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| Status |
Public on Feb 27, 2024 |
| Title |
brain; SD; CFC; CA1; rep8 [protein expression level] |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
treatment: SD;CFC
region: CA1
slide: 4791-LW_S3
roi: 28
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| Extracted molecule |
protein |
| Extraction protocol |
Samples were incubated with the following target panels for the Nanostring GeoMx DSP: (v1.0) Mouse NGS Protein Core, (v1.0) Mouse NGS Alzheimer's Pathology Extended Protein, (v1.0) Mouse NGS Alzheimer's Pathology Protein, (v1.0) Mouse NGS Autophagy Protein, (v1.0) Mouse NGS Cell Death Protein, (v1.0) Mouse NGS Glial Cell Subtyping Protein, (v1.0) Mouse NGS MAPK Signaling Protein, (v1.0) Mouse NGS Neural Cell Typing Protein, (v1.0) Mouse NGS PI3K/AKT Signaling Protein, (v1.0) Mouse NGS Parkinson's Pathology Protein. For extraction, regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x).
Manufactor's protocol for Nanostring GeoMx DSP with NGS readout; Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed ROIs were pooled and purified prior to sequencing.
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| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
DSP-1001660009836-A-G07
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| Data processing |
library strategy: GeoMx NGS readout
Raw FASTQ files were processed via Nanostring's NGS pipeline (v1.0) with default parameters. According to the manufacturer, reads are first processed for quality before trimming adapters and merging paired-end reads. The resulting high quality reads are then aligned to the proprietary Readout Tag Sequence-ID (RTS-ID) barcode. PCR duplicates are removed by matching on the Unique Molecular Index (UMI) and output DCC files are then generated for each region of interest (ROI) or area of illumination (AOI).
Processed DCC files were then mapped to protein targets and collapsed into a single count table using the R package GeoMxTools (v 3.3.0) and themanufactor's reference for each of the target panels ( .pkc files).
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes)
Supplementary files format and content: GeoMx pipeline readable digital counts (DCC) - contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target count table are the raw counts of the probes for a given protein target - or in the case that multiple probes were used, the averaged raw counts.
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| Submission date |
Apr 05, 2023 |
| Last update date |
Feb 27, 2024 |
| Contact name |
Bioinformatics Core |
| E-mail(s) |
bioinformatics@umich.edu
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| Organization name |
University of Michigan
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| Street address |
BRCF Bioinformatics Core, 2800 Plymouth Rd
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| City |
Ann Arbor |
| State/province |
Mi |
| ZIP/Postal code |
48109-2800 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE229081 |
Reactivation of memory-encoding dentate gyrus neurons during memory consolidation is associated with subregion-specific, learning- and sleep-mediated biosynthetic changes [spatial protein expression level] |
| GSE229082 |
Reactivation of memory-encoding dentate gyrus neurons during memory consolidation is associated with subregion-specific, learning- and sleep-mediated biosynthetic changes. |
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| Relations |
| BioSample |
SAMN34084131 |
| SRA |
SRX19887309 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7152141_DSP-1001660009836-A-G07.dcc.gz |
790 b |
(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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