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| Status |
Public on Sep 11, 2020 |
| Title |
mondoa_mis_3 [CtrlMo_3] |
| Sample type |
SRA |
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| Source name |
embryo_mondoa_mis
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| Organism |
Danio rerio |
| Characteristics |
treatment: mondoa-mis injected
Stage: 4 hpf
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| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction was performed as described in the manufacturer’s protocol, with minor modifications. If not otherwise stated, 30 embryos were harvested in 1.5 ml TRIzol. Embryos were disrupted in the TRIzol solution with micropestles (Eppendorf), and 5 x 105 cells in 25 cm2 flasks were harvested with 1.5 ml TRIzol solution. Samples were then stored overnight at –80°C. After thawing the samples on ice, they were passed through a syringe four times (Braun Sterican, 0.45 x 25 mm).
Indexed mRNAseq libraries were generated from morphant samples following the TruSeq mRNA kit protocol (Illumina).
Libraries were sequenced on a HiSeq 1000 system (Illumina) in 3 lanes of a paired-end flow cell. For each end, 50 nucleotides were sequenced. Cluster and sequencing reactions were performed with the TruSeq SBS kit v3-HS and the paired-end cluster v3- cBot-HS kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Description |
CtrlMo_3_CAGATC
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| Data processing |
mapping using STAR 2.3.8
Uniquely mapped reads were counted for each gene locus defined in the Ensembl 96 release. Briefly, we applied SAMtools view (Li et al., 2009) to assign uniquely mapped paired-end reads
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: tab delimited table containing raw counts for each sample
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| Submission date |
Jan 28, 2020 |
| Last update date |
Jul 12, 2022 |
| Contact name |
Benjamin D Weger |
| Organization name |
EPFL
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| Department |
SV
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| Lab |
Naef Lab
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| Street address |
Station 15
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| City |
Lausanne |
| State/province |
VD |
| ZIP/Postal code |
76344 |
| Country |
Germany |
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| Platform ID |
GPL16509 |
| Series (2) |
| GSE144349 |
RNA-seq of mondoa zebrafish morphants |
| GSE144350 |
Regulation of cholesterol biogenesis by the glucose-sensing transcription factor MondoA is required for zebrafish epiboly |
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| Relations |
| BioSample |
SAMN13932537 |
| SRA |
SRX7639409 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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