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| Status |
Public on Jul 28, 2020 |
| Title |
ATAC-seq datasets for chromatin accessibility quantification in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems" |
| Organism |
Rattus norvegicus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
This dataset contains Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat embryonic cortical, hippocampal, and striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 1hr.
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| Overall design |
This experiment contains 18 biological samples, each of which underwent ATAC-seq on an Illumina NextSeq500 instrument. Samples were treated with neurobasal media (vehicle; samples V1C, V2C, V3C, V1H, V2H, V4H, V1S, V2S, V4S), or 10mM KCl (samples K2C, K3C, K4C, K1H, K2H, K4H, K1S, K2S, K3S) . The first letter of sample names denotes acute treatement (V = vehicle, K = KCl). The second digit denotes the unique replicate ID for a given brain region and treatment. The third digit denotes the region of cultured neuron (C = cortex, H = hippocampus, S = striatum). Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.
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| Contributor(s) |
Carullo NN, Phillips RA, Ianov L, Day JJ |
| Citation(s) |
32810208, 37333110, 37938195 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 MH114990 |
Enhancer RNA Regulation of Experience-dependent Neuroepigenetic Processes |
UNIVERSITY OF ALABAMA AT BIRMINGHAM |
JEREMY J DAY |
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| Submission date |
May 14, 2020 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Jeremy Jason Day |
| E-mail(s) |
jjday@uab.edu
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| Phone |
205-996-8960
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| Organization name |
UAB
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| Department |
Neurobiology
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| Lab |
Day
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| Street address |
1825 University Blvd
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| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
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| Platforms (1) |
| GPL20084 |
Illumina NextSeq 500 (Rattus norvegicus) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA632876 |
| SRA |
SRP261642 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150589_AllRegions_ATACPeaks.bed.gz |
1.6 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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