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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 11, 2021 |
| Title |
Naive_DNT_2 |
| Sample type |
SRA |
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| Source name |
spleen T cells of eight-week-old C57BL/6 male mice
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| Organism |
Mus musculus |
| Characteristics |
cell type: TCRalphabeta + T cells
cell subset: naive DN
strain: C57BL/6
tissue: spleen
Sex: male
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
cDNA libraries of TCRab_Tcell, naïve_DNT_1, activated_DNT_1, CD4_Tcell and CD8_Tcell were obtained using Chromium Single Cell 3’ Library & Gel Bead Kit v2. cDNA libraries of Naïve_DNT_2 and activated_DNT_2 were obtained using Chromium Single Cell 3’ Library & Gel Bead Kit v3.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
CD3+NK1.1-TCRαβ+TCRγδ-CD4-CD8-aGal-CD1d-LPC-CD1d-
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| Data processing |
For TCRab_Tcell, naïve_DNT_1, activated_DNT_1, CD4_Tcell and CD8_Tcell samples, 10x Genomics cellranger mkfastq (version 2.1.0) was used to demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files. For Naïve_DNT_2 and activated_DNT_2 samples, 10x Genomics cellranger mkfastq (version 3.1.0) was used to demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
R1 = 16bp cell barcode + 10bp UMI barcode. R2 = biological
For TCRab_Tcell, naïve_DNT_1, activated_DNT_1, CD4_Tcell and CD8_Tcell samples, cellranger count (version 2.1.0) aligns the fastq files to the mm10 genome, filter and count the barcode and UMIs. For Naïve_DNT_2 and activated_DNT_2 samples, cellranger count (version 3.0.1) aligns the fastq files to the mm10 genome, filter and count the barcode and UMIs.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Row information of gene name is in genes.tsv. Column information of cell barcodes is in barcodes.tsv. Matrix file of read counts is in matrix.mtx.
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| Submission date |
Oct 22, 2020 |
| Last update date |
Jun 15, 2021 |
| Contact name |
YangLu Yang |
| E-mail(s) |
lucyyang1991@hotmail.com
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| Organization name |
Beijing Friendship Hospital, Capital Medical University
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| Street address |
Beijing Xicheng District Yongan Road NO.95
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100053 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE129030 |
Transcriptome landscape of double negative T cells by single-cell RNA sequencing |
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| Relations |
| BioSample |
SAMN16519093 |
| SRA |
SRX9346292 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4849476_Naive_DNT_2_barcodes.tsv.gz |
30.9 Kb |
(ftp)(http) |
TSV |
| GSM4849476_Naive_DNT_2_genes.tsv.gz |
244.7 Kb |
(ftp)(http) |
TSV |
| GSM4849476_Naive_DNT_2_matrix.mtx.gz |
46.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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