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| Status |
Public on Aug 02, 2024 |
| Title |
P1 | 016 | Full ROI |
| Sample type |
SRA |
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| Source name |
Head and neck
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Head and neck
aoisurfacearea: 52293.315434
aoinucleicount: 919
roicoordinatex: 8076
roicoordinatey: 29801
rawreads: 16305942
alignedreads: 15526825
deduplicatedreads: 827993
trimmedreads: 16155498
stitchedreads: 15990229
sequencingsaturation: 94.6673386220299
scanwidth: 35417.2109375
scanheight: 88720.9609375
scanoffsetx: 6867
scanoffsety: 4791
loq (human_ngs_whole_transcriptome_atlas_rna_1.0): 39.1206807593481
best response: PR
mortality: Y
date of_last_follow_up/_censored: NM
age: 53
Sex: Male
smoking status: Previous
ecog performance: 1
pfs: 14 mos
p16 status: Positive
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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 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 |
Illumina NovaSeq 6000 |
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| Description |
hnscc_normalised_QC.csv
hnscc_WTA_QC.csv
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| Data processing |
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“
Assembly: sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx Hs_R_NGS_WTA_v1.0 file
Supplementary files format and content: hnscc_WTA_QC.csv: raw count data, hnscc_normalised_QC.csv: normalised count data
Library strategy: Spatial Transcriptomics
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| Submission date |
Jun 29, 2024 |
| Last update date |
Aug 02, 2024 |
| Contact name |
Habib Sadeghirad |
| E-mail(s) |
[email protected]
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| Phone |
0451319292
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| Organization name |
The University of Queensland
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| Street address |
37 Kent St, Woolloongabba, 37 Kent St, Woolloongabba
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| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4102 |
| Country |
Australia |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE259279 |
Transcriptomic and proteomic spatial profiling of tertiary lymphoid aggregates in head and neck cancer reveal spatial tissue dynamics and profiles associated with immunotherapy response. |
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| Relations |
| BioSample |
SAMN42167464 |
| SRA |
SRX25154126 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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