Published June 16, 2023 | Version 2.0
Dataset Open

Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa

Poceviciute, Roberta1 ORCID icon
Bogatyrev, Said R.1 ORCID icon
Romano, Anna E.1 ORCID icon
Dilmore, Amanda H.1 ORCID icon
Mondragón-Palomino, Octavio1 ORCID icon
Takko, Heli1 ORCID icon
Ismagilov, Rustem F.1 ORCID icon
  • 1. ROR icon California Institute of Technology

Description

Raw and processed data and imaging files [0.42 TB total] for the bioRxiv preprint "Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa"

Files

Fig02-FigS02-DataAnalysis-16SrDNA.zip
Files (2.1 GB)
Name Size
FigS13-DataAnalysis-ImageAnalysis-5x.zip
md5:543ff49086032d093dfab59cca71addc
1.7 MB Preview Download
FigS12-DataAnalysis-HydrogelOptimization.zip
md5:e5d113135540ac171d818d1460bb197f
165.9 kB Preview Download
FigS11-DataAnalysis-ProbeCrossreactivity.zip
md5:420553a81abd74f5402da5b57814c191
473.4 MB Preview Download
FigS09-DataAnalysis-UniversalProbeValidation.zip
md5:53f845b05b8dda3a394c0450d2e0cfa7
686.8 MB Preview Download
FigS10-DataAnalysis-TaxonSpecificProbeValidation.zip
md5:970381ff83e43c107ab4816d3a63a5d1
245.5 MB Preview Download
Fig02-FigS02-DataAnalysis-16SrDNA.zip
md5:751beb51deb095d8b60c7fc46f9e4cf5
288.7 kB Preview Download
16SrRNA HCRv3 Probes.xlsx
md5:2e764d4b010bbe21ba14a08c8b4a11ea
9.5 kB Download
FigS08-DataAnalysis-UniversalProbeDesign.zip
md5:6ee9848b899c282e5dbbcd1f85d5da6c
316.7 MB Preview Download
DataSummary.xlsx
md5:712cff3ecc6b604ccb5b8fc8e503f3c3
16.2 kB Download
FigS01-DataAnalysis-GrowthCurves.zip
md5:5eee2b066915d3e006a0bd8dac18f95d
26.0 kB Preview Download
Fig04-Fig06-DataAnalysis-ImageAnalysis.zip
md5:ff0b2470ebadbdd050c8e93917e86fa2
79.8 MB Preview Download
Fig03-DataAnalysis-ImageAnalysis.zip
md5:2a532cc75ba32d67aae640264518b9a7
288.4 MB Preview Download
FigS01-DataAnalysis-RTqPCR.zip
md5:6e56394c14e2ec820761c6c981bb77b3
893.7 kB Preview Download
Supplementary Data 1.xlsx
md5:0f3d457749df8fb79317828f2a213dd5
72.0 kB Download
Supplementary Data 2.xlsx
md5:fd5ea53f821a356961934f4e4307fd4b
21.2 kB Download
Supplementary Data 3.xlsx
md5:d914181ea2a703736081a165b7310c0f
11.1 kB Download
Supplementary Data 4.xlsx
md5:15efbae82692b091ec8302da3abdb891
17.6 kB Download

