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| Status |
Public on Oct 28, 2024 |
| Title |
Transcriptional profile of the rat cardiovascular system at single cell resolution |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We sought to characterize cellular composition across the cardiovascular system of the healthy Wistar rat, an important model in preclinical cardiovascular research. We performed snRNA-seq in 78 samples in 10 distinct regions including the four chambers of the heart, ventricular septum, sinoatrial node, atrioventricular node, aorta, pulmonary artery, and pulmonary veins, which produced 505,835 nuclei. We identified 26 distinct cell types and additional subtypes, with different cellular composition across cardiac regions and tissue-specific transcription for each cell type. Several cell subtypes were region-specific, including a subtype of vascular smooth muscle cells enriched in the large vasculature. We observed tissue-enriched cellular communication networks, including heightened Nppa - Npr1/2/3 signaling in the sinoatrial node. The existence of tissue-restricted cell types suggests regional regulation of cardiovascular physiology. Our detailed transcriptional characterization of each cell type offers the potential to identify novel therapeutic targets and improve preclinical models of cardiovascular disease.
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| Overall design |
78 samples which passed QC are included here. All samples are from healthy Wistar rat cardiovascular tissue, collected from specific tissue regions. The rats are all male 17 week old animals. Multiple tissue region samples were collected from each individual rat, and a total of 16 individual rats were used to collect the snRNA-seq data in this study. Nuclei were isolated from each sample and were used to prepare a 10x 3' v2 library for snRNA-seq.
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| Contributor(s) |
Arduini A, Fleming SJ, Ellinor PT |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 HL092577 |
IDENTIFICATION OF COMMON GENETIC VARIANTS FOR ATRIAL FIBRILLATION AND PR INTERVAL |
MASSACHUSETTS GENERAL HOSPITAL |
Patrick Thomas Ellinor |
| R01 HL157635 |
Using Electrocardiogram Genetics to Inform Arrhythmia Risk |
MASSACHUSETTS GENERAL HOSPITAL |
Patrick Thomas Ellinor |
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| Submission date |
Oct 23, 2024 |
| Last update date |
Oct 28, 2024 |
| Contact name |
Stephen Jordan Fleming |
| E-mail(s) |
[email protected]
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| Organization name |
Broad Institute
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| Lab |
Lab of Patrick Ellinor
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| Street address |
415 Main St.
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (1) |
| GPL25029 |
NextSeq 550 (Rattus norvegicus) |
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| Samples (78)
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| GSM8587464 |
AVN3_a, Atrioventricular node sample from av_3, replicate a |
| GSM8587465 |
AVN3_b, Atrioventricular node sample from av_3, replicate b |
| GSM8587466 |
AV1a, Atrioventricular node sample from av_1, replicate a |
| GSM8587467 |
AV1b, Atrioventricular node sample from av_1, replicate b |
| GSM8587468 |
AV1c, Atrioventricular node sample from av_1, replicate c |
| GSM8587469 |
AV1d, Atrioventricular node sample from av_1, replicate d |
| GSM8587470 |
AV2a, Atrioventricular node sample from av_2, replicate a |
| GSM8587471 |
AV2b, Atrioventricular node sample from av_2, replicate b |
| GSM8587472 |
AV2c, Atrioventricular node sample from av_2, replicate c |
| GSM8587473 |
AV2d, Atrioventricular node sample from av_2, replicate d |
| GSM8587474 |
Aorta5, Aorta sample from aorta_5, replicate 1 |
| GSM8587475 |
Aorta7, Aorta sample from aorta_7, replicate 1 |
| GSM8587476 |
LA2, Left atrium sample from chambers_2, replicate 1 |
| GSM8587477 |
LA3, Left atrium sample from chambers_3, replicate 1 |
| GSM8587478 |
LA6, Left atrium sample from chambers_6, replicate 1 |
| GSM8587479 |
LA8, Left atrium sample from chambers_8, replicate 1 |
| GSM8587480 |
LV11_1B, Left ventricle region 1B sample from chambers_11, replicate 1 |
| GSM8587481 |
LV11_2A, Left ventricle region 2A sample from chambers_11, replicate 1 |
| GSM8587482 |
LV11_2C, Left ventricle region 2C sample from chambers_11, replicate 1 |
| GSM8587483 |
LV11_3B, Left ventricle region 3B sample from chambers_11, replicate 1 |
| GSM8587484 |
LV13_1B, Left ventricle region 1B sample from chambers_13, replicate 1 |
| GSM8587485 |
LV13_2A, Left ventricle region 2A sample from chambers_13, replicate 1 |
| GSM8587486 |
LV13_2C, Left ventricle region 2C sample from chambers_13, replicate 1 |
