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| Status |
Public on Apr 06, 2023 |
| Title |
3D cultured middle aged hematopoietic stem and progenitor cells |
| Sample type |
SRA |
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| Source name |
3D co-cultured
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| Organism |
Mus musculus |
| Characteristics |
cell type: hematopoietic stem and progenitor cells
tissue: 3D co-cultured
strain: WT
age: 12 months
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
After 3D co-cultured, all cells was collected by dissociating with collegen type I and neutral protease, and Lin- cells was sorted by FACS. About 20000 Lin- cells was used to constructe the scRNA-seq libraries.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
cultured-M
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The filtering, normalization, scaling, integrating,dimension reduce, clustering and finding markers were processed the seurat (v4.0.4).
The trajecory inference was processed with slingshot based on the coordinate which was reduced by Diffusion Map.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Oct 31, 2022 |
| Last update date |
Apr 06, 2023 |
| Contact name |
Dandan Cao |
| E-mail(s) |
1931465@tongji.edu.cn
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| Phone |
17853136996
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| Organization name |
Tongji University
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| Street address |
1239 Siping Road, Yangpu District
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE180866 |
Harnessing matrix stiffness to engineer a bone marrow niche for hematopoietic stem cell rejuvenation |
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| Relations |
| BioSample |
SAMN31535916 |
| SRA |
SRX18089634 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6697766_cultured-M_barcodes.tsv.gz |
62.7 Kb |
(ftp)(http) |
TSV |
| GSM6697766_cultured-M_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM6697766_cultured-M_matrix.mtx.gz |
167.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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