Samples were sorted as described above and each replicate indicates a biological replicate that was prepared using different sets of mice on different experimental days. RNA-seq library preparations were performed (Chevrier, N. manuscript in preparation). Briefly, RNA was isolated using MyOne Silane Dynabeads (Thermo Fisher Scientific). RNA was fragmented, and barcoded using 8bp barcodes in conjunction with standard Illumina adaptors. Primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) and samples were amplified with 14 PCR cycles. Libraries were gel purified and quantified using a Qubit high sensitivity DNA kit (Invitrogen) and library quality was confirmed using Tapestation high sensitivity DNA tapes (Agilent Technologies). RNA Sequencing reactions were sequenced on an Illumina HiSeq 2000 or Illumina NextSeq sequencer (Illumina) according to manufacturer’s instructions, sequencing 50bp reads. Analysis was performed using the CLC Genomics Workbench version 8.0.1 RNA-seq analysis software package (Qiagen). Briefly, reads were aligned (mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8) to the mouse genome and differential expression analysis was performed (total count filter cutoff=5.0). Results were normalized to reads per million. Gene-e (Broad Institute) was used to generate heatmaps.
Clc genomics workbench version 8.0.1 rna seq analysis software package
Manufactured by Qiagen
The CLC Genomics Workbench version 8.0.1 is an RNA-seq analysis software package developed by Qiagen. It provides a comprehensive set of tools for the analysis and visualization of RNA sequencing data.
Automatically generated - may contain errors
Lab products found in correlation
Tapestation high sensitivity dna tapes, by Agilent Technologies (4 mentions)
Qubit high sensitivity dna kit, by Thermo Fisher Scientific (4 mentions)
Dynabeads myone silane, by Thermo Fisher Scientific (4 mentions)
Nextseq sequencer, by Illumina (4 mentions)
Hiseq 2000, by Illumina (1 mentions)
Rlt buffer, by Qiagen (1 mentions)
4 protocols using clc genomics workbench version 8.0.1 rna seq analysis software package
1
RNA-seq Library Preparation and Analysis
2
RNA-seq Library Preparation and Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
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RNA-seq was performed as described previously15 (link). Briefly, RNA was isolated using MyOne Silane Dynabeads (Thermo Fisher Scientific). RNA was fragmented, and barcoded using 8bp barcodes in conjunction with standard Illumina adaptors. Primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) and samples were amplified with 14 PCR cycles. Libraries were gel purified and quantified using a Qubit high sensitivity DNA kit (Invitrogen) and library quality was confirmed using Tapestation high sensitivity DNA tapes (Agilent Technologies). RNA Sequencing reactions were sequenced on an Illumina NextSeq sequencer (Illumina) according to the manufacturer’s instructions, sequencing 50bp reads. Analysis was performed using the CLC Genomics Workbench version 8.0.1 RNA-seq analysis software package (Qiagen). Briefly, reads were aligned (mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8) to the mouse genome and differential expression analysis was performed (total count filter cutoff=5.0). Results were normalized to reads per million. Gene-e (Broad Institute) was used to generate heatmaps. The datasets generated during the current study are available on Gene Expression Omnibus (GEO) (Accession number GSE134153) and are available from the corresponding author on reasonable request.
3
RNA-seq library preparation and analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
RNAseq library preparations were performed as previously described75 (link). Briefly, samples were lysed with RLT Buffer (Qiagen) and RNA was isolated using MyOne Silane Dynabeads (Thermo Fisher Scientific). RNA was fragmented and barcoded with 8 bp barcodes. Primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt). Samples were amplified with 14 PCR cycles. Libraries were gel purified and quantified using a Qubit high sensitivity DNA kit (Invitrogen) and library quality was assessed using Tapestation high sensitivity DNA tapes (Agilent Technologies). RNA was sequenced on an Illumina NextSeq sequencer (Illumina) according to manufacturer’s instructions, sequencing 50 bp single end reads. Analysis was performed using the CLC Genomics Workbench version 8.0.1 RNAseq analysis software package (Qiagen). Briefly, reads were aligned (mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8) to the mouse genome and differential expression analysis was performed (total count filter cutoff = 5.0). Results were normalized to reads per million.
4
RNA-seq Library Preparation and Analysis
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