{
"@context": [
"https://www.w3.org/ns/activitystreams",
"https://purl.org/coar/notify"
],
"id": "urn:uuid:c37371fb-1974-4412-a672-cb3d5c172125",
"type": [
"Offer",
"coar-notify:ReviewAction"
],
"actor": {
"id": "https://datalake.inria.fr",
"type": "Service",
"name": "Inria DataLake"
},
"origin": {
"id": "https://datalake.inria.fr",
"type": "Service",
"inbox": "https://prod-datadcis-api.inria.fr/coar/inbox"
},
"target": {
"id": "https://inria.hal.science",
"type": "Service",
"inbox": "https://inbox.hal.science"
},
"object": {
"id": "https://hal.science/hal-05490685v1",
"ietf:cite-as": null,
"sorg:citation": {
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"type": "SoftwareSourceCode",
"name": "DESeq2",
"codeRepository": null,
"referencePublication": null
},
"mentionType": "software",
"mentionContext": [
"The adjusted rawcount matrices were normalized by sequencing depth using DESeq2 size-factors and then gene-counts were divided by median transcript lengths.",
"Differential gene expression analyses between the different groups were done with DESeq2 with functional analyses and visualization performed as described in the previous section for cellular models.",
"Comparisons of interest were performed using the Wald test for differential expression and implemented in the Bioconductor package DESeq2 version 1.16.1."
]
}
}
2026-04-05 07:00:52
urn:uuid:b22a7b8a-a0b6-491c-93f7-932b93640dd8
https://datalake.inria.fr
https://inria.hal.science
["Offer","coar-notify:ReviewAction"]
{
"@context": [
"https://www.w3.org/ns/activitystreams",
"https://purl.org/coar/notify"
],
"id": "urn:uuid:b22a7b8a-a0b6-491c-93f7-932b93640dd8",
"type": [
"Offer",
"coar-notify:ReviewAction"
],
"actor": {
"id": "https://datalake.inria.fr",
"type": "Service",
"name": "Inria DataLake"
},
"origin": {
"id": "https://datalake.inria.fr",
"type": "Service",
"inbox": "https://prod-datadcis-api.inria.fr/coar/inbox"
},
"target": {
"id": "https://inria.hal.science",
"type": "Service",
"inbox": "https://inbox.hal.science"
},
"object": {
"id": "https://hal.science/hal-05490685v1",
"ietf:cite-as": null,
"sorg:citation": {
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"type": "SoftwareSourceCode",
"name": "FlowJo",
"codeRepository": null,
"referencePublication": null
},
"mentionType": "software",
"mentionContext": [
"Images were capture with a SP8-X confocal microscope and the EU fluorescence signal from the nucleus was quantified using the Hoechst signal as a mask for determining the mean fluorescence of the EU signal in each nucleus by analyses using a FlowJo macro program."
]
}
}
2026-04-05 07:00:52
urn:uuid:a3efd525-1585-4a60-a71a-94525c5117b9
https://datalake.inria.fr
https://inria.hal.science
["Offer","coar-notify:ReviewAction"]
{
"@context": [
"https://www.w3.org/ns/activitystreams",
"https://purl.org/coar/notify"
],
"id": "urn:uuid:a3efd525-1585-4a60-a71a-94525c5117b9",
"type": [
"Offer",
"coar-notify:ReviewAction"
],
"actor": {
"id": "https://datalake.inria.fr",
"type": "Service",
"name": "Inria DataLake"
},
"origin": {
"id": "https://datalake.inria.fr",
"type": "Service",
"inbox": "https://prod-datadcis-api.inria.fr/coar/inbox"
},
"target": {
"id": "https://inria.hal.science",
"type": "Service",
"inbox": "https://inbox.hal.science"
},
"object": {
"id": "https://hal.science/hal-05490685v1",
"ietf:cite-as": null,
"sorg:citation": {
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"type": "SoftwareSourceCode",
"name": "OligoAnalyzer",
"codeRepository": null,
"referencePublication": null
},
"mentionType": "software",
"mentionContext": [
"Primers for RT-qPCR were designed using the OligoAnalyzer TM Tool from IDT and are listed in Dataset EV7."
