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| Status |
Public on Apr 15, 2020 |
| Title |
Stomach AQ-seq |
| Sample type |
SRA |
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| Source name |
Stomach
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| Organism |
Mus musculus |
| Characteristics |
tissue: Stomach
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| Extracted molecule |
total RNA |
| Extraction protocol |
Commercially available: Mouse Total RNA Master Panel; Takara
AQ-seq (bias-minimized sRNA-seq) libraries were constructed using total RNAs from fifteen mouse tissues (Mouse Total RNA Master Panel; Takara) as described in our previous study (Kim et al., 2019). Briefly, we mixed 5 μg of total RNAs with 10 fmole of thirty equimolar spike-in RNAs which are miRNA-like non-human/mouse/frog/fish RNAs used for bias evaluation. Small RNAs were enriched by size fractionation by 15% urea-polyacrylamide gel electrophoresis and sequentially ligated to the randomized adapter at the 3′ and 5′ ends. The ligated RNAs were reverse-transcribed using SuperScript III reverse transcriptase (Invitrogen), amplified using Phusion High-Fidelity DNA Polymerase (Thermo Scientific), and subjected to high-throughput sequencing on the MiSeq platform (Illumina).
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
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| Description |
Small RNA-seq
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| Data processing |
FASTQ files were generated by base-calling using Illumina RTA (v1.18) and conversion using bcl2fastq (v1.8.4).
The TruSeq 3′ adapter sequence was removed using cutadapt. For AQ-seq data, 4 nt-long degenerate sequences at the 3′ and 5′ end were trimmed using the FASTX-Toolkit. Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Preprocessed reads were first aligned to the spike-in sequences by BWA with an option of -n 3. Reads mapped to spike-in sequences perfectly or with a single mismatch were considered as reliable spike-in reads.
Reads unmapped to spike-in sequences by BWA with an option of -n 3 were subsequently mapped to the mouse genome (mm10) with the same option. For multi-mapped reads, we selected the alignment results which have the best alignment score, allowing mismatches only at the 3′ end of reads using custom scripts.
Reads were classified into annotations from miRBase release 21 (from www.mirbase.org), RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from gtrnadb.ucsc.edu), and Rfam (from rfam.sanger.ac.uk) by intersectBed in BEDTools.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values (tsv) files containing miRNA names and corresponding read counts.
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| Submission date |
Apr 14, 2020 |
| Last update date |
Apr 15, 2020 |
| Contact name |
Haedong Kim |
| E-mail(s) |
hdkim615@gmail.com
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| Phone |
+82-2-887-1343
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| Organization name |
Seoul National University
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| Department |
Biological Sciences
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| Street address |
1 Gwanak-ro, Gwanak-gu
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| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platform ID |
GPL16417 |
| Series (2) |
| GSE148686 |
A mechanism for microRNA arm switching regulated by uridylation [AQ-seq] |
| GSE148687 |
A mechanism for microRNA arm switching regulated by uridylation |
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| Relations |
| BioSample |
SAMN14598694 |
| SRA |
SRX8117092 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4476695_stomach_aqseq.read_count.tsv.gz |
3.3 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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