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| Status |
Public on May 16, 2024 |
| Title |
actinomycinD_4h-239865 |
| Sample type |
SRA |
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| Source name |
Embryo
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| Organism |
Danio rerio |
| Characteristics |
tissue: Embryo
genotype: WT (TLAB)
treatment: actinomycin D
time: 4 hpf
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| Treatment protocol |
Embryos were collected as soon as they were laid and put into E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, 10−5% methylene blue) containing inhibitors. Embryos were kept in this medium for the duration of the experiment. For this experiment we used already established concentrations for inhibitors: oligomycin (Millipore, 495455) 1µM, actinomycin D (Sigma-Aldrich, A1410) 10µg/ml. Untreated embryos were kept alongside as controls.
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| Growth protocol |
E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, 10−5% methylene blue).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen, 175023525). 1.5µg of total RNA was used for the construction of sequencing libraries.
Samples were submitted to VBCF NGS facility for library preparation and NGS sequencing. Samples were prepared with Quantseq kit (Lexogen) protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Reads mapping to abundant sequences (mitochondrial chromosome, phiX174 genome, and silva zebrafish rRNAs from the SILVA rRNA database) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1) .
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
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| Submission date |
May 13, 2024 |
| Last update date |
May 16, 2024 |
| Contact name |
Anastasia Chugunova |
| E-mail(s) |
anastasia.chugunova@imp.ac.at
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| Organization name |
IMP
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| Lab |
Pauli
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| Street address |
Campus-Vienna-Biocenter 1
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL30614 |
| Series (1) |
| GSE267318 |
Increase in ER-mitochondria contacts and mitochondrial fusion are hallmarks of mitochondrial activation during embryogenesis |
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| Relations |
| BioSample |
SAMN41382139 |
| SRA |
SRX24534896 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8263848_239865_counts.tsv.gz |
116.2 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
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