Cerebellum development: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| (5 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
{{TimeCourse | {{TimeCourse | ||
|TCOverview=Brain development requires intricately controlled expression of specific gene regulatory networks across time. Despite recent development in genomics technology, temporally-dependent large-scale transcriptome analyses across neural development are lacking. The cerebellum is a less complex, anatomically discrete and well-studied part of the mammalian brain that lends itself to such an analysis. To identify active transcription factor networks in developing mouse cerebellum, we analyzed the sequenced CAGE libraries from 12 time points across cerebellar development (embryonic days 11-18 at 24 hour intervals and every 72hrs until postnatal day 9).<br>'''Background'''<br><br>Brain development requires intricately controlled expression of specific gene regulatory networks across time. Despite recent development in genomics technology, temporally-dependent large-scale transcriptome analyses across neural development are lacking. The cerebellum is a less complex, anatomically discrete and well-studied part of the mammalian brain that lends itself to such an analysis. In cerebellum, the rhombic lip (RL) gives rise to the excitatory neurons of the cerebellum: first glutamatergic cerebellar nuclear neurons and then granule cell precursors and unipolar brush cells whereas the ventricular neuroepithelium gives rise to Purkinje cells and other GABAergic interneurons and cerebellar nuclear neurons. The key transcription factors Math1 and Pax6 are expressed in RL and the external germinal layer (EGL), and Ptf1a is expressed in the ventricular neuroepithelium. Cerebellar granule cells go through several epochs of development from their origins in the rhombic lip around E12.5 to the trans-migratory cells that establish the EGL, to the highly proliferative and then migratory population that produces the largest cohort of neurons in the brain. In spite of numerous studies on granule cell development, the understanding of the genetic underpinnings of the establishment of the EGL is limited. By taking advantage of FANTOM5 Cerebellr Developmental Time Course analysis, we plan to identify the transcriptional network controlling the development of cerebellum with primary focus on cerebellar granule cells. | |TCOverview=Brain development requires intricately controlled expression of specific gene regulatory networks across time. Despite recent development in genomics technology, temporally-dependent large-scale transcriptome analyses across neural development are lacking. The cerebellum is a less complex, anatomically discrete and well-studied part of the mammalian brain that lends itself to such an analysis. To identify active transcription factor networks in developing mouse cerebellum, we analyzed the sequenced CAGE libraries from 12 time points across cerebellar development (embryonic days 11-18 at 24 hour intervals and every 72hrs until postnatal day 9).<br>'''Background'''<br><br>Brain development requires intricately controlled expression of specific gene regulatory networks across time. Despite recent development in genomics technology, temporally-dependent large-scale transcriptome analyses across neural development are lacking. The cerebellum is a less complex, anatomically discrete and well-studied part of the mammalian brain that lends itself to such an analysis. In cerebellum, the rhombic lip (RL) gives rise to the excitatory neurons of the cerebellum: first glutamatergic cerebellar nuclear neurons and then granule cell precursors and unipolar brush cells whereas the ventricular neuroepithelium gives rise to Purkinje cells and other GABAergic interneurons and cerebellar nuclear neurons. The key transcription factors Math1 and Pax6 are expressed in RL and the external germinal layer (EGL), and Ptf1a is expressed in the ventricular neuroepithelium. Cerebellar granule cells go through several epochs of development from their origins in the rhombic lip around E12.5 to the trans-migratory cells that establish the EGL, to the highly proliferative and then migratory population that produces the largest cohort of neurons in the brain. In spite of numerous studies on granule cell development, the understanding of the genetic underpinnings of the establishment of the EGL is limited. By taking advantage of FANTOM5 Cerebellr Developmental Time Course analysis, we plan to identify the transcriptional network controlling the development of cerebellum with primary focus on cerebellar granule cells. | ||
