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Sample GSM4476683 Query DataSets for GSM4476683
Status Public on Apr 15, 2020
Title 11-day embryo AQ-seq
Sample type SRA
Source name 11-day embryo
Organism Mus musculus
Characteristics tissue: Embryo
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).
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina MiSeq
Description Small RNA-seq
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, RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from, and Rfam (from by intersectBed in BEDTools.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values (tsv) files containing miRNA names and corresponding read counts.
Submission date Apr 14, 2020
Last update date Apr 15, 2020
Contact name Haedong Kim
Phone +82-2-887-1343
Organization name Seoul National University
Department Biological Sciences
Street address 1 Gwanak-ro, Gwanak-gu
City Seoul
ZIP/Postal code 08826
Country South Korea
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
BioSample SAMN14598647
SRA SRX8117080

Supplementary file Size Download File type/resource
GSM4476683_embryo_11day_aqseq.read_count.tsv.gz 4.6 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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