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| Status |
Public on May 08, 2019 |
| Title |
Transcriptomic profiling of zebrafish livers with nAtf6 overexpression at collected at 78 and 120 hpf |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Activting transcription factor 6 (Atf6) is one of three main mediators of the Unfolded Protein Response and it gets cleaved cleaved in the Golgi and its N-terminal consisting of the bZip domain translocates into the nucleus to generate a transcriptional response (nAtf6). This study carries out RNAseq on an established transgenic overexpression of nAtf6 in zebrafish hepatocytes ( tg(fabp10:nAtf6-cherry; cmlc2:GFP)-C allele). Samples were collected at 78 and 120 hpf to detect gene expression changes at early and late time points after nAtf6 is overexpressed.
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| Overall design |
We used two transgenic lines: Tg(fabp10a: CAAX-EGFP) to use as a marker of the liver for dissction and tg(fabp10:nAtf6-cherry; cmlc2:GFP)-C allele to overexpress nAtf6 specifically in hepatocytes.This experiment was conducted by natural spawnings between tg:(fabp10:nAtf6-cherry; cmlc2:GFP)-C and tg(fabp10a:CAAX-EGFP ). Using GFP to guide microdissscion of 20-25 livers at 78 hpf and 120 hpf . Total RNA isolated using TRIZOL and treated by DNAse I. Libraries were prepared using RiboZero (for 120 hpf samples) or polyA selection (for 78 hpf samples). Samples from 2 clutches collected at 78 hpf and 3 clutches at 120 hpf. Samples were sequenced on NextSeq550 (Illumina)
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| Contributor(s) |
Gummala M, Ramdas Nair A, Sadler (Edepli) KC |
| Citation(s) |
34863900 |
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| Submission date |
May 07, 2019 |
| Last update date |
Feb 29, 2024 |
| Contact name |
Kirsten Sadler Edepli |
| E-mail(s) |
kirsten.edepli@nyu.edu
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| Phone |
971568327587
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| Organization name |
New York University Abu Dhabi
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| Department |
Biology
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| Street address |
PO Box 129188
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| City |
Abu Dhabi |
| State/province |
Abu Dhabi |
| ZIP/Postal code |
000 |
| Country |
United Arab Emirates |
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| Platforms (2) |
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| Samples (10)
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| GSM3754093 |
sibslivr1: 5 dpf Livers non transgenic siblings-1 |
| GSM3754094 |
sibslivr2: 5 dpf Livers non transgenic siblings-2 |
| GSM3754095 |
sibslivr3: 5 dpf Livers non transgenic siblings-3 |
| GSM3754096 |
nATF61: 5 dpf Livers of ATF6 transgenic zebrafish-1 |
| GSM3754097 |
nATF62: 5 dpf Livers of ATF6 transgenic zebrafish-2 |
| GSM3754098 |
nATF63: 5 dpf Livers of ATF6 transgenic zebrafish-3 |
| GSM5145706 |
78 hpf liver from sibling of transgenics overexpressing nAtf6 - Clutch 1 |
| GSM5145707 |
78 hpf liver from sibling of transgenics overexpressing nAtf6 - Clutch 2 |
| GSM5145708 |
78 hpf liver from transgenics overexpressing nAtf6 - Clutch 1 |
| GSM5145709 |
78 hpf liver from transgenics overexpressing nAtf6 - Clutch 2 |
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| This SubSeries is part of SuperSeries: |
| GSE130801 |
Transcriptomic profiling of zebrafish livers at 5 dpf with nAtf6 overexpression or in response to ethanol exposures |
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| Relations |
| BioProject |
PRJNA541476 |
| SRA |
SRP195753 |
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