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Series GSE247719 Query DataSets for GSE247719
Status Public on Mar 05, 2024
Title A Panoramic View of Cell Population Dynamics in Mammalian Aging
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary To elucidate the aging-associated cellular population dynamics throughout the body, here we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissue samples, encompassing a range of organs across different developmental stages, genders, and genotypes. This comprehensive dataset allowed us to identify more than 3,000 unique cellular states and catalog over 200 distinct aging-associated cell populations experiencing significant depletion or expansion. Our panoramic analysis uncovered four distinct, temporally structured aging-related cell population dynamic waves that are organ- and lineage-specific. Moreover, we investigated aging-associated alterations in immune cell populations, revealing both widespread shifts and organ-specific changes. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte-dependent. The breadth and depth of our 'cell-omics' methodology not only enhance our comprehension of cellular aging but also lay the groundwork for exploring the complex regulatory networks among varied cell types in the context of aging and aging-associated diseases.
 
Overall design Single nucleus RNA-seq profiling for C57BL/6 mouse cells from lung, heart, liver, kidney, muscle, stomach, duodenum, jejunum, ileum, colon, brown adipose tissue, inguinal adipose tissue, gonadal adipose tissue cells at 3,6,12,16,23 months. Single nucleus RNA-seq profiling for B6.129S7-Rag1tm1Mom/J and B6.Cg-Prkdcscid/SzJ mouse cells from lung, heart, liver, kidney, muscle, stomach, duodenum, jejunum, brown adipose tissue, inguinal adipose tissue, gonadal adipose tissue cells at 3 and 16 months.
** Please note that the library for each organ is made out of pooled samples. For example, only one library (splitted into 9 sample/part records) was constructed and sequenced for kidney. After demultiplexing, there were over 2000 FASTQ files, which were submitted as multiple SRA experiments due to the maximum file number (256) for each library. All FASTQ files (generated from all corresponding organ *part sample records) are from the same pooled sample and each processed data (linked to the corresponding *part1 sample records) was generated from all pooled samples.
** 20240213_PanSci_all_cells_adata.h5ad: The h5ad file is generated with Scanpy where we pooled all the count matrix and metadata from GSE247719 and GSE212606, containing cells from brain, lung, heart, liver, kidney, muscle, stomach, duodenum, jejunum, ileum, colon, brown adipose tissue, inguinal adipose tissue, gonadal adipose tissue.
 
Contributor(s) Zhang Z, Schaefer C, Jiang W, Lu Z, Lee J, Sziraki A, Abdulraouf A, Zhou W, Cao J
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA1036289
Submission date Nov 14, 2023
Last update date Jul 01, 2024
Contact name Zehao Zhang
E-mail(s) zzhang03@rockefeller.edu
Organization name The Rockefeller University
Lab Laboratory of single-cell genomics and population dynamics
Street address 1230 York Ave, The Rockefeller University
City New York
State/province NY
ZIP/Postal code 10065-7949
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (78)
GSM7899256 PanSci, mouse kidney, part1
GSM7899257 PanSci, mouse kidney, part2
GSM7899258 PanSci, mouse kidney, part3

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE247719_20240213_PanSci_all_cells_adata.h5ad.gz 29.8 Gb (ftp)(http) H5AD
GSE247719_PanSci_01_Kidney_adata.h5ad 13.8 Gb (ftp)(http) H5AD
GSE247719_PanSci_02_Lung_adata.h5ad 7.8 Gb (ftp)(http) H5AD
GSE247719_PanSci_03_Heart_adata.h5ad 6.8 Gb (ftp)(http) H5AD
GSE247719_PanSci_04_Liver_adata.h5ad 6.0 Gb (ftp)(http) H5AD
GSE247719_PanSci_05_Muscle_adata.h5ad 1.8 Gb (ftp)(http) H5AD
GSE247719_PanSci_06_Stomach_adata.h5ad 2.1 Gb (ftp)(http) H5AD
GSE247719_PanSci_07_BAT_adata.h5ad 4.1 Gb (ftp)(http) H5AD
GSE247719_PanSci_08_iWAT_adata.h5ad 1.8 Gb (ftp)(http) H5AD
GSE247719_PanSci_09_gWAT_adata.h5ad 2.9 Gb (ftp)(http) H5AD
GSE247719_PanSci_10_Ileum_adata.h5ad 3.7 Gb (ftp)(http) H5AD
GSE247719_PanSci_11_Colon_adata.h5ad 3.7 Gb (ftp)(http) H5AD
GSE247719_PanSci_12_Jejunum_adata.h5ad 3.4 Gb (ftp)(http) H5AD
GSE247719_PanSci_13_Duodenum_adata.h5ad 1.8 Gb (ftp)(http) H5AD
GSE247719_PanSci_B_cell_adata.h5ad 2.1 Gb (ftp)(http) H5AD
GSE247719_PanSci_Myeloid_cell_adata.h5ad 3.2 Gb (ftp)(http) H5AD
GSE247719_PanSci_T_cell_adata.h5ad 1.8 Gb (ftp)(http) H5AD
GSE247719_RAW.tar 42.7 Gb (http)(custom) TAR (of CSV, MTX)
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