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| Status |
Public on Sep 30, 2024 |
| Title |
UIP-A10 | 004 | Full ROI |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
patient id: M24
annotation: fibrosis
condition: IPF
roi replicate: 004
anno: fibrosis
lot human_ngs_whole_transcriptome_atlas_rna: HWTA21001
patid: M24
disease: Y
batch: first
type: IPF
anno type: fibrosis_IPF
outcome: Good
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| Treatment protocol |
not applicable
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| Growth protocol |
not applicable
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| Extracted molecule |
other |
| Extraction protocol |
FFPE sections underwent immunofluorescence with morphology markers (DNA SYTO 13, pan-cytokeratin Alexa Fluor 532, alpha-smooth muscle actin PE-Cy5, and CD45 Alexa Fluor 593) to locate lung microenvironments of interest
in situ RNA probes conjugated to barcodes by a photocleavable linker were hybridized to the sections
Regions of interest were exposed to UV light to decouple the barcoding oligo from RNA probes. Decoupled oligos were collected, indexed by ROI location, and sequenced on Nextseq 1000/2000. GeoMx NGS pipeline (Illumina) was used to produce DCC files from FASTQ files on the GeoMX DSP software.
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| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Description |
GeoMx_NGS_Pipeline_2.3.3.10
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| Data processing |
Probe count and sample metadata files were obtained from GeoMx DSP control center/v3.0.0.113. standR package was used to perform data exploration and normalization (Liu et al 2023 NAR).
Raw or log2 normalized count output from 'assay' function of standR package
Assembly: hg38
Supplementary files format and content: DCC: output from GeoMX NGS pipeline (Nanostring)
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| Submission date |
Feb 06, 2024 |
| Last update date |
Sep 30, 2024 |
| Contact name |
Marco Mura |
| E-mail(s) |
marco.mura@lhsc.on.ca
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| Organization name |
Western University
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| Department |
Medicine, Respirology
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| Lab |
A6-150
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| Street address |
800 Commissioners Road E
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| City |
London |
| State/province |
Ontario |
| ZIP/Postal code |
N6A5W9 |
| Country |
Canada |
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| Platform ID |
GPL30173 |
| Series (2) |
| GSE255174 |
The spatial transcriptomic landscape of fibrosing ILDs [Nanostring] |
| GSE255175 |
The spatial transcriptomic landscape of fibrosing ILDs |
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| Relations |
| BioSample |
SAMN39843420 |
| SRA |
SRX23550206 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8065235_DSP-1001250002565-C-A05.dcc.gz |
47.6 Kb |
(ftp)(http) |
DCC |
SRA Run Selector |
| Raw data are available in SRA |
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