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Sample GSM7151919 Query DataSets for GSM7151919
Status Public on Feb 27, 2024
Title brain; Sleep; CFC; Hilus; rep2
Sample type SRA
 
Source name brain
Organism Mus musculus
Characteristics tissue: brain
treatment: Sleep;CFC
region: Hilus
slide: S1
roi: 13
molecule type: targeted RNA
Extracted molecule other
Extraction protocol Samples were incubated with the following target panels for the Nanostring GeoMx DSP: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA (Lot# MWTA12001). 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.
 
Library strategy OTHER
Library source other
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description DSP-1001660005875-G-B02
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.
 
Submission date Apr 05, 2023
Last update date Feb 27, 2024
Contact name Bioinformatics Core
E-mail(s) bioinformatics@umich.edu
Organization name University of Michigan
Street address BRCF Bioinformatics Core, 2800 Plymouth Rd
City Ann Arbor
State/province Mi
ZIP/Postal code 48109-2800
Country USA
 
Platform ID GPL24247
Series (2)
GSE229080 Reactivation of memory-encoding dentate gyrus neurons during memory consolidation is associated with subregion-specific, learning- and sleep-mediated biosynthetic changes [spatial RNA expression level]
GSE229082 Reactivation of memory-encoding dentate gyrus neurons during memory consolidation is associated with subregion-specific, learning- and sleep-mediated biosynthetic changes.
Relations
BioSample SAMN34084960
SRA SRX19888080

Supplementary file Size Download File type/resource
GSM7151919_DSP-1001660005875-G-B02.dcc.gz 67.3 Kb (ftp)(http) DCC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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