Other

Raw data files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/0_D1.20199/

   R4P-p091-20xC-ImarisSurfaceFiles.zip 4.4 kB Download

   R4P-p091-D28C3M1-EJ-5x_Stitch.czi 2.9 GB Download

   R4P-p091-D29C2M1-EJ-5x_Stitch.czi 2.6 GB Download

   R4P-p091-D29C4M2-EJ-1.czi 7.3 GB Download

   R4P-p091-D29C4M2-EJ-1.ims 11.1 GB Download

   R4P-p091-D29C4M2-EJ-3.czi 4.6 GB Download

   R4P-p091-D29C4M2-EJ-3.ims 8.1 GB Download

   R4P-p091-D29C4M2-EJ-5x_Stitch.czi 2.0 GB Download

   R4P-p091-D31C1M1-EJ-5x_Stitch.czi 3.4 GB Download

   R4P-p121-Bfrag-v3EC-v3BAC-20x.czi 1.5 GB Download

   R4P-p121-Ecoli-v3EC-v3BAC-20x.czi 1.5 GB Download

   R4P-p124-20xC-ImarisSurfaceFiles.zip 486.2 kB Download

   R4P-p124-D28C1M1-EJ-5x_Stitch.czi 1.1 GB Download

   R4P-p124-D28C2M1-EJ-5x_Stitch.czi 1.4 GB Download

   R4P-p124-D28C3M1-EJ-1.czi 5.3 GB Download

   R4P-p124-D28C3M1-EJ-1.ims 7.4 GB Download

   R4P-p124-D28C3M1-EJ-2.czi 5.2 GB Download

   R4P-p124-D28C3M1-EJ-2.ims 7.6 GB Download

   R4P-p124-D28C3M1-EJ-3.czi 4.3 GB Download

   R4P-p124-D28C3M1-EJ-3.ims 6.4 GB Download

   R4P-p124-D28C3M1-EJ-5x_Stitch.czi 1.1 GB Download

   R4P-p124-D28C4M1-EJ-1.czi 4.8 GB Download

   R4P-p124-D28C4M1-EJ-1.ims 9.7 GB Download

   R4P-p124-D28C4M1-EJ-2.czi 4.8 GB Download

   R4P-p124-D28C4M1-EJ-2.ims 7.0 GB Download

   R4P-p124-D28C4M1-EJ-3.czi 4.1 GB Download

   R4P-p124-D28C4M1-EJ-3.ims 6.6 GB Download

   R4P-p124-D28C4M1-EJ-4.czi 5.0 GB Download

   R4P-p124-D28C4M1-EJ-4.ims 7.4 GB Download

   R4P-p124-D28C4M1-EJ-5.czi 5.7 GB Download

   R4P-p124-D28C4M1-EJ-5.ims 8.9 GB Download

   R4P-p124-D28C4M1-EJ-5x_Stitch.czi 1.2 GB Download

   R4P-p124-D28C4M1-EJ-6.czi 5.4 GB Download

   R4P-p124-D28C4M1-EJ-7.czi 5.8 GB Download

   R4P-p124-D28C4M1-EJ-7.ims 8.6 GB Download

   R4P-p124-D29C1M2-EJ-1.czi 5.8 GB Download

   R4P-p124-D29C1M2-EJ-1.ims 8.3 GB Download

   R4P-p124-D29C1M2-EJ-2.czi 4.6 GB Download

   R4P-p124-D29C1M2-EJ-2.ims 6.6 GB Download

   R4P-p124-D29C1M2-EJ-3.czi 4.2 GB Download

   R4P-p124-D29C1M2-EJ-3.ims 6.6 GB Download

   R4P-p124-D29C1M2-EJ-5x_Stitch.czi 918.4 MB Download

   R4P-p124-D29C2M2-EJ-1.czi 6.1 GB Download

   R4P-p124-D29C2M2-EJ-1.ims 9.5 GB Download

   R4P-p124-D29C2M2-EJ-2.czi 6.0 GB Download

   R4P-p124-D29C2M2-EJ-2.ims 8.3 GB Download

   R4P-p124-D29C2M2-EJ-3.czi 3.9 GB Download

   R4P-p124-D29C2M2-EJ-4.czi 5.5 GB Download

   R4P-p124-D29C2M2-EJ-4.ims 7.8 GB Download

   R4P-p124-D29C2M2-EJ-5x_Stitch.czi 1.2 GB Download

   R4P-p124-D29C3M2-EJ-5x_Stitch.czi 1.3 GB Download

   R4P-p124-D29C4M2-EJ-5x_Stitch.czi 1.3 GB Download

   R4P-p124-D30C1M3-EJ-5x_Stitch.czi 877.9 MB Download

