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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 30, 2023 |
| Title |
PyMT cells |
| Sample type |
SRA |
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| Source name |
BONE MARROW
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| Organism |
Mus musculus |
| Characteristics |
tissue: BONE MARROW
cell type: Bone marrow stromal cells
genotype: PyMT mouse
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted and isolated using the Single Cell RNA purification kit (Norgen) according to the manufacturer’s instructions for bulk RNAseq experiments. For single cell experiments, sorted cells were loaded on a Chromium Controller using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 according to manufacturer’s instructions.
RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech/Takara) for bulk RNAseq and Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v2 or v3 Reagent Kit (10x Genomics) according to manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
SC_PyMT_Raw_Counts.csv
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| Data processing |
[scRNAseq] The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0.
[Bulk RNAseq] Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore!
[Bulk RNAseq] The raw sequencing data was initially aligned on the murine reference genome mm10, using STAR aligner (v2.5.3a) (Dobin et al., 2013). Raw read counts matrix was made with STAR (using the parameter –quantMode Gene- Counts).
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes metadata and cluster informations
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| Submission date |
Sep 25, 2023 |
| Last update date |
Sep 30, 2023 |
| Contact name |
Julie Helft |
| E-mail(s) |
gerber.helft@gmail.com, julie.helft@inserm.fr, jason.cosgrove@curie.fr, yoann.missolo-koussou@curie.fr, yohan.gerber@curie.fr
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| Organization name |
Institut Curie
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| Department |
U932
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| Street address |
26 Rue D'ulm
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| City |
France |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE243964 |
Breast cancer remotely imposes a myeloid bias on hematopoietic stem cells by reprogramming the bone marrow niche |
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| Relations |
| BioSample |
SAMN37531496 |
| SRA |
SRX21877399 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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