{"id":780,"date":"2026-05-11T14:54:32","date_gmt":"2026-05-11T18:54:32","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/microarray\/?page_id=780"},"modified":"2026-05-19T15:48:44","modified_gmt":"2026-05-19T19:48:44","slug":"spatial-bio-seq-parameters","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/microarray\/recommendations\/spatial-bio-seq-parameters\/","title":{"rendered":"10X Spatial Sequencing Parameters"},"content":{"rendered":"\n\n\n\n\n\n\n\n\n\n\n\n\n
Assay Name<\/strong><\/td>\nSample Type<\/strong><\/td>\nSlide Type<\/strong><\/td>\nMinimum<\/span> No. of Sequencing Reads Needed1<\/sup><\/strong><\/td>\n<\/tr>\n
<\/span><\/td>\n<\/span><\/td>\n<\/span><\/td>\n(per 100% Coverage of Capture Area)<\/td>\n<\/tr>\n
Visium HD Spatial Gene Expression2<\/sup><\/span><\/td>\nFresh-Frozen<\/span><\/td>\n6.5 mm<\/span><\/td>\n700 M<\/span><\/td>\n<\/tr>\n
<\/td>\nFixed-Frozen<\/span><\/td>\n6.5 mm<\/span><\/td>\n500 M<\/span><\/td>\n<\/tr>\n
<\/td>\nFFPE<\/span><\/td>\n6.5 mm<\/span><\/td>\n275 M<\/span><\/td>\n<\/tr>\n
Visium HD Spatial Gene Expression3<\/sup><\/span><\/td>\nFresh-Frozen<\/span><\/td>\n11.0 mm<\/span><\/td>\n2.1 B<\/span><\/td>\n<\/tr>\n
<\/td>\nFixed-Frozen<\/span><\/td>\n11.0 mm<\/span><\/td>\n1.5 B<\/span><\/td>\n<\/tr>\n
<\/td>\nFFPE<\/span><\/td>\n11.0 mm<\/span><\/td>\n825 M<\/span><\/td>\n<\/tr>\n
Visium HD 3′ Spatial Gene Expression4<\/sup><\/span><\/td>\nFresh-Frozen<\/span><\/td>\n6.5 mm<\/span><\/td>\n550 M<\/span><\/td>\n<\/tr>\n
Visium CytAssist Spatial Gene Expression5<\/sup><\/span><\/td>\nAny<\/span><\/td>\n6.5 mm<\/span><\/td>\n125 M<\/span><\/td>\n<\/tr>\n
<\/td>\nAny<\/span><\/td>\n11.0 mm<\/span><\/td>\n375.5 M<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

1.\u00a0 To determine minimum<\/span> number of reads needed per sample, multiply the percent of capture area covered with the sample tissue by the number of reads needed if 100% of the capture area is covered for your tissue type. E.g., Tissue Sample A was fresh-frozen and covered 15% of the capture area of a Visium HD Spatial 6.5mm slide. Therefore minimum<\/span> reads needed = 0.15 x 700,000,000 or\u00a0 105,000,000 (105 M).<\/sup><\/p>\n

2.\u00a0 See 10X Genomics protocol CG000685 – Visium HD Spatial Gene Expression Reagent Kits<\/sup><\/p>\n

3.\u00a0 See 10X Genomics protocol CG001679 – Visium HD Spatial Gene Expression 2.0<\/sup><\/p>\n

4.\u00a0 See 10X Genomics protocol CG000805 – Visium HD 3′ Spatial Gene Expression<\/sup><\/p>\n

5.\u00a0 See 10X Genomics protocol CG000494 – Visium CytAssist Spatial Gene and Protein Expression Reagent Kits<\/sup><\/p>\n","protected":false},"excerpt":{"rendered":"

Assay Name Sample Type Slide Type Minimum No. of Sequencing Reads Needed1 (per 100% Coverage of Capture Area) Visium HD Spatial Gene Expression2 Fresh-Frozen 6.5 mm 700 M Fixed-Frozen 6.5 mm 500 M FFPE 6.5 mm 275 M Visium HD Spatial Gene Expression3 Fresh-Frozen 11.0 mm 2.1 B Fixed-Frozen 11.0 mm 1.5 B FFPE 11.0 […]<\/p>\n","protected":false},"author":4084,"featured_media":0,"parent":68,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"page-templates\/no-sidebars.php","meta":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/microarray\/wp-json\/wp\/v2\/pages\/780"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/microarray\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/microarray\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/microarray\/wp-json\/wp\/v2\/users\/4084"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/microarray\/wp-json\/wp\/v2\/comments?post=780"}],"version-history":[{"count":20,"href":"https:\/\/www.bumc.bu.edu\/microarray\/wp-json\/wp\/v2\/pages\/780\/revisions"}],"predecessor-version":[{"id":821,"href":"https:\/\/www.bumc.bu.edu\/microarray\/wp-json\/wp\/v2\/pages\/780\/revisions\/821"}],"up":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/microarray\/wp-json\/wp\/v2\/pages\/68"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/microarray\/wp-json\/wp\/v2\/media?parent=780"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}