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| Status |
Public on Jun 10, 2021 |
| Title |
L11_ROI63_TME [ICP20th-L11-ICPKilo-ROI63-TME-C08] |
| Sample type |
SRA |
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| Source name |
NSCLC tumor
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| Organism |
Homo sapiens |
| Characteristics |
sample_id: ICP20th-L11-ICPKilo-ROI63-TME-C08
tissue: L11
slide.name: ICPKilo
roi: ROI63
aoi.name: TME
aoi.annotation: TME
mask.type: grid/seg
rawreads: 328133
trimmedreads: 328013
stitchedreads: 311874
alignedreads: 309655
deduplicatedreads: 219063
sequencingsaturation: 29.2557846635772
uid: ICP20th-L11-ICPKilo-ROI63-TME-C08
neggeomean_02: 2.32607375183708
neggeosd_02: 1.83870802310369
geolod2.5_02: 10.6636383619911
normfactorneg_02: 0.677202032741246
neggeomean_01: 4.88611421611458
neggeosd_01: 1.65663745525296
geolod2.5_01: 17.2596627378817
normfactorneg_01: 0.725987153751643
normfactorq3: 0.572162960202964
normfactorhk: 0.404478421406593
roi x position: 7200
roi y position: 6000
nuclei: 643
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently 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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| Data processing |
Library strategy: GeoMx-Seq
Adapter trimming with trim galore, trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file 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: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.
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| Submission date |
May 20, 2021 |
| Last update date |
Jun 10, 2021 |
| Contact name |
Patrick Danaher |
| Organization name |
NanoString Technologies, Inc.
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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) |
| GSE174749 |
GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on 191 ROIs from a NSCLC tumor. [NSCLC_191_grid] |
| GSE175927 |
GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay |
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| Relations |
| BioSample |
SAMN19284822 |
| SRA |
SRX10947933 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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