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| Status |
Public on Mar 01, 2022 |
| Title |
DSP-1001250007851-H-D02 |
| Sample type |
SRA |
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| Source name |
Human FFPE kidney
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| Organism |
Homo sapiens |
| Characteristics |
slide name: disease3
class: DKD
region: glomerulus
pathology: abnormal
nuclei: 69
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were incubated with the human 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.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
RNA ISH
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| 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: Kidney_Sample_Annotations.txt: txt file containing sample annotations
Supplementary_files_format_and_content: Kidney_Raw_BioProbeCountMatrix.txt: txt file containing raw probe counts for each AOI
Supplementary_files_format_and_content: Kidney_Raw_TargetCountMatrix.txt: txt file containing collapsed target-level counts for each AOI
Supplementary_files_format_and_content: Kidney_Q3Norm_TargetCountMatrix.txt: txt file containing Q3 normalized target-level counts for each AOI
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| Submission date |
Dec 03, 2021 |
| Last update date |
Mar 02, 2022 |
| Contact name |
Stephanie Zimmerman |
| E-mail(s) |
[email protected]
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| Organization name |
NanoString Technologies
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| Street address |
530 Fairview Ave N
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL21697 |
| Series (2) |
| GSE190088 |
Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human kidney] |
| GSE190089 |
Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling |
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| Relations |
| BioSample |
SAMN23582956 |
| SRA |
SRX13298729 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5713040_DSP-1001250007851-H-D02.dcc.gz |
51.8 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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