   R4P-p124-D30C2M3-EJ-1.czi 3.9 GB Download

   R4P-p124-D30C2M3-EJ-1.ims 5.9 GB Download

   R4P-p124-D30C2M3-EJ-2.czi 4.4 GB Download

   R4P-p124-D30C2M3-EJ-2.ims 8.1 GB Download

   R4P-p124-D30C2M3-EJ-3.czi 4.2 GB Download

   R4P-p124-D30C2M3-EJ-3.ims 6.2 GB Download

   R4P-p124-D30C2M3-EJ-5x_Stitch.czi 1.2 GB Download

   R4P-p124-D30C3M3-EJ-5x_Stitch.czi 1.3 GB Download

   R4P-p124-D30C4M3-EJ-5x_Stitch.czi 1.1 GB Download

   R4P-p124-D31C1M4-EJ-1.czi 3.7 GB Download

   R4P-p124-D31C1M4-EJ-1.ims 5.6 GB Download

   R4P-p124-D31C1M4-EJ-2.czi 3.8 GB Download

   R4P-p124-D31C1M4-EJ-2.ims 5.6 GB Download

   R4P-p124-D31C1M4-EJ-3.czi 6.2 GB Download

   R4P-p124-D31C1M4-EJ-3.ims 8.7 GB Download

   R4P-p124-D31C1M4-EJ-5x_Stitch.czi 949.5 MB Download

   R4P-p124-D31C2M4-JE-5x_Stitch.czi 1.5 GB Download

   R4P-p124-D31C3M4-EJ-1.czi 5.3 GB Download

   R4P-p124-D31C3M4-EJ-1.ims 7.4 GB Download

   R4P-p124-D31C3M4-EJ-2.czi 5.4 GB Download

   R4P-p124-D31C3M4-EJ-2.ims 7.8 GB Download

   R4P-p124-D31C3M4-EJ-3.czi 4.9 GB Download

   R4P-p124-D31C3M4-EJ-3.ims 3.4 GB Download

   R4P-p124-D31C3M4-EJ-4.czi 5.3 GB Download

   R4P-p124-D31C3M4-EJ-5x_Stitch.czi 1.1 GB Download

   R4P-p124-D31C4M4-EJ-1.czi 5.3 GB Download

   R4P-p124-D31C4M4-EJ-1.ims 2.9 GB Download

   R4P-p124-D31C4M4-EJ-2.czi 4.8 GB Download

   R4P-p124-D31C4M4-EJ-2.ims 6.9 GB Download

   R4P-p124-D31C4M4-EJ-3.czi 5.6 GB Download

   R4P-p124-D31C4M4-EJ-4.czi 5.8 GB Download

   R4P-p124-D31C4M4-EJ-4.ims 8.1 GB Download

   R4P-p124-D31C4M4-EJ-5x_Stitch.czi 1.5 GB Download

   R4P-p125-D31C4M4-CD455-WGA2-Crop.ims 371.2 MB Download

   R4P-p125-D31C4M4-CD455-WGA2.czi 4.2 GB Download

   R4P-p125-D31C4M4-CD455-WGA2.ims 1.9 GB Download

   R4P-p125-D31C4M4-EpCAM5-WGA2-Crop.ims 810.8 MB Download

   R4P-p125-D31C4M4-EpCAM5-WGA2.czi 4.6 GB Download

   R4P-p125-D31C4M4-EpCAM5-WGA2.ims 2.3 GB Download

   R4P-p127-20xCS-ImarisSurfaceFiles.zip 3.3 kB Download

   R4P-p127-D28C4M1-EJ-20xCS-1.czi 8.4 GB Download

   R4P-p127-D28C4M1-EJ-20xCS-1_Linear unmixing.czi 1.3 GB Download

   R4P-p127-D28C4M1-EJ-20xCS-1_Linear unmixing.ims 869.6 MB Download

   R4P-p127-D28C4M1-EJ-20xCS-2.czi 8.2 GB Download

   R4P-p127-D28C4M1-EJ-20xCS-2_Linear unmixing.czi 1.3 GB Download

   R4P-p127-D28C4M1-EJ-20xCS-2_Linear unmixing.ims 824.7 MB Download

   R7P-p008-A4B8P0-A1B.01P4.czi 651.1 MB Download

   R7P-p008-A4B8P0-A4B0P4.czi 789.7 MB Download

   R7P-p040-Ecoli-CFB560bV2-BacteroidesV3-20x.czi 1.1 GB Download

   R7P-p041-EUB338v2-UNIVv3-1.czi 1.6 GB Download

   R7P-p041-EUB338v2-UNIVv3-2.czi 1.2 GB Download

Additional details

Funding
Created:
June 16, 2023
Modified:
July 11, 2023