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| Status |
Public on Aug 15, 2019 |
| Title |
Wildtype X. laevis at NF stage 47, Biological Replicate 2 |
| Sample type |
SRA |
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| Source name |
Whole-brain tissue
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| Organism |
Xenopus laevis |
| Characteristics |
group (control/thioridazine): Control
developmental stage: 47
biological replicate: 2
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| Treatment protocol |
Pharmacological exposures to induce brain defects were conducted on neurula stage embryos (NF stage 14-26) that had been reared at 14 ˚C prior to exposure. During the exposure windows, experimental and controls embryos were kept at 18 ˚C, after the exposure they were returned to 14 ˚C until they reached feeding-tadpole stages. Pharmacological treatments included: 90 µM thioridazine (Tocris). Plate densities during exposures were kept at 50 embryos per 10 mL of media.
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| Growth protocol |
All experiments utilizing Xenopus laevis were conducted in accordance with the guide for Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committee at Tufts University. Embryo culturing was carried out as previously described (Caine and McLaughlin, 2013). Embryos and tadpoles were reared in 0.1x Marc’s Modified Ringer’s solution (MMR, 10mM NaCl, 0.2 mM KCl, 0.1 mM CaCl, 0.2 mM MgCl2, 0.5 MM HEPES, 1 µM EDTA, pH 7.5) at 14-23 ˚C. The 0.1x MMR rearing media was refreshed at least three times a week. Feeding stage tadpoles were fed Sera Micron powdered growth food three times a week. Embryos and tadpoles were staged based on Nieuwkoop and Faber (P.D. Nieuwkoop and J. Faber, 1994).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were generated with the Qiagen RNeasy Mini kit and DNAse treated prior to generating cDNA libraries for RNAseq.
RNAseq cDNA libraries were constructed with the Illumina Truseq RNA Library Preparation Kit v2, following the manufacturer’s protocol. We applied Quibit analysis to quantify the RNAseq cDNA libraries, which were then pooled and run on Illumina Hi-Seq 2500 at the Tufts University Core Facility to generate 100-bp single end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were trimmed to remove adapter sequences and filtered to remove any low-quality reads with Trimmomatic.
Trimmed reads were mapped to the Xenopus laevis genome v9.1 with HISAT2.
Transcript count tables were generated with HTSeq-count.
Differential gene analysis was carried out using the DESeq2 package in R (Love et al., 2014).
Genome_build: Xenopus laevis genome v9.1
Supplementary_files_format_and_content: Tabular sheet, gene counts.
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| Submission date |
Apr 02, 2019 |
| Last update date |
Aug 17, 2019 |
| Contact name |
Kelly McLaughlin |
| E-mail(s) |
[email protected]
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| Organization name |
Tufts University
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| Department |
Biology
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| Lab |
McLaughlin Lab
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| Street address |
200 Boston Avenue
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| City |
Medford |
| State/province |
MA |
| ZIP/Postal code |
02155 |
| Country |
USA |
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| Platform ID |
GPL18936 |
| Series (1) |
| GSE129234 |
Differential gene expression analysis between pre-metamorphic WT control X. laevis tadpoles and tadpoles with thioridazine-induced brain abnormalities. |
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| Relations |
| BioSample |
SAMN11318726 |
| SRA |
SRX5626436 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3703273_htseq-count_on_C47_Brain_R2.tabular.txt.gz |
137.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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