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Salmon quant — N061011 untreated (SRR1039520)
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21 items
Salmon quant — N61311 untreated (SRR1039508)
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21 items
Salmon Index — GENCODE v44 transcriptome
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17 items
Salmon quant — N061011 dex (SRR1039521)
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21 items
Salmon quant — N61311 dex (SRR1039509)
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21 items
Salmon quant — N080611 dex (SRR1039517)
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21 items
Bulk DE — dex vs untreated (DESeq2 + apeglm)
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73 items
Salmon quant — N052611 untreated (SRR1039512)
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21 items
Salmon quant — N080611 untreated (SRR1039516)
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21 items
Salmon quant — N052611 dex (SRR1039513)
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21 items
Uploads
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18 items
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May 08, 2026 at 12:42
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Mike Love persona demo — canonical bulk RNA-seq DE pipeline on the Himes 2014
airway smooth muscle dataset (GSE52778 / SRP033351). PMID 24926665.
4 donors × (untreated vs dexamethasone), 8 paired-end Illumina HiSeq samples.
Pipeline: Salmon quant (8 samples, auto-detect index) → bulk_de
(tximport + DESeq2 + apeglm shrinkage + BH FDR).
Design formula: ~ donor + treatment
Contrast: treatment_dex_vs_untreated
Data: The 8 FASTQ pairs and the GENCODE v44 Salmon index are pre-staged in
MinIO under projects/rnaseq-demo-airway-himes2014/. The salmon_quant stages
have forward_reads / reverse_reads set to the per-sample filenames and will
find the salmon_index/ directory automatically from the input manifest.
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