|TCQuality_control=Bioanalyzer analysis was performed to check RNA quality. All RNA samples used for the time series achieved high RNA Integrity (RIN) Score. 34 out of 36 samples had RIN score of 9.7 or higher (10 being the best).<br><html><img src=' | |TCQuality_control=Bioanalyzer analysis was performed to check RNA quality. All RNA samples used for the time series achieved high RNA Integrity (RIN) Score. 34 out of 36 samples had RIN score of 9.7 or higher (10 being the best).<br><html><img src='/resource_browser/images/TC_qc/1000px-Mouse_cerebellum.png' onclick='javascript:window.open("/resource_browser/images/TC_qc/1000px-Mouse_cerebellum.png", "imgwindow", "width=1000,height=500");' style='width:700px;cursor:pointer'/></html>Figure 2: CAGE expression of marker genes in TPM.<br><br>References:<br>[1] Ha TJ, Swanson D, Kirova R, Yeung J, Choi K, Tong Y, Chesler E, Goldowitz D (2012) Genome-wide microarray comparison reveals downstream genes of Pax6 in the developing mouse cerebellum. Euro J Neurosci (In Press).<br>[2] Tong Y, Ha TJ, Liu L, Nishimoto A, Reiner A, Goldowitz D (2011) Spatial and temporal requirements for huntingtin (Htt) in neuronal migration and survival during brain development. J Neurosci 31:14794-14799.<br>[3] Swanson, D.J., Y. Tong, and D. Goldowitz, Disruption of cerebellar granule cell development in the Pax6 mutant, Sey mouse. Brain Res Dev Brain Res, 2005. 160(2): p. 176-93.<br>[4] Goldowitz, D. and K. Hamre, The cells and molecules that make a cerebellum. Trends Neurosci, 1998. 21(9): p. 375-82.<br> | ||
|TCSample_description=Mice were housed in a room with 12/12 hr light/dark controlled environment. Embryos were obtained from timed pregnant females at midnight of the day when a vaginal plug was detected; this was considered embryonic day 0 (E0). Pregnant females were cervically dislocated and embryos were harvested from the uterus. The cerebellum was isolated from each embryo, pooled with littermates of like genotype, and snap-frozen in liquid nitrogen. 3-4 replicate pools of 3-10 whole cerebella samples were collected from 12 time points across cerebellar development (embryonic days 11-18 at 24 hour intervals and every 72hrs until postnatal day 9)<br>Laser capture microdissection (LCM), a technique that can isolate specific cell types of interest from regions of tissue, was used to obtain pure populations of granule cells from early-stages of mouse cerebellar development. Fresh frozen brain tissue from mouse embryo (aged E13, 15 and 18) were collected and cyro-sectioned into 8 µm thick sections. The sections were then stained with cresyl violet for histological identification of the EGL. Veritas automated LCM system (Arcturus Veritus) was used to capture cells from external granular layer with infrared laser. Finally, the captured cells were lysed and RNA from pure granule cell population was extracted.<br> | |TCSample_description=Mice were housed in a room with 12/12 hr light/dark controlled environment. Embryos were obtained from timed pregnant females at midnight of the day when a vaginal plug was detected; this was considered embryonic day 0 (E0). Pregnant females were cervically dislocated and embryos were harvested from the uterus. The cerebellum was isolated from each embryo, pooled with littermates of like genotype, and snap-frozen in liquid nitrogen. 3-4 replicate pools of 3-10 whole cerebella samples were collected from 12 time points across cerebellar development (embryonic days 11-18 at 24 hour intervals and every 72hrs until postnatal day 9)<br>Laser capture microdissection (LCM), a technique that can isolate specific cell types of interest from regions of tissue, was used to obtain pure populations of granule cells from early-stages of mouse cerebellar development. Fresh frozen brain tissue from mouse embryo (aged E13, 15 and 18) were collected and cyro-sectioned into 8 µm thick sections. The sections were then stained with cresyl violet for histological identification of the EGL. Veritas automated LCM system (Arcturus Veritus) was used to capture cells from external granular layer with infrared laser. Finally, the captured cells were lysed and RNA from pure granule cell population was extracted.<br> | ||
|Time_Course= | |Time_Course= | ||
|category_treatment= | |category_treatment=Development | ||
|collaborators=Daniel Goldowitz | |collaborators=Daniel Goldowitz | ||
|description=mouse_cerebellum | |description=mouse_cerebellum | ||
| Line 14: | Line 14: | ||
|series=DEVELOPMENTAL TISSUE SERIES | |series=DEVELOPMENTAL TISSUE SERIES | ||
|species=Mouse (Mus musculus) | |species=Mouse (Mus musculus) | ||
|tet_config= | |tet_config=https://fantom.gsc.riken.jp/5/suppl/tet/Cerebellum_development.tsv.gz | ||
|tet_file=https://fantom.gsc.riken.jp/5/tet#!/search/?filename=mm9.cage_peak_phase1and2combined_tpm_ann_decoded.osc.txt.gz&file=1&c=1&c=440&c=441&c=442&c=443&c=444&c=445&c=446&c=447&c=448&c=449&c=450&c=451&c=452&c=453&c=454&c=455&c=456&c=457&c=458&c=459&c=460&c=461&c=462&c=463&c=464&c=465&c=466&c=467&c=468&c=469&c=470&c=471&c=472&c=473&c=474&c=475 | |||
