Immunofluorescence and In Situ hybridization images in the postmortem human entorhinal cortex

Neurons located in layer II of the entorhinal cortex (ECII) are the primary site of pathological tau accumulation and neurodegeneration at preclinical stages of Alzheimer’s disease (AD). Exploring the alterations that underlie the early degeneration of these cells is essential to develop therapies that curb the disease before symptom onset. Here we performed cell-type specific profiling of human EC at the onset of AD neuropathology.
This dataset represents slide scanner images of the pathology in these EC (AD neuropathology); DAB1-RELN co-staining to test Reelin pathway activity; RBFOX1-RELN co-staining to test for expression of RBFOX1 across neuron types in the EC, and chromogenic and fluorescent ISH images to follow-up on single-nucleus RNAseq findings (see manuscript).
  

AD neuropathology: Thioflavin-S staining and 6E10 (Biolegend, 1:500, Alexa 647) amyloid staining on postmortem EC from the 10 individuals described in the linked manuscript. All individuals were asymptomatic at death. C1 to C5 are Braak stage 0, AD1 to AD5 are Braak stage II. C5 and AD1 were further excluded from the analysis because C5 has plaques (as opposed to C1-C4) and AD1 does not (as opposed to AD2 to AD5).

In the DAB1-RELN folder: Immunofluorescence for DAB1 (LSbio - LS-B9240, 1/250) - Alexa 647 and RELN (Invitrogen PA5- 47537, 1/50) -Alexa 488 on postmortem EC from six different human individuals (from Netherlands Brain Bank), without AD neuropathology (6402, 6404, 6406) or with incipient AD neuropathology (6403, 6405, 6407) - see extended data on the linked manuscript. Nuclei are counterstained with DAPI.

In the RBFOX1-RELN folder: Immunofluorescence for RBFOX1 (Biolegend #862706) - Alexa 546 and RELN (Invitrogen PA5- 47537, 1/50) - Alexa 488 on postmortem EC from six different human individuals (from Netherlands Brain Bank), without AD neuropathology (9694, 9696, 9699) or with incipient AD neuropathology (9695, 9697, 9698) - see extended data on the linked manuscript. Nuclei are counterstained with DAPI.

In the chromogenic ISH folder: Chromogenic duplex in situ hybridization on postmortem FFPE sections of EC from control individuals (from NIH NeuroBioBank - Harvard Brain Bank). Images are available for:

individual S13266 - female - 55 years - RELN(green dye)/BMPR1B(red dye)

individual S01509 - male - 36 years - RELN(green dye)/BMPR1B(red dye)

individual S13266 - female - 55 years - RELN(red dye)/RORB(green dye)

individual S01509 - male - 36 years - RELN(red dye)/RORB(green dye)

individual S13266 - female - 55 years - RELN(green dye)/GPC5(red dye)

individual S08880 - male - 52 years - RELN(green dye)/GPC5(red dye)

individual S018190 - duplex negative control(red and green dyes).

All sections are counterstained with Hematoxylin and imaged at 40x on a vectra polaris slide scanner.

In the fluorescent ISH folder: Multiplex fluorescent in situ hybridization on postmortem EC. Both raw images and images unmixed in the PhenoImager HT folder are available.

Individual 15069 - male control 64 years - VIP (Opal 520)/NPTX2 (Opal 690)/PAX6 (Opal 780)/LAMP5 (Opal 570)

Individual 15069 - male control 64 years - NPTX2 (Opal 570)/CBLN4 (Opal 690)/LAMP5 (Opal 780)

Individual 15069 - male control 64 years - NPTX2 (Opal 570)/HTR3A (Opal 690)/RELN (Opal 520)/GPC5 (Opal 780)

Individual 17017 - female Amyloid positive, Braak stage II, 67 years - SNX31 (Opal 690)/GPC5 (Opal 780)/RELN (Opal 520)

Individual 17017 - female Amyloid positive, Braak stage II, 67 years - 3-plex negative control (Opal 570, 690, 780)

All sections are counterstained with DAPI and imaged at 20x on a vectra polaris slide scanner.

Reference of the Advanced Cell Diagnostics in situ hybridization probes: RELN #413051, GPC5 #521731, SNX31 #1661551, NPTX2 #464831, CBLN4 #572621, LAMP5 #487691, PAX6 #588881, VIP #452751, HTR3A #310681, BMPR1B #468031, RORB #446061