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| Status |
Public on Nov 02, 2023 |
| Title |
Animal C15 Gray Matter ROI 127 |
| Sample type |
SRA |
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| Source name |
Fetal brain
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| Organism |
Macaca nemestrina |
| Characteristics |
tissue: Fetal brain
brain reigion: GM
zika infection: mock
animal id: C15
region of interest (roi) identifer: 127
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| Extracted molecule |
total RNA |
| Extraction protocol |
Unstained 5 µm-thick tissue sections cut from PFA-fixed, paraffin-embedded specimens were mounted on Colorfrost microscope slides
In situ hybridizations with the GeoMx Whole Transcriptome Atlas Panel (WTA, 18,676 total targets) were performed in Buffer R
Rabbit polyclonal anti-Olig2 antibody was incubated first at 1:100 in Buffer W, followed by Goat anti-rabbit AF647 for visualization. The remaining morphology markers were collectively diluted in Buffer W at the following concentrations: 1:50 RBFOX3 (NeuN), 1:400 GFAP, and STYO 83 for nuclei visualization
Each slide was scanned with a 20X objective and default scan parameters on a GeoMx Digitial Spatial Profiler
ROI placement: Geometric 500 µm diameter circle ROIs were placed in the subcortex (Superficial WM; n=3/section), WM tracts (Deep WM; n=3/section), and cortical layers IV-VI (GM; n=3/section). One maximum area (660 µm X 785 µm) ROI was placed at the GM/WM interface on each section
ALOI segmentation: Segmentation mask was applied to the GM/WM interface maximum area to select Olig2+, GFAP+, and NeuN+ areas of interest (AOI).
Sequencing libraries were generated by PCR from the photo-released indexing oligos and ROI-specific Illumina adapter sequences and unique i5 and i7 sample indices were added
Total target counts per DSP collection plate for sequencing were calculated from the total samples areas (µm2). For WTA libraries, the target sequencing depth was 100 counts/µm2. Pooled libraries were sequenced at 2×27 base pairs and with the dual-indexing workflow on an Illumina NovaSeq
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
GeoMx DSP
ROI_127_GM_C15
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| Data processing |
library strategy: GeoMx DSP
Reads were trimmed, merged, and aligned to retrieve probe identity, and the unique molecular identifier of each read was used to remove PCR duplicates converting reads to digital counts for each target within an individual AOI
Supplementary files format and content: CountsROI_matrix.csv - ontains raw counts for the 94 samples that passed min limit of quantification of 2
Supplementary files format and content: normROI_matrix.csv - contains log2 Q3 normalized counts for 94 samples
Supplementary files format and content: countsAOI_matrix.csv - contains raw counts for the 18 samples that passed the minimum limit of quantification 2
Supplementary files format and content: normAOI_matrix.csv - contains log2 Q3 normalized counts for 18 samples
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| Submission date |
Mar 16, 2023 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Michael Gale, Jr |
| E-mail(s) |
uw_galelab_geo@uw.edu
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| Organization name |
University of Washington
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| Department |
Immunology
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| Street address |
750 Republican St. E360, Box 358059
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| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL33261 |
| Series (1) |
| GSE227533 |
Spatial transcriptomics on Zika virus infected fetal brains of nonhuman primates |
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| Relations |
| BioSample |
SAMN33788047 |
| SRA |
SRX19695751 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7102308_DSP-1001660009883-B-B08.dcc.gz |
72.8 Kb |
(ftp)(http) |
DCC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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