|time_points= | |time_points= | ||
|time_span=17 days | |time_span=17 days | ||
|timepoint_design= | |timepoint_design=Embryonic stages | ||
|tissue_cell_type= | |tissue_cell_type=Cerebellum | ||
|zenbu_config= | |zenbu_config=https://fantom.gsc.riken.jp/zenbu/gLyphs/#config=6TQrz0bWBFyvEW7cEPvKVD | ||
}} | }} | ||
Latest revision as of 17:27, 14 March 2022
| Series: | DEVELOPMENTAL TISSUE SERIES |
|---|---|
| Species: | Mouse (Mus musculus) |
| Genomic View: | Zenbu |
| Expression table: | FILE |
| Link to TET: | TET |
| Sample providers : | Daniel Goldowitz |
| Germ layer: | ectoderm |
| Primary cells or cell line: | primary cells |
| Time span: | 17 days |
| Number of time points: | 12 |
| Overview |
|---|
|
Brain development requires intricately controlled expression of specific gene regulatory networks across time. Despite recent development in genomics technology, temporally-dependent large-scale transcriptome analyses across neural development are lacking. The cerebellum is a less complex, anatomically discrete and well-studied part of the mammalian brain that lends itself to such an analysis. To identify active transcription factor networks in developing mouse cerebellum, we analyzed the sequenced CAGE libraries from 12 time points across cerebellar development (embryonic days 11-18 at 24 hour intervals and every 72hrs until postnatal day 9). |
| Sample description |
|---|
|
Mice were housed in a room with 12/12 hr light/dark controlled environment. Embryos were obtained from timed pregnant females at midnight of the day when a vaginal plug was detected; this was considered embryonic day 0 (E0). Pregnant females were cervically dislocated and embryos were harvested from the uterus. The cerebellum was isolated from each embryo, pooled with littermates of like genotype, and snap-frozen in liquid nitrogen. 3-4 replicate pools of 3-10 whole cerebella samples were collected from 12 time points across cerebellar development (embryonic days 11-18 at 24 hour intervals and every 72hrs until postnatal day 9) |
| Quality control |
|---|
|
Bioanalyzer analysis was performed to check RNA quality. All RNA samples used for the time series achieved high RNA Integrity (RIN) Score. 34 out of 36 samples had RIN score of 9.7 or higher (10 being the best). |
Figure 2: CAGE expression of marker genes in TPM.Profiled time course samples
Only samples that passed quality controls (Arner et al. 2015) are shown here. The entire set of samples are downloadable from FANTOM5 human / mouse samples
| 10114-102E6 | cerebellum | embryo E11 | biol_rep1 (E11R1) |
| 10115-102E7 | cerebellum | embryo E12 | biol_rep1 (E12R1) |
| 10116-102E8 | cerebellum | embryo E13 | biol_rep1 (E13R1) |
| 10117-102E9 | cerebellum | embryo E14 | biol_rep1 (E14R1) |
| 10118-102F1 | cerebellum | embryo E15 | biol_rep1 (E15R1) |
| 10119-102F2 | cerebellum | embryo E16 | biol_rep1 (E16R1) |
| 10120-102F3 | cerebellum | embryo E17 | biol_rep1 (E17R1) |
| 10121-102F4 | cerebellum | embryo E18 | biol_rep1 (E18R1) |
| 10122-102F5 | cerebellum | neonate N00 | biol_rep1 (P0R1) |
| 10123-102F6 | cerebellum | neonate N03 | biol_rep1 (P3R1) |
| 10124-102F7 | cerebellum | neonate N06 | biol_rep1 (P6R1) |
| 10125-102F8 | cerebellum | neonate N09 | biol_rep1 (P9R1) |
| 10126-102F9 | cerebellum | embryo E11 | biol_rep2 (E11R2) |
| 10127-102G1 | cerebellum | embryo E12 | biol_rep2 (E12R2) |
| 10128-102G2 | cerebellum | embryo E13 | biol_rep2 (E13R2) |
| 10129-102G3 | cerebellum | embryo E14 | biol_rep2 (E14R2) |
| 10130-102G4 | cerebellum | embryo E15 | biol_rep2 (E15R2) |
| 10131-102G5 | cerebellum | embryo E16 | biol_rep2 (E16R2) |
| 10132-102G6 | cerebellum | embryo E17 | biol_rep2 (E17R2) |
| 10133-102G7 | cerebellum | embryo E18 | biol_rep2 (E18R2) |
| 10134-102G8 | cerebellum | neonate N00 | biol_rep2 (P0R2) |
| 10135-102G9 | cerebellum | neonate N03 | biol_rep2 (P3R2) |
| 10136-102H1 | cerebellum | neonate N06 | biol_rep2 (P6R2) |
| 10137-102H2 | cerebellum | neonate N09 | biol_rep2 (P9R2) |
| 10138-102H3 | cerebellum | embryo E11 | biol_rep3 (E11R3) |
| 10139-102H4 | cerebellum | embryo E12 | biol_rep3 (E12R3) |
| 10140-102H5 | cerebellum | embryo E13 | biol_rep3 (E13R3) |
| 10141-102H6 | cerebellum | embryo E14 | biol_rep3 (E14R3) |
| 10142-102H7 | cerebellum | embryo E15 | biol_rep3 (E15R3) |
| 10143-102H8 | cerebellum | embryo E16 | biol_rep3 (E16R3) |
| 10144-102H9 | cerebellum | embryo E17 | biol_rep3 (E17R3) |
| 10145-102I1 | cerebellum | embryo E18 | biol_rep3 (E18R3) |
| 10146-102I2 | cerebellum | neonate N00 | biol_rep3 (P0R3) |
| 10147-102I3 | cerebellum | neonate N03 | biol_rep3 (P3R3) |
| 10148-102I4 | cerebellum | neonate N06 | biol_rep3 (P6R3) |
| 10149-102I5 | cerebellum | neonate N09 | biol_rep3 (P9R3) |
