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| Status |
Public on Jan 05, 2022 |
| Title |
Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System Characterized by Whole Genome Bisulfite Sequencing (WGBS) |
| Organism |
Xenopus laevis |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Xenopus is uniquely suited for identifying core features of successful CNS axon regeneration, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. We performed bisulfite whole genome bisulfite methylation sequencing (WGBS) on juvenile frog eye after optic nerve injury, and on hindbrain samples from tadpole and juvenile frog after spinal cord injury during the peak phase of axon regeneration, to compare tissue-related and injury-induced differences in DNA methylation among them.
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| Overall design |
Whole Genome Bisulfite Sequencing (WGBS: 15XGenome coverage per sample) was performed on 21 samples (3 biological replicates; 7 tissues/conditions): operated juvenile frog eye and contralateral unoperated eye after optic nerve injury at 11 days post optic nerve crush, plus surgically naïve frog eyes, with 6 pooled eyes for each sample; tadpole hindbrain after spinal cord transection plus age-matched unoperated controls at 7 days post spinal cord transection, with 5 pooled hindbrains for each sample; juvenile frog hindbrain at 7 days after spinal cord transection, plus unoperated hindbrain control, with 5 pooled hindbrains for each sample.
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| Web link |
https://0-doi-org.brum.beds.ac.uk/10.1186/s12864-021-08247-0
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| Contributor(s) |
Szaro BG, Reverdatto S, Zhang X, Sammons MA, Gibbs KM |
| Citation(s) |
34979916 |
| Submission date |
Sep 03, 2021 |
| Last update date |
Jan 05, 2022 |
| Contact name |
Ben Gregory Szaro |
| E-mail(s) |
bgs86@albany.edu
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| Phone |
518-591-8852
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| Organization name |
University at Albany, SUNY
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| Department |
Biological Sciences
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| Lab |
Life Sciences 1059
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| Street address |
1400 Washington Avenue
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| City |
Albany |
| State/province |
NY |
| ZIP/Postal code |
12222 |
| Country |
USA |
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| Platforms (1) |
| GPL20998 |
Illumina HiSeq 1000 (Xenopus laevis) |
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| Samples (21)
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| GSM5556097 |
XL1 Tadpole hindbrain, Spinal Cord Transected, Replicate 1 |
| GSM5556098 |
XL2 Tadpole hindbrain, Spinal Cord Transected, Replicate 2 |
| GSM5556099 |
XL3 Tadpole hindbrain, Spinal Cord Transected, Replicate 3 |
| GSM5556100 |
XL4 Tadpole hindbrain, Unoperated, Replicate 1 |
| GSM5556101 |
XL5 Tadpole hindbrain, Unoperated, Replicate 2 |
| GSM5556102 |
XL6 Tadpole hindbrain, Unoperated, Replicate 3 |
| GSM5556103 |
XL7 Frog hindbrain, Unoperated , Replicate 1 |
| GSM5556104 |
XL8 Frog hindbrain, Unoperated , Replicate 2 |
| GSM5556105 |
XL9 Frog hindbrain, Unoperated , Replicate 3 |
| GSM5556106 |
XL10 Frog hindbrain, Spinal cord transected, Replicate 1 |
| GSM5556107 |
XL10 Frog hindbrain, Spinal cord transected, Replicate 2 |
| GSM5556108 |
XL10 Frog hindbrain, Spinal cord transected, Replicate 3 |
| GSM5556109 |
XL13 Frog eye, Unoperated animal, Replicate 1 |
| GSM5556110 |
XL14 Frog eye, Unoperated animal, Replicate 2 |
| GSM5556111 |
XL15 Frog eye, Unoperated animal, Replicate 3 |
| GSM5556112 |
XL16 Frog eye, Optic nerve crush, Operated eye, Replicate 1 |
| GSM5556113 |
XL17 Frog eye, Optic nerve crush, Operated eye, Replicate 2 |
| GSM5556114 |
XL18 Frog eye, Optic nerve crush, Operated eye, Replicate 3 |
| GSM5556115 |
XL19 Frog eye, Optic nerve crush, Unoperated eye, Replicate 1 |
| GSM5556116 |
XL20 Frog eye, Optic nerve crush, Unoperated eye, Replicate 2 |
| GSM5556117 |
XL21 Frog eye, Optic nerve crush, Unoperated eye, Replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE183357 |
Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System |
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| Relations |
| BioProject |
PRJNA760352 |
| SRA |
SRP335531 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE183355_MS-CpG_ONjv-11d_NA_XL13-15.bw |
656.1 Mb |
(ftp)(http) |
BW |
| GSE183355_MS-CpG_ONjv-11d_TX_XL16-18.bw |
660.6 Mb |
(ftp)(http) |
BW |
| GSE183355_MS-CpG_ONjv-11d_UO_XL19-21.bw |
667.9 Mb |
(ftp)(http) |
BW |
| GSE183355_MS-CpG_SCjv-1w_TX_XL10-12.bw |
660.4 Mb |
(ftp)(http) |
BW |
| GSE183355_MS-CpG_SCjv_UO_XL7-9.bw |
656.1 Mb |
(ftp)(http) |
BW |
| GSE183355_MS-CpG_SCtd-1w_TX_XL1-3.bw |
656.9 Mb |
(ftp)(http) |
BW |
| GSE183355_MS-CpG_SCtd-1w_UO_XL4-6.bw |
659.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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