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| Status |
Public on Sep 06, 2016 |
| Title |
wt2_4h.rep1 |
| Sample type |
SRA |
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| Source name |
embryos
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| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: embryos
time-window: 2-4h
genotype: gfp-vas,Pr Dr/TM3
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| Growth protocol |
Flies were kept at 25ºC with 12 hours light/dark cycles
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s protocol. The small-RNA fraction was isolated from the total RNA sample using a modification protocol of mirVana™ (MirVANA kit, Invitrogen) as Gu et al Methods Mol Biol 2011, 725:251
2S rRNA depletion using a protocol from Seitz H et al, Curr Biol 2008, 18:147
RNA libraries were prepared for sequencing using a protocol from Gu et al Methods Mol Biol 2011, 725:251.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
small RNA
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| Data processing |
Illumina CASAVA-1.8.2 software used for basecalling.
Prior to read mapping, small-RNA reads were processed using the FASTX-Toolkit to demultiplex, remove adaptor sequences (CTGTAGGCACCATCAAT) and the first 4 bases (corresponding to random barcode).
Sequence quality reads (phred quality ≥ 20 in 100% of nucleotides), reads length (18-30 nt) were filted. Fastq files were collapsed to fasta files.
Filtered reads were mapped to Drosophila Genome Release 5.50 using Bowtie 0.12.8 with parameters -f -v 0 --best --sam --al.
Genome_build: flybase: dmel-all-chromosome-r5.50
Supplementary_files_format_and_content: tab-delimited text file of sequence that were trimmed adaptor and the first 4 bases (corresponding to barcode), all bases quality score ≥ 20 for each Sample. Sequence count included.
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| Submission date |
Jun 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Howard D Lipshitz |
| E-mail(s) |
howard.lipshitz@utoronto.ca
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| Organization name |
University of Toronto
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| Department |
Molecular Genetics
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| Street address |
1 King's College Circle
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| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5S1A8 |
| Country |
Canada |
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| Platform ID |
GPL17275 |
| Series (1) |
| GSE82194 |
The Smaug RNA-binding protein is essential for microRNA synthesis during the Drosophila maternal-to-zygotic transition |
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| Relations |
| BioSample |
SAMN05199502 |
| SRA |
SRX1817509 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2186325_wt2_4h.rep1.txt.gz |
10.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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