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Sample GSM6499506

Query DataSets for GSM6499506

Status

Public on May 01, 2024

Title

Moderate 1

Sample type

SRA

Source name

Blood

Organism

Rattus norvegicus

Characteristics

strain: Sprague-Dawley
tissue: Blood
treatment: Moderate SHB
disease state: PTU-induced model

Treatment protocol

18 10-12-weeks old SD rats were randomly divided into six groups. The normal control group (rats were not subjected to any disposal, Normal group); the blank control group (rats were administered intragastrically by of propylthiouracil PTU 0.01/kg one day for 28 days, Blank group); the positive drug control group (rats subjected to nodular goiter were administered intragastrically with levothyroxin sodium tablets (LST) 0.07 mg/kg one day for one day 28 days, LST group); the light concentration of QMTG prescription group (rats subjected to goiter were administered intragastrically with QMTG 0.63 g/kg one day for 28 days, Light group); the moderate concentration of QMTG prescription group (rats subjected to nodular goiter were administered with intragastrically QMTG 1.26 g/kg one day for 28 days, Moderate group); the high concentration of QMTG prescription group (rats subjected to nodular goiter were administered intragastrically with QMTG 2.52 g/kg one day for 28 days, High group).

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA libraries according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq2000/2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 2500

Data processing

Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic location
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: Rattus_norvegicus Ensembl relaese-94
Supplementary files format and content: Excel file reports sequence and normalized expression of all miRNAs

Submission date

Aug 20, 2022

Last update date

May 01, 2024

Contact name

Yang Li

E-mail(s)

leeyeungwestchina@outlook.com

Organization name

West China Hospital of Sichuan University

Street address

No.37 Guoxue Alley, Wuhou District,