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{{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='https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/1000px-Mouse_cerebellum.png' onclick='javascript:window.open("https://fantom5-collaboration.gsc.riken.jp/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>
|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=
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|series=DEVELOPMENTAL TISSUE SERIES
|series=DEVELOPMENTAL TISSUE SERIES
|species=Mouse (Mus musculus)
|species=Mouse (Mus musculus)
|tet_config=http://fantom.gsc.riken.jp/5/suppl/tet/Cerebellum_development.tsv.gz
|tet_config=https://fantom.gsc.riken.jp/5/suppl/tet/Cerebellum_development.tsv.gz
|tet_file=http://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
|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=Embryonic stages
|timepoint_design=Embryonic stages
|tissue_cell_type=Cerebellum
|tissue_cell_type=Cerebellum
|zenbu_config=http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=7IO5l4PoAZjknqRIeAnm6C
|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).
Background

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.

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)
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.

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.

References:
[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).
[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.
[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.
[4] Goldowitz, D. and K. Hamre, The cells and molecules that make a cerebellum. Trends Neurosci, 1998. 21(9): p. 375-82.

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


10114-102E6cerebellumembryo E11biol_rep1 (E11R1)
10115-102E7cerebellumembryo E12biol_rep1 (E12R1)
10116-102E8cerebellumembryo E13biol_rep1 (E13R1)
10117-102E9cerebellumembryo E14biol_rep1 (E14R1)
10118-102F1cerebellumembryo E15biol_rep1 (E15R1)
10119-102F2cerebellumembryo E16biol_rep1 (E16R1)
10120-102F3cerebellumembryo E17biol_rep1 (E17R1)
10121-102F4cerebellumembryo E18biol_rep1 (E18R1)
10122-102F5cerebellumneonate N00biol_rep1 (P0R1)
10123-102F6cerebellumneonate N03biol_rep1 (P3R1)
10124-102F7cerebellumneonate N06biol_rep1 (P6R1)
10125-102F8cerebellumneonate N09biol_rep1 (P9R1)
10126-102F9cerebellumembryo E11biol_rep2 (E11R2)
10127-102G1cerebellumembryo E12biol_rep2 (E12R2)
10128-102G2cerebellumembryo E13biol_rep2 (E13R2)
10129-102G3cerebellumembryo E14biol_rep2 (E14R2)
10130-102G4cerebellumembryo E15biol_rep2 (E15R2)
10131-102G5cerebellumembryo E16biol_rep2 (E16R2)
10132-102G6cerebellumembryo E17biol_rep2 (E17R2)
10133-102G7cerebellumembryo E18biol_rep2 (E18R2)
10134-102G8cerebellumneonate N00biol_rep2 (P0R2)
10135-102G9cerebellumneonate N03biol_rep2 (P3R2)
10136-102H1cerebellumneonate N06biol_rep2 (P6R2)
10137-102H2cerebellumneonate N09biol_rep2 (P9R2)
10138-102H3cerebellumembryo E11biol_rep3 (E11R3)
10139-102H4cerebellumembryo E12biol_rep3 (E12R3)
10140-102H5cerebellumembryo E13biol_rep3 (E13R3)
10141-102H6cerebellumembryo E14biol_rep3 (E14R3)
10142-102H7cerebellumembryo E15biol_rep3 (E15R3)
10143-102H8cerebellumembryo E16biol_rep3 (E16R3)
10144-102H9cerebellumembryo E17biol_rep3 (E17R3)
10145-102I1cerebellumembryo E18biol_rep3 (E18R3)
10146-102I2cerebellumneonate N00biol_rep3 (P0R3)
10147-102I3cerebellumneonate N03biol_rep3 (P3R3)
10148-102I4cerebellumneonate N06biol_rep3 (P6R3)
10149-102I5cerebellumneonate N09biol_rep3 (P9R3)
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