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| Status |
Public on Aug 18, 2024 |
| Title |
BM lin- Flt3+ Kitint-lo H/H, GEX |
| Sample type |
SRA |
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| Source name |
BM
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| Organism |
Mus musculus |
| Characteristics |
tissue: BM
cell line: C57BL/6
cell type: lin- Flt3+ Kitint-lo BM cells
genotype: H/H
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
BM and spleens were harvested from two WT and two Irf8 +32H/H mice. The BM samples were depleted of lin+ cells expressing CD3e, CD8b, CD11b, CD19, B220, ly-6G, TER-119, and NK1.1. Each sample was stained with fluorochrome-conjugated antibodies and labeled with a unique Antibody Capture TotalSeq B antibody (Biolegend) before sorting for lin- Flt3+ Kitint-lo cells. Two samples from each genotype were pooled and resuspended in PBS with 0.04% BSA at a final concentration of approximately 1,000 cells/mL. The spleen samples were enriched for CD11c-expressing cells, similarly stained with fluorochrome-conjugated antibodies and labeled with a unique Antibody Capture TotalSeq B antibody (Biolegend), before further sort-purification for CD11c+ cells. All four samples were pooled and resuspended in PBS with 0.04% BSA at approximately 1,000 cells/mL. These were loaded on a 10× Genomics Chromium Single Cell Controller at GTAC@MGI at Washington University School of Medicine.
Library preparation was performed using the 10× Genomics Next GEM Single Cell 3’ Reagents Kit v3. Libraries were sequenced using an Illumina Novaseq 6000 sequencer, producing 150 bp paired-end reads. Sequencing targeted depths of 1B reads for the gene expression (GEX) library and 100M reads for the hashtag oligo (HTO) library, respectively.
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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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| Data processing |
The Cell Ranger pipeline v8.0.0 was used for aligning reads to the mm10 reference genome, single cell counting, barcode processing, and sample demultiplexing.
Assembly: mm10
Supplementary files format and content: TSV files of per biological replicate
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| Submission date |
Jun 17, 2024 |
| Last update date |
Aug 18, 2024 |
| Contact name |
Feiya Ou |
| E-mail(s) |
feiya.ou@wustl.edu
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| Organization name |
Washington University in St. Louis
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| Department |
Pathology & Immunology
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| Lab |
Murphy Lab
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| Street address |
4939 Children's Place
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE270060 |
Optimization of the Irf8 +32 kb enhancer disrupts dendritic cell lineage segregation [scRNA-seq] |
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| Relations |
| SRA |
SRX24955230 |
| BioSample |
SAMN41880928 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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