Metadata schema additions for RNAseq (w/ probes) for GeoMX (NGS)

[HerrLufty]

Select the target metadata schema name (can be multiple), or choose 'Other' if not listed.

RNAseq (with probes)

If 'Other' is selected, please enter the schema name below.

No response

Describe the change request (use a numbered list if many).

add umi_size = 14; NOTE: hold on this as it may impact pipelines and/or soft assay rules decision engine; [investigating

add library_preparation_kit

• 10X Genomics; Visium Spatial for FFPE Gene Expression Kit, Mouse Transcriptome, 1 slide, 4 reactions; PN 1000339 Attached (CG000407.pdf, pg. 7)

add sample_indexing_kits

• NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-AB Attached (GeoMx_RNA_Flyer.pdf, pg. 4)
• NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-CD Attached (GeoMx_RNA_Flyer.pdf, pg. 4)
• NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-EF Attached (GeoMx_RNA_Flyer.pdf, pg. 4)
• NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-GH Attached (GeoMx_RNA_Flyer.pdf, pg. 4)

add sequencing_reagent_kits

• Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (200 Cycles); PN 20028318 NovaSeq 6000 Reagents link
• Illumina; NextSeq 2000 P3 Reagents Kit (100 Cycles); PN 20040559 NextSeq Reagents link

add oligo_probe_panels

• 10x Genomics; Visium Mouse Transcriptome Probe Kit - Small; PN 1000365 Attached (CG000407.pdf, pg. 11)
• NanoString Technologies; GeoMx Human Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-HuWTA-4 Attached (GeoMx_RNA_Flyer.pdf, pg. 4)
• NanoString Technologies; GeoMx Mouse Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-MsWTA-4 Attached (GeoMx_RNA_Flyer.pdf, pg. 4)

GeoMx_RNA_Flyer.pdf CG000407.pdf

[johardi]

Closes with https://github.com/hubmapconsortium/dataset-metadata-spreadsheet/commit/84ac08d6a19352efa34a880f2a13936f2954f7bd