RNA sequencing libraries were generated using the Illumina® Stranded mRNA Prep (Illumina, San Diego, CA). Samples were processed following the manufacturer’s instructions. The resulting libraries were multiplexed and sequenced with 100 basepairs (bp) Paired-End reads (PE100) to a depth of approximately 25 million reads per sample on an Illumina NovaSeq 6000. Samples were demultiplexed using bcl2fastq Conversion Software (Illumina, San Diego, CA, United States).
Stranded mrna prep
Manufactured by Illumina
Sourced in United States
The Stranded mRNA Prep is a laboratory equipment that prepares stranded mRNA samples for sequencing. It is designed to preserve the directionality of the mRNA molecules, allowing for accurate identification of the coding and non-coding strands.
Automatically generated - may contain errors
Lab products found in correlation
Novaseq 6000, by Illumina (10 mentions)
Bcl2fastq conversion software, by Illumina (3 mentions)
Rneasy kit, by Qiagen (3 mentions)
Rneasy plus mini kit, by Qiagen (2 mentions)
Rneasy tissue kit, by Qiagen (2 mentions)
Hiseq 4000, by Illumina (2 mentions)
Rneasy mrna extraction kit, by Qiagen (2 mentions)
Fastselect, by Qiagen (2 mentions)
Nextseq 500, by Illumina (2 mentions)
Ercc spike in control, by Thermo Fisher Scientific (2 mentions)
Nanodrop 2000, by Thermo Fisher Scientific (2 mentions)
Rneasy mini kit, by Qiagen (2 mentions)
Agilent high sensitivity d1000 screentape, by Agilent Technologies (2 mentions)
Qubit dsdna hs assay kit, by Thermo Fisher Scientific (2 mentions)
Nextseq 500 550 high output kit v2, by Illumina (2 mentions)
D1000 screentape, by Agilent Technologies (2 mentions)
Rna screentape, by Agilent Technologies (2 mentions)
Nextseq 550, by Illumina (2 mentions)
Novaseq platform, by Illumina (1 mentions)
Tapestation 4200, by Agilent Technologies (1 mentions)
27 protocols using stranded mrna prep
1
Illumina Stranded mRNA Sequencing
2
mRNA Sequencing with Illumina NextSeq
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated using the RNeasy Plus Mini Kit (74134, QIAGEN). mRNA-seq samples were pooled and sequenced on NextSeq 2000 P2 using Illumina® Stranded mRNA Prep and paired-end sequencing. Three independent replicates were used for RNA-seq analysis.
3
RNA-seq analysis of human fibroblast cultures
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
RNA was extracted from cultured HF or i-HF using the RNeasy kit (Qiagen). RNA quality control, library preparation, and sequencing were performed using the Génome Québec platform. RNA quality was assessed using the Perkin Elmer LabChip (RIN > 6.5). Illumina Stranded mRNA Prep was used for library preparation. Paired-end sequencing (PE100) was performed on the Illumina NovaSeq platform, achieving an average sequencing depth of 25 million reads per sample. Quality control was performed using FastQC. Reads were trimmed using trimmomatic (v0.39), aligned to the human genome GRCh38 using STAR2.7.9, and quantified using RSEM 1.3.1. Differential expression analysis and Student’s t-test statistical analysis were conducted using R (v4.3.1) and RStudio (v2023.09.01+494) software with the ggplot2 package (v3.4.4) for data visualization. The gene set enrichment analysis (GSEA) results were analyzed with the fgsea package (v3.18) from Bioconductor using reactome_cell_cycle, reactome_DNA_repair, and reactome_regulation_of_TP53_activity gene sets from the Molecular Signatures Database (MsigDB, v2023.2.Hs). GO_Biological_Process_2023 from Enrichr packages (v3.2) was used for gene ontology analysis. The raw sequencing data generated in this study have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE266663.
4
RNA Sequencing of Hippocampus and Cortex
5
RNA-seq Analysis of Transcriptome Profiles
6
RNA Extraction and RNA-seq Library Preparation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Cells were plated in 25-cm2 dishes at 75% confluence, and total RNA was extracted and purified from cells using the NucleoSpin® RNA Plus kit (Macherey-Nagel, Strasbourg, France) according to the manufacturer’s recommendations. Each RNA sample (three replicates per group) was validated for RNA integrity using an 18S/28S ratio. Then, 1 µg of total RNA from each sample (n = 10) was used for library preparation. Library preparation was realized following the manufacturer’s recommendations (Illumina Stranded mRNA Prep). Final samples pooled libraries prep were sequenced on ILLUMINA NovaSeq 6000 with SP-200 cartridge (2 × 800 millions of 100 bases reads), corresponding to 2 × 26 millions of reads per sample after demultiplexing. This work benefited from equipment and services from the iGenSeq core facility, at ICM (Paris, France).
