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Links from GEO DataSets

Items: 20

1.

Deciphering cell states and genealogies of human hematopoiesis with single-cell multi-omics [Extended donors]

(Submitter supplied) The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived hematopoietic stem cells (HSCs). Perturbations to this process underlie a diverse set of diseases, but the clonal contributions to human hematopoiesis and how this changes with age remain incompletely understood. While recent insights have emerged from barcoding studies in model systems, simultaneous detection of cell states and phylogenies from natural barcodes in humans has been challenging, which has limited the ability to explore functional differences between HSC clones. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL24676
9 Samples
Download data: H5, RDS, TSV, TXT
Series
Accession:
GSE261078
ID:
200261078
2.

Deciphering cell states and genealogies of human hematopoiesis with single-cell multi-omics [Crispr_Mouse_Batch2]

(Submitter supplied) The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived hematopoietic stem cells (HSCs). Perturbations to this process underlie a diverse set of diseases, but the clonal contributions to human hematopoiesis and how this changes with age remain incompletely understood. While recent insights have emerged from barcoding studies in model systems, simultaneous detection of cell states and phylogenies from natural barcodes in humans has been challenging, which has limited the ability to explore functional differences between HSC clones. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24247
4 Samples
Download data: H5, TAR, TSV
Series
Accession:
GSE259285
ID:
200259285
3.

Deciphering cell states and genealogies of human hematopoiesis with single-cell multi-omics [Crispr_Mouse_Batch1]

(Submitter supplied) The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived hematopoietic stem cells (HSCs). Perturbations to this process underlie a diverse set of diseases, but the clonal contributions to human hematopoiesis and how this changes with age remain incompletely understood. While recent insights have emerged from barcoding studies in model systems, simultaneous detection of cell states and phylogenies from natural barcodes in humans has been challenging, which has limited the ability to explore functional differences between HSC clones. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24247
4 Samples
Download data: H5, TAR, TSV, TXT
Series
Accession:
GSE259284
ID:
200259284
4.

Deciphering cell states and genealogies of human hematopoiesis with single-cell multi-omics [Young2]

(Submitter supplied) The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived hematopoietic stem cells (HSCs). Perturbations to this process underlie a diverse set of diseases, but the clonal contributions to human hematopoiesis and how this changes with age remain incompletely understood. While recent insights have emerged from barcoding studies in model systems, simultaneous detection of cell states and phylogenies from natural barcodes in humans has been challenging, which has limited the ability to explore functional differences between HSC clones. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL24676
9 Samples
Download data: H5, MTX, TSV
Series
Accession:
GSE219248
ID:
200219248
5.

Deciphering cell states and genealogies of human hematopoiesis with single-cell multi-omics [Young1_T2]

(Submitter supplied) The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived hematopoietic stem cells (HSCs). Perturbations to this process underlie a diverse set of diseases, but the clonal contributions to human hematopoiesis and how this changes with age remain incompletely understood. While recent insights have emerged from barcoding studies in model systems, simultaneous detection of cell states and phylogenies from natural barcodes in humans has been challenging, which has limited the ability to explore functional differences between HSC clones. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL24676
9 Samples
Download data: H5, MTX, TSV
Series
Accession:
GSE219167
ID:
200219167
6.

Deciphering cell states and genealogies of human hematopoiesis with single-cell multi-omics [Young 1]

(Submitter supplied) The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived hematopoietic stem cells (HSCs). Perturbations to this process underlie a diverse set of diseases, but the clonal contributions to human hematopoiesis and how this changes with age remain incompletely understood. While recent insights have emerged from barcoding studies in model systems, simultaneous detection of cell states and phylogenies from natural barcodes in humans has been challenging, which has limited the ability to explore functional differences between HSC clones. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL24676
9 Samples
Download data: H5, MTX, TSV
Series
Accession:
GSE219106
ID:
200219106
7.

Deciphering cell states and genealogies of human hematopoiesis with single-cell multi-omics [Aged 2]

(Submitter supplied) The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived hematopoietic stem cells (HSCs). Perturbations to this process underlie a diverse set of diseases, but the clonal contributions to human hematopoiesis and how this changes with age remain incompletely understood. While recent insights have emerged from barcoding studies in model systems, simultaneous detection of cell states and phylogenies from natural barcodes in humans has been challenging, which has limited the ability to explore functional differences between HSC clones. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL24676
6 Samples
Download data: H5, MTX, TSV
Series
Accession:
GSE219057
ID:
200219057
8.

Deciphering cell states and genealogies of human hematopoiesis with single-cell multi-omics

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. The main processed data are organized in the following two Figshare links: Seurat objects: https://doi.org/10.6084/m9.figshare.23290004 ReDeeM-V output: https://doi.org/10.6084/m9.figshare.24418966.v1
Organism:
Homo sapiens; Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL24676 GPL24247
56 Samples
Download data: H5, RDS, TAR, TSV, TXT
Series
Accession:
GSE219015
ID:
200219015
9.

Deciphering cell states and genealogies of human hematopoiesis with single-cell multi-omics [Aged 1]

(Submitter supplied) The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived hematopoietic stem cells (HSCs). Perturbations to this process underlie a diverse set of diseases, but the clonal contributions to human hematopoiesis and how this changes with age remain incompletely understood. While recent insights have emerged from barcoding studies in model systems, simultaneous detection of cell states and phylogenies from natural barcodes in humans has been challenging, which has limited the ability to explore functional differences between HSC clones. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL24676
6 Samples
Download data: H5, MTX, TSV
Series
Accession:
GSE219014
ID:
200219014
10.

