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| Status |
Public on May 14, 2024 |
| Title |
scRNA-seq_αLP_hashtag |
| Sample type |
SRA |
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| Source name |
Bone Marrow
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: WT and G3SEKO
tissue: Bone Marrow
cell type: lymphoid progenitor
antibodies/tags: Anti-MHC classI, WT:TotalSeq-A307, A308, A309; G3SEKO:TotalSeq-A310, A311, A312)
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| Extracted molecule |
protein |
| Extraction protocol |
Bone marrow cells were harvested from the cut-off of both ends of the femur, tibia and pelvis, humerus, and scapula of mice using a centrifuge. Lineage-positive cells were depleted using a MOJO Hematopoietic Isolation Kit. αLP were sorted using FACSAriaII.
Hashtag labeled sorted cells were combined, trapped, and reverse-transcribed using BD Rhapsody (BD) according to the manufacturer's instructions. Single-cell RNA sequencing was performed using the platform of TAS-Seq.
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| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
After adaptor removal by Cutadpat, gene-expression libraries were aligned to the mm10 reference transcriptome by Bowtie2, and count matrices were generated using modified BD Rhapsody workflow. Valid cell barcodes were identified as cell barcodes above the inflection threshold of the knee-plot of total read counts of each cell barcode identified by the DropletUtils package. Sample origins and doublets were identified based on fold change of the normalized read counts of the hashtags. The count matrices were imported and analyzed using Seurat v.4.
Assembly: GRCm38
Supplementary files format and content: count matrix
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| Submission date |
Nov 16, 2022 |
| Last update date |
May 14, 2024 |
| Contact name |
Arifumi Iwata |
| Organization name |
Chiba University
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| Department |
Department of Allergy and Clinical Immunology
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| Street address |
1-8-1 Inohana, Chuou-ku
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| City |
Chiba-shi |
| State/province |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE218154 |
Single cell RNA sequencing for α lymphoid progenitor |
| GSE218155 |
ILC2 development requires GATA3-related super-enhancers after lineage commitment |
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| Relations |
| BioSample |
SAMN31760873 |
| SRA |
SRX18290231 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6735565_Hashtag_top1M_Tag2.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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