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| Status |
Public on Jun 10, 2021 |
| Title |
L11_ROI71_TME [ICP20th-L11-ICPKilo-ROI71-TME-D12] |
| Sample type |
SRA |
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| Source name |
NSCLC tumor
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| Organism |
Homo sapiens |
| Characteristics |
sample_id: ICP20th-L11-ICPKilo-ROI71-TME-D12
tissue: L11
slide.name: ICPKilo
roi: ROI71
aoi.name: TME
aoi.annotation: TME
mask.type: grid/seg
rawreads: 521427
trimmedreads: 521105
stitchedreads: 495614
alignedreads: 491795
deduplicatedreads: 331827
sequencingsaturation: 32.5273742107992
uid: ICP20th-L11-ICPKilo-ROI71-TME-D12
neggeomean_02: 2.83894288492673
neggeosd_02: 1.82376357837027
geolod2.5_02: 12.7519911059853
normfactorneg_02: 0.826516309291701
neggeomean_01: 4.74570832201423
neggeosd_01: 1.72429602792223
geolod2.5_01: 18.5280882985564
normfactorneg_01: 0.705125407398745
normfactorq3: 0.920591390487961
normfactorhk: 0.959670711579838
roi x position: 5400
roi y position: 5500
nuclei: 588
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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 |
SAMN19286123 |
| SRA |
SRX10948154 |
| 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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