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| Status |
Public on Jul 01, 2022 |
| Title |
gemin3_hom_2 |
| Sample type |
SRA |
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| Source name |
Homozygous gemin3 mutants, repeat 2
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| Organism |
Danio rerio |
| Characteristics |
strain background: TAB-5
genotype/variation: Homozygous gemin3 mutants
Stage: 7 dpf
tissue: whole fish embryos
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| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were placed in Qiazol, and RNA was extracted by using Qiagen miRNeasy Mini Kit.
Prepare one paired end index library from each total RNA sample, pool 24 libraries, load pool on NovaSeq6000_S4, run as indexed 150 base paired end reads
embryos were placed in Qiazol, and RNA was extracted by using Qiagen miRNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads are trimmed using Trimmomatic v0.36
Trimmed reads are aligned using STAR 2.5.4a (mRNA) or "hisat2 2.2.1.0 --no-softclip --no-spliced-alignment --rna-strandness R --new-summary" (miRNA)
abundance is measured by RSEM ("rsem-calculate-expression --paired-end --forward-prob 0.0 --alignments -p 16 --seed 987347 --calc-ci --calc-pme --estimate-rspd --time --no-bam-output" for mRNA-Seq, "rsem-calculate-expression --forward-prob 1.0 --alignments -p 16 --seed 987347 --calc-ci --calc-pme --estimate-rspd --time --no-bam-output --fragment-length-mean 22 --fragment-length-sd 10 --seed-length 15" for miRNA-Seq)
Genome_build: danRer10/Ensembl release 91 for mRNA-Seq, miRBase mature miRNA for microRNA-Seq
Supplementary_files_format_and_content: RSEM output, gene abundance
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| Submission date |
Jul 12, 2019 |
| Last update date |
Jul 01, 2022 |
| Contact name |
zelin chen |
| E-mail(s) |
zelin.chen@nih.gov
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| Organization name |
NIH
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| Department |
NHGRI
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| Lab |
Burgess
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| Street address |
50 South Dr.
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL24995 |
| Series (1) |
| GSE134187 |
the role of SMN complex in tissue regeneration |
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| Relations |
| BioSample |
SAMN12259843 |
| SRA |
SRX6434712 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3938543_G3_2hom.genes.results.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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