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zscreen_pilot_data / raw_counts_data /data_shape_summary.md
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Z-Screen Dataset: Global Data Map & Architecture Summary

This report maps the structural dimensions, screening configurations, cell lines, libraries, and device associations for the current dataset.

This dataset contains transcriptomic counts representing 768,162 nanowells profiled across 49 devices (0–48), testing 14 libraries against 6 cell lines / clone variants.

Nanowell Architecture: Each row/observation in the data represents a single nanowell rather than an individual cell. Each physical nanowell is 90 microns in diameter by 120 microns tall and holds approximately 2–10 cells.

📊 High-Level Metrics

Metric Count Details
Total Wells (Observations) 768,162 Mapped 1-to-1 across MasterFile, chemistry, and counts.h5ad
Total Features (Genes) 46,944 Gene expression profiles stored in counts.h5ad
Screening Devices 49 Numbered 0 to 48
Unique Cell Lines 6 HEK293, HEK293-clone, A549, H1650, THP1, AEC7
Screened Libraries 14 9 Named control compounds/control libraries, 3 OBOC libraries, 2 Control bead libraries
Unique Compounds / Precursors 142,227 78 named controls, 142,149 OBOC building blocks, and controls

🧪 Libraries & Nomenclature Breakdown

The screening libraries and control sets are classified using the following nomenclature:

  • ZEL Prefix: Represents One-Bead One-Compound (OBOC) combinatorial libraries (testing building block precursor fragments, e.g., ZEL024, ZEL028-2, ZEL031).
  • ZIC Prefix: Represents named control compounds (testing targeted, fully synthesized compounds, e.g., target inhibition screen ZIC008).
  • No-Compound Controls:
    • ZEL026-2 represents a set of no-compound control beads (not a combinatorial library).
    • ZIC005 & ZIC005-2 represent no-compound controls (with ZIC005 profiling water/vehicle controls).
Library Nomenclature Category Unique Compound IDs Unique SMILES Unique Names Nanowell Count
ZIC008 Named Control Compounds 35 35 35 256,052
ZEL024 OBOC Combinatorial Library 13,934 13,934 1 175,285
ZEL028-2 OBOC Combinatorial Library 117,950 117,950 1 134,821
ZEL026-2 No-Compound Control Beads 0 0 1 95,583
ZEL031 OBOC Combinatorial Library 10,265 10,265 1 43,241
ZIC009 Named Control Compounds 31 31 31 31,107
ZIC002 Named Control Compounds 7 0 7 10,999
ZIC005-2 No-Compound Control 0 0 1 7,891
ZIC001 Named Control Compounds 2 2 2 6,569
ZIC006 Named Control Compounds 1 1 1 2,099
ZIC004 Named Control Compounds 1 1 1 1,913
ZIC003 Named Control Compounds 2 0 2 1,880
ZIC007 Named Control Compounds 4 4 4 565
ZIC005 No-Compound Control (Water) 1 1 1 157
Total 142,227 142,218 79 768,162

🧫 Cell Line Screen Matrix

The table below shows the nanowell count distribution for each library screened across each cell line:

Library A549 AEC7 H1650 HEK293 HEK293-clone THP1 Total Wells
ZEL024 0 0 21,545 153,740 0 0 175,285
ZEL026-2 26,718 36,827 17,086 0 14,952 0 95,583
ZEL028-2 42,435 0 26,694 65,692 0 0 134,821
ZEL031 20,868 0 431 0 0 21,942 43,241
ZIC001 0 0 1,229 3,858 0 1,482 6,569
ZIC002 0 0 806 9,558 0 635 10,999
ZIC003 0 0 378 919 0 583 1,880
ZIC004 122 0 411 0 0 1,380 1,913
ZIC005 0 0 109 0 0 48 157
ZIC005-2 0 7,891 0 0 0 0 7,891
ZIC006 207 0 631 0 0 1,261 2,099
ZIC007 0 0 452 0 0 113 565
ZIC008 84,952 91,448 26,382 19,010 34,260 0 256,052
ZIC009 0 31,107 0 0 0 0 31,107

📱 Devices Analysis & Metadata Mapping

1. Is each device an individual cell line?

Yes. Every physical screening device (0–48) runs exactly one cell line (no cell line mixing on-chip).

