul125-3/neuronul125-3_R2.fq.gz f73d5a209eabd0aec54518e51488f9cf Rawdata/neuronflag-2/neuronflag-2_R1.fq.gz 97553dfcd99f99f3a8fad2718aff9ab7 Rawdata/neuronul125-1/neuronul125-1_R1.fq.gz b209228208141888866619371c7459d8 Rawdata/neuronul125-1/neuronul125-1_R2.fq.gz cbe4fc92cf6e7ef38831e22f8df368c2 Rawdata/neuronul125-2/neuronul125-2_R1.fq.gz 40b771fd770f846ea9242989e1f8bb03 Rawdata/neuronflag-1/neuronflag-1_R2.fq.gz 0204c0b2b3d059bd2d2aa9dfe77099b3 Rawdata/neuronflag-3/neuronflag-3_R2.fq.gz