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| Status |
Public on Oct 13, 2021 |
| Title |
TECs control batch2 |
| Sample type |
SRA |
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| Source name |
thymic epithelial cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8 weeks old
tissue: thymus
cell type: thymic epithelial cells
genotype: Aire+/+
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using Chromium Single Cell 3′ Reagent Kits v2 and v3 Chemistry
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina bcl2fastq software was used for generating FASTQ files FASTQ files were processed using Fastp, and reads were demultiplexed and mapped to the mm10 reference genome via Cell Ranger (v3.0.0). Processing data by the Cell Ranger pipeline was performed using the HOKUSAI supercomputer at RIKEN and the NIG supercomputer at ROIS National Institute of Genetics. Expression count matrices were prepared by counting unique molecule identifiers.
Supplementary files format and content are described at http://software.10xgenomics.com/single-cell/overview/welcome
Genome_build: mm10
Supplementary_files_format_and_content: Unfiltered feature-barcode matrices containing all barcodes in MEX format
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| Submission date |
Nov 26, 2020 |
| Last update date |
Oct 13, 2021 |
| Contact name |
Hideyuki Yoshida |
| E-mail(s) |
[email protected]
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| Organization name |
RIKEN IMS
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| Street address |
1-7-22 Suehiro-cho
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| City |
Tsurumi-ku, Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE155331 |
Transcriptional regulation by Aire in medullary thymic epithelial cells revisited |
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| Relations |
| BioSample |
SAMN16926622 |
| SRA |
SRX9590438 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4946388_ctrl2_barcodes.tsv.gz |
20.0 Mb |
(ftp)(http) |
TSV |
| GSM4946388_ctrl2_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM4946388_ctrl2_matrix.mtx.gz |
98.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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