Clonal analysis of lineage fate in unperturbed hematopoiesis

(Submitter supplied) The classical tenet of hematopoiesis posits well-accepted lineage trees that arise from progressively restricted oligopotent and unipotent progenitor populations. However, because fate in hematopoiesis has mostly been studied in the context of transplantation, it is unclear whether these lineage branches and such proposed oligopotent progenitors exist in an unperturbed hematopoietic system. Here, we utilize endogenous transposon tagging to trace the fate of thousands of progenitors and stem cells over time to re-evaluate these dogmas. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
5 Samples
Download data: CSV
Series
Accession:
GSE90742
ID:
200090742
11.

Simultaneous lineage and transcriptome analysis of hematopoietic stem cell fates

(Submitter supplied) Bone marrow transplantation therapy relies on the life-long regenerative capacity of hematopoietic stem cells (HSCs). HSCs present a wide complexity of regenerating behaviours at the clonal level, but the mechanisms underlying this diversity are still unclear. Recent advances in single cell sequencing have described transcriptional differences amongst HSCs, providing a possible explanation for their functional heterogeneity. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
90 Samples
Download data: CSV, TSV, TXT
Series
Accession:
GSE134242
ID:
200134242
12.

Epigenetic Memory Underlies Cell Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells

(Submitter supplied) Stem cells determine homeostasis and repair of many tissues and are increasingly recognized as functionally heterogeneous. To define the extent of and molecular basis for heterogeneity we overlaid functional, transcriptional and epigenetic attributes of hematopoietic stem cells (HSCs) at a clonal level using endogenous fluorescent tagging. Endogenous HSC had clone-specific functional attributes in vivo. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
21 Samples
Download data: BED, TDF, TXT
Series
Accession:
GSE87527
ID:
200087527
13.

Mapping genotypes to chromatin accessibility profiles in single cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Other; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
55 Samples
Download data: CSV, MTX, TSV, TXT
Series
Accession:
GSE204912
ID:
200204912
14.

Mapping genotypes to chromatin accessibility profiles in single cells [Genotyping GoT-ChA amplicon]

(Submitter supplied) Processed scATAC-seq sequencing data from myelofibrosis patients and raw sequencing data from scATAC-seq cell mixing experiments
Organism:
Homo sapiens
Type:
Other
Platform:
GPL24676
27 Samples
Download data: CSV
Series
Accession:
GSE204911
ID:
200204911
15.

Mapping genotypes to chromatin accessibility profiles in single cells [scATAC-seq; Pt01-19;Pt-02 DOGMAseq]

(Submitter supplied) Processed scATAC-seq sequencing data from myelofibrosis patients and raw sequencing data from scATAC-seq cell mixing experiments
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
28 Samples
Download data: CSV, MTX, TSV, TXT
Series
Accession:
GSE203251
ID:
200203251
16.

Resolving fate and transcriptome of hematopoietic stem cell clones

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
35 Samples
Download data: MTX, TSV
Series
Accession:
GSE152557
ID:
200152557
17.

Resolving fate and transcriptome of hematopoietic stem cell clones [LT_ST_HSC]

(Submitter supplied) Hematopoietic stem cell (HSC) differentiation into mature lineages has been studied under physiological conditions in vivo by genetic barcoding-driven lineage tracing. HSC clones differ in output (differentiation-inactive versus differentiation-active), and in fates (multilineage versus lineage-restricted). Single-cell sequencing data revealed transcriptome diversity of HSC and progenitors, and suggested differentiation pathways. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
4 Samples
Download data: MTX, TSV
Series
Accession:
GSE152555
ID:
200152555
18.

Resolving fate and transcriptome of hematopoietic stem cell clones [multiple cell types]

(Submitter supplied) Hematopoietic stem cell (HSC) differentiation into mature lineages has been studied under physiological conditions in vivo by genetic barcoding-driven lineage tracing. HSC clones differ in output (differentiation-inactive versus differentiation-active), and in fates (multilineage versus lineage-restricted). Single-cell sequencing data revealed transcriptome diversity of HSC and progenitors, and suggested differentiation pathways. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
31 Samples
Download data: MTX, TSV
Series
Accession:
GSE144273
ID:
200144273
19.

An Epigenetic Component of Hematopoietic Stem Cell Aging Amenable to Reprogramming Into a Young State

(Submitter supplied) Aging of hematopoietic stem cells (HSCs) leads to several functional changes, including alterations affecting self-renewal and differentiation. While it is well established that many of the age-induced changes are intrinsic to HSCs, less is known about the stability of this state. Here, we entertained the hypothesis that HSC aging is driven by the acquisition of permanent genetic mutations. To examine this issue at a functional level in vivo, we applied induced pluripotent stem (iPS) cell reprogramming of aged hematopoietic progenitors and allowed the resulting aged-derived iPS cells to reform hematopoiesis via blastocyst complementation. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
16 Samples
Download data: CEL
Series
Accession:
GSE44923
ID:
200044923
20.

Accumulating mitochondrial DNA mutations drive premature hematopoietic aging phenotypes molecularly distinct from physiologic stem cell aging

(Submitter supplied) Somatic stem cells mediate tissue maintenance for the lifetime of an organism. Despite the well-established longevity that is a prerequisite for such function, accumulating data argue for compromised stem cell function with age. Identifying the mechanisms underlying age-dependent stem cell dysfunction is therefore key to understand the aging process. Using a model that carries a proofreading defective mitochondrial DNA polymerase, we demonstrate hematopoietic defects reminiscent of premature HSC aging including anemia, lymphopenia and myeloid lineage skewing. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS3976
Platform:
GPL1261
16 Samples
Download data: CEL
Series
Accession:
GSE27686
ID:
200027686
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