 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 02, 2019 |
| Title |
Characterization of Npas4 and heterodimer DNA binding in stimulated and silenced rat neurons |
| Organism |
Rattus norvegicus |
| Experiment type |
Other
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We evaluated genome-wide DNA binding of NPAS4, ARNT1, ARNT2, H3K27ac, and RNAPII by chromatin immunoprecipitation sequencing (ChIP-seq) in mature primary hippocampal neurons (rat, DIV 28) that were pharmacologically silenced (“–”; 24 hours in TTX, CPP, and NBQX) or silenced and then treated with PTX for two hours (“+”) to trigger the production of AP- and EPSP-induced NPAS4.
|
| |
|
| Overall design |
ChIP-seq for Npas4, Arnt1, Arnt2, H3K27ac, and RNAPII were performed in stimulated and silenced cultured rat neurons, with 2 biological replicated of each ChIP.
|
| |
|
| Contributor(s) |
Brigidi GS, B Hayes MG, Delos Santos NP, Hartzell A, Texari L, Lin P, Bartlett A, Ecker JR, Benner C, Heinz S, Bloodgood BL |
| Citation(s) |
31585079 |
| |
| Submission date |
Mar 04, 2019 |
| Last update date |
Jan 07, 2020 |
| Contact name |
Michael Hayes |
| E-mail(s) |
mhayes8520@gmail.com
|
| Phone |
4805288547
|
| Organization name |
University of California, San Diego
|
| Department |
Medicine
|
| Lab |
Sven Heinz
|
| Street address |
UCSD Campus Direct, Room 105H/GPL, 9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL20084 |
Illumina NextSeq 500 (Rattus norvegicus) |
|
| Samples (24)
|
|
| Relations |
| BioProject |
PRJNA525418 |
| SRA |
SRP187430 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE127793_RNAPII_gene_expression_rpkm.txt.gz |
618.7 Kb |
(ftp)(http) |
TXT |
| GSE127793_ptx_arnt1_peaks.bed.gz |
1.6 Mb |
(ftp)(http) |
BED |
| GSE127793_ptx_arnt2_peaks.bed.gz |
932.4 Kb |
(ftp)(http) |
BED |
| GSE127793_ptx_h3k27ac_regions.bed.gz |
776.6 Kb |
(ftp)(http) |
BED |
| GSE127793_ptx_npas4_peaks.bed.gz |
470.5 Kb |
(ftp)(http) |
BED |
| GSE127793_rat_neuron_chip_PTX_Arnt2_comb.bw |
236.5 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_PTX_Arnt_comb.bw |
322.7 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_PTX_H3K27ac_comb.bw |
290.4 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_PTX_Input_comb.bw |
409.2 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_PTX_Npas4_comb.bw |
411.8 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_PTX_RNAPII_comb.bw |
369.4 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_TTX_Arnt2_comb.bw |
235.4 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_TTX_Arnt_comb.bw |
320.0 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_TTX_H3K27ac_comb.bw |
265.9 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_TTX_Input_comb.bw |
401.0 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_TTX_Npas4_comb.bw |
300.4 Mb |
(ftp)(http) |
BW |
| GSE127793_rat_neuron_chip_TTX_RNAPII_comb.bw |
368.8 Mb |
(ftp)(http) |
BW |
| GSE127793_ttx_arnt1_peaks.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE127793_ttx_arnt2_peaks.bed.gz |
601.1 Kb |
(ftp)(http) |
BED |
| GSE127793_ttx_h3k27ac_regions.bed.gz |
863.0 Kb |
(ftp)(http) |
BED |
| GSE127793_ttx_npas4_peaks.bed.gz |
1.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...