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| Status |
Public on Jul 29, 2024 |
| Title |
Block_3_023 |
| Sample type |
SRA |
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| Source name |
287909
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 287909
origin: LTRC
batch: 1B
roi area: 138052.8
negative probe_geometric_mean: 12.974
negative probe_standard_deviation: 1.543198
limit of_quantification: 30.897071
genesdetected: 3192
genedetectionrate: 0.17090539
age: 36
Sex: Female
ethnicity: not hispanic or latino
race: Caucasian
smoking: former
muc5b rs35705950_genotype: GT
disease: IPF
segment roi_morphology: transition
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| Treatment protocol |
Formalin-fixed, paraffin-embedded lung tissues from 75 age-matched donors who were either unaffected (21) or had IPF (54) were arranged into tissue macroarray blocks at National Jewish Health by our histopathologist (D.H.). 310 regions were acquired which fell into one of five categories: Airway, alveolus, transition zones characterized by fibroblastic foci, dense fibrosis, or honeycomb cysts guided by our pathologist (C.D.C.). Specimens were genotyped for the IPF risk variant in the promoter for the MUC5B gene, rs35705950 G:T, with 7 control specimens and 31 IPF specimens containing at least one copy of the variant allele.
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| Growth protocol |
Formalin-fixed, paraffin-embedded tissues were obtained from the Lung Tissue Research Consortum or from patients undergoing lung transplant at the University of Colorado (Colorado Multi-Institutional Review Board protocol #15-1147).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Barcoded, UMI-labelled probes targeting specific mRNA were hybridized to formalin-fixed, paraffin-embedded tissues and acquired at Nanostring (Seattle, WA) or the University of Colorado Anschutz Medical Campus (Aurora, CO).
A commercially available protocol was followed (Nanostring, Seattle, WA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
In-situ hybridization
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| Data processing |
Samples were acquired on a Nanostring GeoMx DSP instrument using standard protocols.
Barcoded UMIs from regions of interest were acquired via a photoactivatable linker, sequenced, demuliplexed, and quantified using the R software package "GeoMxWorkflows" according to the vignette (https://bioconductor.org/packages/devel/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html). Raw counts and segments were filtered according to the default quality control thresholds in the vignette, with the modification that segments from which less than 2% of genes in the genome were detected were excluded. Raw counts were normalized using the variant stabilizing transformation function from the DESeq package (https://github.com/thelovelab/DESeq2). Covariates, including donor ("Tissue_ID"), batch, aquisition area ("rounded_area"), region of interest ("Segment"), diagnosis ("Disease"), and MUC5B promoter genotype according to a dominant model (either "G" for GG homozygotes, or "T" for heerozygous or homozygous variants, "Geno"). Downstream analysis used linear mixed effects modeling including region of interest area and batch as fixed effects and donor as a random effect for specimens with multiple regions from the same donor using the "lme4" wrapper, "lmerSeq" (https://github.com/stop-pre16/lmerSeq).
Supplementary files format and content: Variance stabilizing transformed count values.
Supplementary files format and content: dcc
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| Submission date |
May 15, 2024 |
| Last update date |
Jul 29, 2024 |
| Contact name |
Ivana Yang |
| E-mail(s) |
[email protected]
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| Organization name |
University of Colorado
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| Street address |
1635 Aurora Ct
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| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE267521 |
The MUC5B IPF risk variant promotes a distal airway secretory phenotype and loss of alveolar markers |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM8268120_DSP-1009880006782-A-H03.dcc.gz |
62.1 Kb |
(ftp)(http) |
DCC |
| Raw data not provided for this record |
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