7
Transcriptome Profiling of Saccharomyces cerevisiae
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Sequencing libraries were prepared by the University of Chicago Genomics Facility from DNase I treated RNA using Qiagen FastSelect (Qiagen #334215) and Illumina Stranded mRNA Prep (Illumina #20020595) kits. Paired end 200 bp sequencing was performed on an Illumina NovaSeq 6000.
Sequencing reads were trimmed using TrimGalore (v0.6.10,https://github.com/FelixKrueger/TrimGalore ) using default settings (e.g. trim_galore --paired --fastqc_args '--outdir fastqc/' -j 4 -o trimmed --basename F02 AD-JB-F02_S44_R1_001.fastq.gz AD-JB-F02_S44_R2_001.fastq.gz). They were mapped using STAR v2.7.10b84 (link) (e.g. STAR --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --sjdbGTFfile spike_saccharomyces_cerevisiae_R64–3-1_20210421_geneid.gff3 --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon CDS --sjdbGTFtagExonParentGene gene_id --runThreadN 4 --alignMatesGapMax 20000 --limitBAMsortRAM 1445804817 --genomeDir STAR_spike_saccharomyces_cerevisiae_R64–3-1_20210421 –outFileNamePrefix mapped_reads/F02/F02_ --readFilesIn trimmed/F02_val_1.fq.gz trimmed/F02_val_2.fq.gz). The estimated counts and TPMs were generated using kallisto v0.48.085 (link) (e.g. kallisto quant -i spike_Scerevisiae_orf_coding_all_Scerevisiae_rna_coding.fasta.idx -o kallisto_quant/F02 --fr-stranded --bootstrap-samples=50 -t 1 trimmed/F02_val_1.fq.gz trimmed/F02_val_2.fq.gz).
Sequencing reads were trimmed using TrimGalore (v0.6.10,
8
Transcriptional Response to IACS-9571 and dTRIM24
9
Muscle Transcriptome Response to Exercise
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
RNA was extracted from pulverized muscle biopsy samples at baseline (pre‐exercise) and 3.5‐h after exercise (post‐exercise) using the Qiagen RNeasy mRNA extraction kit and sent to the Mayo Clinic Genome Analysis Core for sequencing as previously described (Kunz et al., 2019 (link); Lalia et al., 2017 (link)). Briefly, libraries were prepared using the Illumina Stranded mRNA Prep and sequenced on an Illumina HiSeq 4000. Reads were aligned using STAR RNA‐seq aligner. Differential expression analysis was carried out using a negative binomial generalized log‐linear model in the edgeR R package. Gene set enrichment analysis was performed using Broads GSEA software. All gene sets that were negatively enriched with an FDR corrected p‐value (using the Benjamini‐Hochberg procedure) < 0.05 were reported.
10
Transcriptome Profiling of Saccharomyces cerevisiae
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Sequencing libraries were prepared by the University of Chicago Genomics Facility from DNase I treated RNA using Qiagen FastSelect (Qiagen #334215) and Illumina Stranded mRNA Prep (Illumina #20020595) kits. Paired end 200 bp sequencing was performed on an Illumina NovaSeq 6000.
Sequencing reads were trimmed using TrimGalore (v0.6.10,https://github.com/FelixKrueger/TrimGalore ) using default settings (e.g. trim_galore --paired --fastqc_args ‘--outdir fastqc/’ -j 4 -o trimmed --basename F02 AD-JB-F02_S44_R1_001.fastq.gz AD-JB-F02_S44_R2_001.fastq.gz). They were mapped using STAR v2.7.10b85 (link) (e.g. STAR --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --sjdbGTFfile spike_saccharomyces_cerevisiae_R64-3-1_20210421_geneid.gff3 -- sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon CDS -- sjdbGTFtagExonParentGene gene_id --runThreadN 4 --alignMatesGapMax 20000 -- limitBAMsortRAM 1445804817 --genomeDir STAR_spike_saccharomyces_cerevisiae_R64-3-1_20210421 --outFileNamePrefix mapped_reads/F02/F02_ --readFilesIn trimmed/F02_val_1.fq.gz trimmed/F02_val_2.fq.gz). The estimated counts and TPMs were generated using kallisto v0.48.086 (link) (e.g. kallisto quant -i spike_Scerevisiae_orf_coding_all_Scerevisiae_rna_coding.fasta.idx -o kallisto_quant/F02 -- fr-stranded --bootstrap-samples=50 -t 1 trimmed/F02_val_1.fq.gz trimmed/F02_val_2.fq.gz).
Sequencing reads were trimmed using TrimGalore (v0.6.10,
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!