]
}
}
{
"@context": [
"https://www.w3.org/ns/activitystreams",
"https://purl.org/coar/notify"
],
"id": "urn:uuid:9b4e3406-af46-401c-813f-b8e8c73894db",
"type": [
"Offer",
"coar-notify:ReviewAction"
],
"actor": {
"id": "https://datalake.inria.fr",
"type": "Service",
"name": "Inria DataLake"
},
"origin": {
"id": "https://datalake.inria.fr",
"type": "Service",
"inbox": "https://prod-datadcis-api.inria.fr/coar/inbox"
},
"target": {
"id": "https://inria.hal.science",
"type": "Service",
"inbox": "https://inbox.hal.science"
},
"object": {
"id": "https://hal.science/hal-05490685v1",
"ietf:cite-as": null,
"sorg:citation": {
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"type": "SoftwareSourceCode",
"name": "survival",
"codeRepository": null,
"referencePublication": null
},
"mentionType": "software",
"mentionContext": [
"Patient survival was computed in R using packages survival v3.2 and survminer v0.4.9.",
"Correlation with patient survival showed that cluster 3 (HR = 5.84, Log-rank p.val = 0.034) and fibroblast score (HR = 3.46, Log-rank p.val = 0.027) were strongly associated with poor survival (Fig. 4C).",
"Cluster 3 showed strongest association with poor survival as did the fibroblast score (Fig. EV5D).",
"Patient survival was computed in R using packages survival v3.2 and survminer v0.4.9.",
"Scoring of a considered list of genes to determine patient survival was defined as the geometrical mean of representative genes of the transcriptional signature.",
"At the end of follow-up, 14 (36%) patients died with median overall survival of 47 months (range: 8.3-231.1 months).",
"Moreover, tRCC EMT was associated with enrichment in mesenchymal cancer cells and myCAFs that both strongly associated with poor survival.",
"Deconvolution with the ccRCC tumor cell signatures again revealed the strong myCAF-mes association and both cell populations strongly associated with poor survival (Figs.",
"Similarly, deconvolution revealed that EMT tumors were enriched in myCAFs and that enrichment in both mesenchymal tumor cells and myCAFs were strongly associated with poor survival.",
"Correlation with patient survival showed that cluster 3 (HR = 5.84, Log-rank p.val = 0.034) and fibroblast score (HR = 3.46, Log-rank p.val = 0.027) were strongly associated with poor survival (Fig. 4C).",
"Furthermore, using transcriptional signatures derived from clear cell renal carcinoma (ccRCC), we revealed that tRCC tumors with EMT signatures were enriched in myofibroblastic cancer-associated fibroblasts (myCAFs) whose presence correlated with poorer survival.",
"So as not to compare stratified tRCC patients with nonstratified ccRCC patients that represent a heterogenous collection of tumors with different EMT and metabolic states, we stratified ccRCC tumors based on our previously reported single-cell RNAseq signatures that defined an EMT gradient associated with poor survival and an OxPhos to glycolysis switch (Davidson et al, 2023)."
]
}
}
2026-04-05 07:00:52
urn:uuid:714d6411-2a07-4679-a336-283a97fe76ec
https://datalake.inria.fr
https://inria.hal.science
["Offer","coar-notify:ReviewAction"]
{
"@context": [
"https://www.w3.org/ns/activitystreams",
"https://purl.org/coar/notify"
],
"id": "urn:uuid:714d6411-2a07-4679-a336-283a97fe76ec",
"type": [
"Offer",
"coar-notify:ReviewAction"
],
"actor": {
"id": "https://datalake.inria.fr",
"type": "Service",
"name": "Inria DataLake"
},
"origin": {
"id": "https://datalake.inria.fr",
"type": "Service",
"inbox": "https://prod-datadcis-api.inria.fr/coar/inbox"
},
"target": {
"id": "https://inria.hal.science",
"type": "Service",
"inbox": "https://inbox.hal.science"
},
"object": {
"id": "https://hal.science/hal-05490685v1",
"ietf:cite-as": null,
"sorg:citation": {
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"type": "SoftwareSourceCode",
"name": "UCSC genome browser",
"codeRepository": null,
"referencePublication": null
},
"mentionType": "software",
"mentionContext": [
"Visualization of ChIP-seq signal at specific gene loci of interest was achieved using the UCSC genome browser (https://genome.ucsc.edu/)."
]
}
}