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| Status |
Public on Nov 01, 2021 |
| Title |
thymus_Female_002_rep1 |
| Sample type |
SRA |
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| Source name |
Thymus
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Fisher 344
tissue: Thymus
age (weeks): 2
Sex: Female
replicate: 1
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| Treatment protocol |
Each whole organ was individually ground into a fine powder
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| Growth protocol |
pair-housed under standard conditions
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from ~30 mg of ground tissue by using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, including treatment with DNase.
Small RNA libraries were constructed using Illumina TruSeq Small RNA Library Prep kit.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The adapter sequences were removed with fastp 0.23.2 software (http://opengene.org/fastp/fastp.0.23.2), followed by a quality filter and a length filter. Reads with more than 2 “N” bases were discarded. The clipped reads with length between 16 and 35 nt were retained for alignment to various transcript types, including miRNA (miRbase v22.1, http://www.mirbase.org/), piRNA (piRBase, http://www.regulatoryrna.org/database/piRNA/download.html), tRNA (GtRNAdb, http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Rnorv7/Rnorv7-seq.html), other RNA (NCBI transcriptome, https://www.ncbi.nlm.nih.gov/genome/73), and the rat genome (Rn7, https://hgdownload.soe.ucsc.edu/downloads.html#mammals). The alignment was performed with Bowtie 1.3.1 (http://bowtie-bio.sourceforge.net/manual.shtml) with less than 2 mismatched bases allowed.
miRDeep2.0.1.3 was used for novel miRNA predicting and mapping.
Genome_build: rat genome rn7 download from UCSC and miRBase v22.1.
Sequence of novel miRNAs are available in file on series record.
Supplementary_files_format_and_content: read count
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| Submission date |
Apr 17, 2021 |
| Last update date |
Feb 11, 2022 |
| Contact name |
Leming Shi |
| E-mail(s) |
lemingshi@fudan.edu.cn
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| Phone |
+86-18616827008
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| Organization name |
Fudan University
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| Department |
School of Life Sciences
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| Lab |
Center for Pharmacogenomics
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| Street address |
2005 Songhu Road
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| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE172269 |
Landscape of rat microRNA BodyMap across 11 organs, four ages, and two sexes |
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| Relations |
| BioSample |
SAMN18789433 |
| SRA |
SRX10627183 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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