An RNA-Seq template that adapts to your lab's study design.
This RNA-Seq template ships with a 10-step protocol covering RNA extraction quality through differential expression analysis, validated library prep references, pre-wired sample sheet fields, and structured inputs for RIN, library yields, fragment sizes, expected read depth, sequencer parameters, and downstream analysis pipeline. Your lab edits the configuration to match your study design and instrument, instead of rebuilding the sample sheet and run notes from scratch every cohort.
See exactly how the template loads in ELabELN.
This is the live ELabELN experiment view, the same screen your lab works in every day. Switch between a blank start and a fully populated example, then expand any section to see what the template pre-fills.
What this RNA-Seq template ships with.
This RNA-Seq template ships configured for a bulk RNA sequencing differential expression study, with a 10-step protocol covering total RNA QC through STAR alignment, featureCounts quantification, and DESeq2 differential expression. The protocol assumes a polyA-selected, strand-specific library prep (NEBNext Ultra II Directional RNA Library Prep Kit), Illumina NextSeq 2000 sequencing with a P2 100-cycle paired-end 75 kit, and Snakemake-orchestrated alignment and DE analysis. A 24-sample cohort (HER2 siRNA knockdown vs scrambled control across three breast cancer cell lines, three biological replicates each) is the example study.
Structured fields capture sample, library, and sequencing run metadata in typed inputs (sample group, biological replicate, RIN, library concentration, average fragment size, index sequence, expected read depth, sequencer instrument and kit, paired-end length), so sample sheets and run parameters are queryable across cohorts instead of buried in free text. RNA preps, library prep kits, sequencing reagents, and index sets link to the ELabELN inventory so kit-lot and index-pool traceability flow into every cohort record without manual entry. The spreadsheet editor captures the cohort sample sheet (sample ID, group, replicate, library yield, index, expected reads) plus a top-DEG summary table from the downstream DESeq2 run.
The template is intended as a tested baseline for academic and life sciences research labs running differential expression studies, transcriptomic profiling, or biomarker discovery. Configure the study design (case vs control, time course, multi-condition), swap the library prep chemistry (polyA, total RNA with rRNA depletion, smRNA, 3'-only), change the sequencing platform, or move from bulk to single-cell by editing the library prep and analysis sections. ELabELN's tamper-evident audit trail captures every sample sheet, every library QC, and every analysis run, so the resulting record supports cohort-level reproducibility documentation, multi-PI collaboration on shared transcriptomic resources, and FDA 21 CFR Part 11 review when the lab's quality system requires it.
Every ELN section, pre-populated for RNA-Seq.
The template populates the existing ELabELN sections your lab already works with: Main Text, Extra Fields, Steps, Compounds, Links, and more. Your team edits instead of building from scratch.
Main Text
Study design summary, library prep notes, expected DEG results, written in the TinyMCE editor.
- Hypothesis + design scaffold
- Library prep validation notes
- Linked to RNA extraction
Extra Fields
Twelve structured, typed fields grouped by Sample, Library, and Sequencing Run.
- Sample group, RIN, library conc
- Index seq, expected depth
- Queryable across cohorts
Steps
Ten-step workflow checklist covering RNA QC through DESeq2 DEG analysis.
- Extract, prep, pool, sequence
- Each tick timestamped
- Sequencer run auto-logged
Compounds
Library prep kit, sequencing kit, index sets, and RNA-Seq controls pre-linked from the compound database.
- Kit lots carried automatically
- Index pool tracking inline
- Low-stock warnings before run
Links & Resources
Pre-wired to your lab's RNA-Seq SOPs, the bioinformatics Snakemake workspace, and reference genome.
- NEBNext Ultra II SOP
- Snakemake DEG workflow ref
- GRCh38 reference linked
Storage & Files
RNA aliquots, prepped library aliquots, raw FASTQ paths, and DESeq2 result attachments.
- -80 °C RNA + library storage
- Attachment slots labelled
- CSV + HTML report ready
Use this template for your next RNA-Seq cohort.
Edit the configuration to match your study design and library chemistry, run the cohort from a tested baseline, and capture every sample sheet, library QC, and DEG result in a structured record. Browse other templates built for the workflows real labs actually use.
Common questions
Can I configure the template for my library chemistry and study design?
Yes. Every section is editable. Swap in different library prep chemistries (polyA selection, total RNA with rRNA depletion, small RNA, 3-prime-only, exome capture), change the sequencing platform (NextSeq, NovaSeq, MiSeq, MGI DNBSEQ), adjust the read length and paired-end configuration, or change the downstream analysis pipeline. Save your edits as a private template scoped to your lab, or publish back to the ELabELN template library.
Does the template work for single-cell RNA-Seq?
This template is configured for bulk RNA-Seq. The structural pattern (sample sheet, library QC, sequencing run, alignment, quantification) carries over to single-cell, but the specific fields, library prep chemistry (10x Chromium, BD Rhapsody, Smart-seq3, Parse), and downstream pipelines (Cell Ranger, Seurat, Scanpy) are different enough that a dedicated single-cell template is more useful. The ELabELN team can scaffold a single-cell variant during onboarding.
How does the template handle the bioinformatics analysis side?
The template captures the analysis parameters and result references rather than running the analysis itself. The Snakemake or Nextflow workspace, reference genome version, alignment tool version (STAR), quantifier (featureCounts, Salmon, kallisto), and DE method (DESeq2, edgeR, limma-voom) are recorded as typed fields. Result files (count matrix, normalized counts, DE results table, HTML report) attach as files. The structured record means cross-cohort comparison of pipeline versions and parameter choices is straightforward.
Is it included in every ELabELN plan?
Yes. Every published template in the ELabELN library is available to all ELabELN subscribers, with unlimited users.
Can my whole lab use this template?
Yes. ELabELN includes unlimited users, so the PI, wet-lab postdocs, computational analysts, and rotating collaborators can all use the template without per-seat charges. Granular permissions let the PI control who can edit wet-lab versus bioinformatics sections.
How quickly can my lab start running RNA-Seq cohorts in ELabELN?
ELabELN Standard cloud deployment is typically live in 1-2 days. Once the instance is provisioned, this template loads from the library in a single click, with the study design, library chemistry, and analysis pipeline editable to match the cohorts your lab actually runs.