LncRNA-seq of Rattus norvegicus: 8 weeks female liver - SRA

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SRX8106244: LncRNA-seq of Rattus norvegicus: 8 weeks female liver
1 ILLUMINA (Illumina HiSeq 4000) run: 43.6M spots, 13.1G bases, 4.5Gb downloads

Design: A total amount of 3 g RNA per sample was used for RNA-seq library construction. Firstly, Due to some lncRNAs lacking the poly (A) tail, the ribosomal RNA was removed from total RNA by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturers recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, the dTTP of dNTPs was replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 L USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq 4000 PE Cluster Kit (Illumia, NEB, USA) according to the manufacturers instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.

Submitted by: China Agricultural University

Study: Genome-Wide Identified and Functional Prediction of Long Non-coding RNAs involved in the Heat Stress Response in Sprague-Dawley Rats

PRJNA624751 • SRP256142 • All experiments • All runs

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Heat stress, as one of the major factor among kinds of abiotic stresses that influences the human and animal survival and development. However, Our understanding of the contribution of lncRNAs to the cellular heat stress response is still highly rudimentary. Therefore, in the present study, we performed a transcriptomic analysis of rat liver and adrenal gland following exposure to heat stress to identify related DEGs, DElncRNAs and key pathways.

Sample: Liver_H120_3

SAMN14582908 • SRS6472000 • All experiments • All runs

Organism: Rattus norvegicus

Library:

Name: liver_H120_3

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: RANDOM PCR

Layout: PAIRED

Runs: 1 run, 43.6M spots, 13.1G bases, 4.5Gb

Run	# of Spots	# of Bases	Size	Published
SRR11535186	43,648,769	13.1G	4.5Gb	2020-12-31

ID:: 10555696

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