Collections / Adult Mouse Controlled Cortical Impact Visium Spatial Transcriptomics

Adult Mouse Controlled Cortical Impact Visium Spatial Transcriptomics

Here we investigated the topographical relationship of early transcriptional responses to a single, focal TBI in mice by controlled cortical impact (CCI). Guided by the presence of the anterior commissure (AC) in coronal sections at the rostro-caudal point of impact, we compared gene expression changes in the neocortex (CTX) and corpus callosum-external capsule (CC-EC), striatum (STR) and AC. Injury-induced gene expression changes were detected in the CTX, CC-EC and STR but not AC and were principally segregated based on cytoarchitecture, and secondarily by proximity to the site of impact. Additionally, unbiased spatial clustering revealed a positive relationship between proximity to the impact and the number of acutely differentially expressed genes within the laminar CTX. Next, we examined the effects of systemic depletion of neutrophils and monocytes on spatial gene expression changes in the injured brain.

Datasets34
Size~1.7 GB
AssayVisium
Samplemouse · brain
KindTime course
PMID:41250842 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse313407")
coll.ordered_artifacts.df()                 # the 34 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
Member datasets · 34
Visium
Mouse brain
GSM9367525
mouse brain traumatic brain injury 64 MB 3,258 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size64 MB
Obs3,258
bronze H&E
Open in Vitessce
Visium
Mouse brain
GSM9367547
mouse brain traumatic brain injury 54 MB 2,717 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size54 MB
Obs2,717
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367532
mouse brain traumatic brain injury 45 MB 2,858 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size45 MB
Obs2,858
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367522
mouse brain traumatic brain injury 45 MB 2,546 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size45 MB
Obs2,546
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367548
mouse brain traumatic brain injury 59 MB 2,999 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size59 MB
Obs2,999
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367541
mouse brain traumatic brain injury 46 MB 2,459 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size46 MB
Obs2,459
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367529
mouse brain traumatic brain injury 41 MB 2,345 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size41 MB
Obs2,345
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367545
mouse brain traumatic brain injury 53 MB 2,730 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size53 MB
Obs2,730
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367531
mouse brain traumatic brain injury 43 MB 2,620 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size43 MB
Obs2,620
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367535
mouse brain traumatic brain injury 52 MB 2,749 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size52 MB
Obs2,749
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367544
mouse brain traumatic brain injury 50 MB 2,635 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size50 MB
Obs2,635
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367519
mouse brain traumatic brain injury 35 MB 1,866 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size35 MB
Obs1,866
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367520
mouse brain traumatic brain injury 56 MB 2,824 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size56 MB
Obs2,824
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367543
mouse brain traumatic brain injury 54 MB 2,750 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size54 MB
Obs2,750
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367534
mouse brain traumatic brain injury 38 MB 2,230 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size38 MB
Obs2,230
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367526
mouse brain traumatic brain injury 48 MB 2,294 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size48 MB
Obs2,294
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367518
mouse brain traumatic brain injury 59 MB 3,027 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size59 MB
Obs3,027
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367524
mouse brain traumatic brain injury 52 MB 2,724 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size52 MB
Obs2,724
bronze H&E Open in Vitessce
Visium
Mouse brain
GSM9367533
mouse brain traumatic brain injury 47 MB 2,916 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size47 MB
Obs2,916
bronze H&E
Open in Vitessce
Visium
Mouse brain
GSM9367542
mouse brain traumatic brain injury 53 MB 2,706 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size53 MB
Obs2,706
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367521
mouse brain traumatic brain injury 58 MB 2,990 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size58 MB
Obs2,990
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367530
mouse brain traumatic brain injury 42 MB 2,732 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size42 MB
Obs2,732
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367528
mouse brain traumatic brain injury 53 MB 2,602 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size53 MB
Obs2,602
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367549
mouse brain traumatic brain injury 52 MB 2,844 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size52 MB
Obs2,844
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367550
mouse brain traumatic brain injury 46 MB 2,741 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size46 MB
Obs2,741
bronze H&E Open in Vitessce
Visium
Mouse brain
GSM9367536
mouse brain traumatic brain injury 55 MB 2,499 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size55 MB
Obs2,499
bronze H&E
Open in Vitessce
Visium
Mouse brain
GSM9367538
mouse brain traumatic brain injury 51 MB 2,449 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size51 MB
Obs2,449
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367540
mouse brain traumatic brain injury 55 MB 2,810 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size55 MB
Obs2,810
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367517
mouse brain traumatic brain injury 63 MB 2,939 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size63 MB
Obs2,939
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367523
mouse brain traumatic brain injury 41 MB 2,288 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size41 MB
Obs2,288
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367537
mouse brain traumatic brain injury 59 MB 3,136 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size59 MB
Obs3,136
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367546
mouse brain traumatic brain injury 52 MB 2,660 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size52 MB
Obs2,660
bronze H&E Open in Vitessce
Visium
Mouse brain
GSM9367539
mouse brain traumatic brain injury 59 MB 2,844 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size59 MB
Obs2,844
bronze H&E
Open in Vitessce
Visium
Mouse brain
GSM9367527
mouse brain traumatic brain injury 50 MB 2,514 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size50 MB
Obs2,514
bronze H&E Open in Vitessce

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