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| Status |
Public on Jul 28, 2020 |
| Title |
RNA-seq datasets for enhancer RNA quantification in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems" |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
This dataset contains total RNA sequencing results from rat embryonic cortical, hippocampal, and striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 1hr prior to RNA extraction.
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| Overall design |
This experiment contains 19 biological samples, each of which underwent directional, 75bp paired-end total RNA-seq on an Illumina NextSeq500 instrument. Samples were treated with neurobasal media (vehicle; samples V1C, V2C, V3C, V1H, V2H, V3H, V2S, V4S, V6S, V8S), or 10mM KCl (samples K1C, K2C, K3C, K1H, K2H, K3H, K1S, K5S, K7S) . The first letter of sample names denotes acute treatement (V = vehicle, K = KCl). The second digit denotes the unique replicate ID. The third digit denotes the region of cultured neuron (C = cortex, H = hippocampus, S = striatum). NEBnext rRNA depletion kit was used to remove ribosomal RNA to include both polyadenylated and non-polyadenylated RNA. Samples were sequenced across multiple lanes of the Illumina instrument, designated as L001, L002, L003, L004 in raw file names. Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.
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| Contributor(s) |
Carullo NV, 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 13, 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 (19)
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| Relations |
| BioProject |
PRJNA632596 |
| SRA |
SRP261474 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150499_Supplementary_Data_Table_RNA.txt.gz |
18.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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