| GSM8587487 |
LV13_3B, Left ventricle region 3B sample from chambers_13, replicate 1 |
| GSM8587488 |
LV14_1B, Left ventricle region 1B sample from chambers_14, replicate 1 |
| GSM8587489 |
LV14_2A, Left ventricle region 2A sample from chambers_14, replicate 1 |
| GSM8587490 |
LV14_2C, Left ventricle region 2C sample from chambers_14, replicate 1 |
| GSM8587491 |
LV14_3B, Left ventricle region 3B sample from chambers_14, replicate 1 |
| GSM8587492 |
LV1_2B, Left ventricle region 2B sample from chambers_1, replicate 1 |
| GSM8587493 |
LV2_2B, Left ventricle region 2B sample from chambers_2, replicate 1 |
| GSM8587494 |
LV3_2B, Left ventricle region 2B sample from chambers_3, replicate 1 |
| GSM8587495 |
LV4_2B, Left ventricle region 2B sample from chambers_4, replicate 1 |
| GSM8587496 |
LV5_2B, Left ventricle region 2B sample from chambers_5, replicate 1 |
| GSM8587497 |
LV6_2B, Left ventricle region 2B sample from chambers_6, replicate 1 |
| GSM8587498 |
LV7_2B, Left ventricle region 2B sample from chambers_7, replicate 1 |
| GSM8587499 |
RA2, Right atrium sample from chambers_2, replicate 1 |
| GSM8587500 |
RA3, Right atrium sample from chambers_3, replicate 1 |
| GSM8587501 |
RA6_12, Right atrium sample from chambers_6, replicate 1 |
| GSM8587502 |
RA8, Right atrium sample from chambers_8, replicate 1 |
| GSM8587503 |
RV1_2G, Right ventricle region 2G sample from chambers_1, replicate 1 |
| GSM8587504 |
RV2_2G, Right ventricle region 2G sample from chambers_2, replicate 1 |
| GSM8587505 |
RV3_2G, Right ventricle region 2G sample from chambers_3, replicate 1 |
| GSM8587506 |
RV4_2G, Right ventricle region 2G sample from chambers_4, replicate 1 |
| GSM8587507 |
RV5_2G, Right ventricle region 2G sample from chambers_5, replicate 1 |
| GSM8587508 |
RV6_2G, Right ventricle region 2G sample from chambers_6, replicate 1 |
| GSM8587509 |
RV7_2G, Right ventricle region 2G sample from chambers_7, replicate 1 |
| GSM8587510 |
SA1b, Sinoatrial node sample from sa_1, replicate b |
| GSM8587511 |
SA1c, Sinoatrial node sample from sa_1, replicate c |
| GSM8587512 |
SA1d, Sinoatrial node sample from sa_1, replicate d |
| GSM8587513 |
SA2a, Sinoatrial node sample from sa_2, replicate a |
| GSM8587514 |
SA2b, Sinoatrial node sample from sa_2, replicate b |
| GSM8587515 |
SA2c, Sinoatrial node sample from sa_2, replicate c |
| GSM8587516 |
SA2d, Sinoatrial node sample from sa_2, replicate d |
| GSM8587517 |
Aorta_2_06072019, Aorta sample from aorta_2, replicate 1 |
| GSM8587518 |
Aorta_3a_06072019, Aorta sample from aorta_3, replicate 1 |
| GSM8587519 |
Aorta_3b_06072019, Aorta sample from aorta_3, replicate 1 |
| GSM8587520 |
Aorta_4_06072019, Aorta sample from aorta_4, replicate 1 |
| GSM8587521 |
PA1_a, Pulmonary arteries sample from pa_1, replicate a |
| GSM8587522 |
PA1_b, Pulmonary arteries sample from pa_1, replicate b |
| GSM8587523 |
PA2_a, Pulmonary arteries sample from pa_2, replicate a |
| GSM8587524 |
PA2_b, Pulmonary arteries sample from pa_2, replicate b |
| GSM8587525 |
PA2_c, Pulmonary arteries sample from pa_2, replicate c |
| GSM8587526 |
PV3_a, Pulmonary veins sample from pv_3, replicate a |
| GSM8587527 |
PV3_b, Pulmonary veins sample from pv_3, replicate b |
| GSM8587528 |
PV4_a, Pulmonary veins sample from pv_4, replicate a |
| GSM8587529 |
PV4_b, Pulmonary veins sample from pv_4, replicate b |
| GSM8587530 |
Pulmonary_veins_1a, Pulmonary veins sample from pv_1, replicate a |
| GSM8587531 |
Pulmonary_veins_1b, Pulmonary veins sample from pv_1, replicate b |
| GSM8587532 |
Pulmonary_veins_2a, Pulmonary veins sample from pv_2, replicate a |
| GSM8587533 |
Pulmonary_veins_2b, Pulmonary veins sample from pv_2, replicate b |
| GSM8587534 |
SAN3_a, Sinoatrial node sample from sa_3, replicate a |
| GSM8587535 |
SAN3_b, Sinoatrial node sample from sa_3, replicate b |
| GSM8587536 |
Sept_Apex_1, Septum apex sample from septum_1, replicate 1 |
| GSM8587537 |
Sept_Apex_2, Septum apex sample from septum_2, replicate 1 |
| GSM8587538 |
Sept_Apex_3, Septum apex sample from septum_3, replicate 1 |
| GSM8587539 |
Sept_NBase_1, Septum base sample from septum_1, replicate 1 |
| GSM8587540 |
Sept_NBase_2, Septum base sample from septum_2, replicate 1 |
| GSM8587541 |
Sept_NBase_3, Septum base sample from septum_3, replicate 1 |
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| Relations |
| BioProject |
PRJNA1176479 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE280111_RAW.tar |
2.6 Gb |
(http)(custom) |
TAR (of H5) |
| GSE280111_Supplementary_Table_1_study_design_and_cellranger_QC_metrics.xlsx |
24.2 Kb |
(ftp)(http) |
XLSX |
| GSE280111_rn6.broad.cardiac.3.gtf.gz |
626.7 Kb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
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