2. Is each device a unique library?

No. Every device contains multiple libraries (ranging from 2 to 8 libraries pooled per device).

3. How many devices contain no-compound controls?

  • No-Compound Controls: Present in 24 devices (Devices 8, 9, 17, 18, 21, 22, 29, 30, and 33 through 48, representing capture_only roles and water vehicle control sets).
  • OBOC Combinatorial Libraries: Present in 24 devices (Devices 0–7, 10, 12–16, 19, 20, 23–28, 31, 32).
  • Only 1 Device (Device 11) contains named control compounds exclusively with no-compound or combinatorial controls.

🗺️ Detailed Device Map

The device-by-device configuration shows cell line mapping and library counts:

Device ID Cell Line Libraries Mapped Wells Count Control Roles
Device 0 HEK293 ZEL024, ZIC002, ZIC001 27,361 OBOC Library (25,310), Named Controls (2,051)
Device 1 HEK293 ZEL024, ZIC002, ZIC001 22,011 OBOC Library (20,398), Named Controls (1,613)
Device 2 HEK293 ZEL024, ZIC002, ZIC001 32,906 OBOC Library (30,307), Named Controls (2,599)
Device 3 HEK293 ZEL024, ZIC002, ZIC001 30,518 OBOC Library (28,064), Named Controls (2,454)
Device 4 HEK293 ZEL024, ZIC003, ZIC002, ZIC001 30,013 OBOC Library (26,973), Named Controls (3,040)
Device 5 HEK293 ZEL024, ZIC003, ZIC002, ZIC001 25,266 OBOC Library (22,688), Named Controls (2,578)
Device 6 H1650 ZEL024, ZIC002, ZIC005, ZIC001, ZIC003 20,099 OBOC Library (19,253), Named Controls (846 - including ZIC005 Water Control)
Device 7 H1650 ZEL024, ZIC003, ZIC005, ZIC002, ZIC001 2,555 OBOC Library (2,292), Named Controls (263 - including ZIC005 Water Control)
Device 8 H1650 ZEL026-2, ZIC007, ZIC004, ZIC006, ZIC003, ZIC002, ZIC001 12,422 No-Compound Control Beads (10,369), Named Controls (2,053)
Device 9 H1650 ZEL026-2, ZIC006, ZIC003, ZIC004, ZIC002, ZIC001, ZIC007 7,571 No-Compound Control Beads (6,717), Named Controls (854)
Device 10 THP1 ZIC006, ZEL031, ZIC007, ZIC004, ZIC005, ZIC002, ZIC003, ZIC001 3,748 OBOC Library (2,837), Named Controls (911 - including ZIC005 Water Control)
Device 11 A549 ZIC006, ZIC004 257 Named Controls (257)
Device 12 THP1 ZEL031, ZIC004, ZIC006, ZIC003, ZIC002, ZIC001 23,696 OBOC Library (19,105), Named Controls (4,591)
Device 13 A549 ZIC008, ZEL031 13,602 Named Controls (7,771), OBOC Library (5,831)
Device 14 A549 ZIC008, ZEL031 9,878 Named Controls (5,583), OBOC Library (4,295)
Device 15 A549 ZIC008, ZEL031 16,898 Named Controls (11,376), OBOC Library (5,522)
Device 16 A549 ZIC008, ZEL031 12,261 Named Controls (7,041), OBOC Library (5,220)
Device 17 A549 ZIC008, ZEL026-2, ZIC004 13,675 Named Controls (9,757), No-Compound Control Beads (3,918)
Device 18 A549 ZIC008, ZEL026-2, ZIC004 11,332 Named Controls (8,428), No-Compound Control Beads (2,904)
Device 19 H1650 ZIC008, ZEL031 6,390 Named Controls (6,283), OBOC Library (107)
