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| Status |
Public on Oct 01, 2014 |
| Title |
Zeb_fish_Emb_t_24h |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Danio rerio |
| Characteristics |
genotype/variation: WT
developmental stage: embryo 24h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit (Illumina) according to manufacturer’s guide. For each library, 10 ug of total RNA was separated on 15% urea-PAGE. RNA of 15-29 nt was gel-purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated (NEB). After gel purification of 3’ adaptor-ligated RNA, the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse-transcribed by SuperScript II (Life Technologies) and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500.
Total RNA was extracted using TRIzol reagent for each experimental condition.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
small RNA-Seq
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| Data processing |
The base calling was done by Illumina Pipeline (CASAVA) v1.8.2.
The 3′ adaptor sequences starting with “TGGAATTC” were removed, and the sequence reads with short length (<16 nt) or artifacts (e.g. long homopolymer) or low quality (Phred quality <30 in >15% of nucleotides) were filtered out using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC, respectively. The BWA short-read aligner (Li and Durbin, 2009) version 0.7.5a-r405 was used for the alignment, with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region.
Each aligned read was classified using intersectBed in Bedtools (Quinlan and Hall, 2010) with annotations retrieved from RefSeq, GtRNAdb, FlyBase, RepeatMasker, Rfam, and miRBase.
We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample-wise normalization of miRNA read counts was done by TMM normalization (Robinson and Oshlack, 2010) using edgR package (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html).
Genome_build: dm3 (GCF_000001215.2); danRer7 (GCA_000002035.2)
Supplementary_files_format_and_content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre-processed reads of each class of RNA; dme_miRNA-TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.
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| Submission date |
Sep 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yeon Choi |
| E-mail(s) |
[email protected]
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| Phone |
+82-2-887-1343
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| Organization name |
Seoul National University
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| Department |
School of Biological Sciences
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| Lab |
Narry Kim Lab
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| Street address |
Building 504 Room 501, School of Biological Sciences, Seoul National University, 1 Gwanangno, Gwanak-gu
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| City |
Seoul |
| ZIP/Postal code |
151-742 |
| Country |
South Korea |
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| Platform ID |
GPL14875 |
| Series (1) |
| GSE61931 |
Adenylation of maternally inherited microRNAs by Wispy |
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| Relations |
| BioSample |
SAMN03085464 |
| SRA |
SRX718003 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1517418_Zeb_fish_Emb_t_24h_1.classcount.csv.gz |
656 b |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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