Status
Public on Mar 01, 2022
Title
DSP-1010910372678-B-A02
Sample type
SRA
Source name
FxF E13.5 embryo
Characteristics
slide name: BRK086 G5S5
scan name: BRK086 G5S5
panel: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA
roi: 022
area: 11082.27
tissue: Lung
tissue_substructure: Epithelium
tissue_region: Distal
molecule: other: mRNA ISH
Extracted molecule
total RNA
Extraction protocol
Samples were incubated with the mouse Whole Transcriptome Atlas RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. 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)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.
Library strategy
OTHER
Library source
transcriptomic
Library selection
other
Instrument model
NextSeq 2000
Data processing
Library strategy: GeoMx Seq
GeoMx NGS Pipeline v2.3.3.10 with the following parameters: quality-trim-score = 20, 2color-trimming = True, adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3, barcode-max-mismatch = 1, stitching-max-mismatch = 2
Genome_build: NA
Supplementary_files_format_and_content: Digital Count Conversion (DCC) files: format outputted from GeoMx NGS Pipeline, 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: RawCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, probe information, and raw probe count matrix for each probe and sample
Supplementary_files_format_and_content: CollapsedTargetCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, processing information, and target-level count matrix for each gene target and sample
Supplementary_files_format_and_content: NormalizedTargetCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, processing information, and Q3 normalized target-level count matrix for each gene target and sample
Submission date
Oct 26, 2021
Last update date
Mar 02, 2022
Contact name
Stephanie Zimmerman
Organization name
NanoString Technologies
Street address
530 Fairview Ave N
City
Seattle
State/province
WA
ZIP/Postal code
98109
Country
USA
Series (2)
GSE186594
Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [E13.5 mouse embryo]
GSE190089
Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
Relations
Supplementary file
Size
Download
File type/resource
GSM5657105_DSP-1010910372678-B-A02.dcc.gz
64.6 Kb
(ftp) (http)
DCC
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record