Device 20 H1650 ZIC008, ZEL031 14,227 Named Controls (13,903), OBOC Library (324)
Device 21 A549 ZEL026-2, ZIC008 27,839 Named Controls (15,125), No-Compound Control Beads (12,714)
Device 22 A549 ZIC008, ZEL026-2 18,240 Named Controls (11,058), No-Compound Control Beads (7,182)
Device 23 A549 ZIC008, ZEL028-2 23,608 OBOC Library (20,152), Named Controls (3,456)
Device 24 H1650 ZIC008, ZEL028-2 14,178 OBOC Library (12,056), Named Controls (2,122)
Device 25 A549 ZIC008, ZEL028-2 27,712 OBOC Library (22,283), Named Controls (5,429)
Device 26 H1650 ZIC008, ZEL028-2 18,712 OBOC Library (14,638), Named Controls (4,074)
Device 27 HEK293 ZIC008, ZEL028-2 17,999 OBOC Library (14,494), Named Controls (3,505)
Device 28 HEK293 ZIC008, ZEL028-2 15,808 OBOC Library (12,865), Named Controls (2,943)
Device 29 HEK293-clone ZIC008, ZEL026-2 27,829 Named Controls (19,951), No-Compound Control Beads (7,878)
Device 30 HEK293-clone ZIC008, ZEL026-2 21,383 Named Controls (14,309), No-Compound Control Beads (7,074)
Device 31 HEK293 ZIC008, ZEL028-2 27,521 OBOC Library (20,770), Named Controls (6,751)
Device 32 HEK293 ZIC008, ZEL028-2 23,374 OBOC Library (17,563), Named Controls (5,811)
Device 33 AEC7 ZIC008, ZEL026-2, ZIC009 11,498 Named Controls (7,910), No-Compound Control Beads (3,588)
Device 34 AEC7 ZEL026-2, ZIC008, ZIC009 11,250 Named Controls (7,340), No-Compound Control Beads (3,910)
Device 35 AEC7 ZIC008, ZEL026-2, ZIC009 9,165 Named Controls (6,075), No-Compound Control Beads (3,090)
Device 36 AEC7 ZIC008, ZEL026-2, ZIC009 12,111 Named Controls (8,004), No-Compound Control Beads (4,107)
Device 37 AEC7 ZIC008, ZEL026-2, ZIC009 13,390 Named Controls (9,358), No-Compound Control Beads (4,032)
Device 38 AEC7 ZEL026-2, ZIC008, ZIC009 17,504 Named Controls (12,360), No-Compound Control Beads (5,144)
Device 39 AEC7 ZIC008, ZEL026-2, ZIC009 21,192 Named Controls (13,801), No-Compound Control Beads (7,391)
Device 40 AEC7 ZIC008, ZEL026-2, ZIC009 16,318 Named Controls (10,753), No-Compound Control Beads (5,565)
Device 41 AEC7 ZIC008, ZIC005-2, ZIC009 2,929 Named Controls (2,587), No-Compound Control (342)
Device 42 AEC7 ZIC008, ZIC009, ZIC005-2 4,660 Named Controls (3,990), No-Compound Control (670)
Device 43 AEC7 ZIC008, ZIC005-2, ZIC009 11,537 Named Controls (9,698), No-Compound Control (1,839)
Device 44 AEC7 ZIC008, ZIC005-2, ZIC009 10,472 Named Controls (8,618), No-Compound Control (1,854)
Device 45 AEC7 ZIC008, ZIC005-2, ZIC009 7,223 Named Controls (6,209), No-Compound Control (1,014)
Device 46 AEC7 ZIC008, ZIC005-2, ZIC009 8,258 Named Controls (7,242), No-Compound Control (1,016)
Device 47 AEC7 ZIC008, ZIC009, ZIC005-2 5,983 Named Controls (5,136), No-Compound Control (847)
Device 48 AEC7 ZIC008, ZIC005-2, ZIC009 3,783 Named Controls (3,474), No-Compound Control (309)