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| Status |
Public on Jun 26, 2023 |
| Title |
Hnf4ctrl.Hnf4dTEC.Pdpn-CD104-.mTEClo.rep#1-7.FBC |
| Sample type |
SRA |
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| Source name |
Thymus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Foxn1(cre/+) Hnf4a(fl/+) Hnf4g(+/-) and Foxn1(cre/+) Hnf4a(fl/fl) Hnf4g(-/-)
cell type: mTEClo
hashid: HT1-ACCCACCAGTAAGAC (hnf4ctrl_r1); HT2-GGTCGAGAGCATTCA (hnf4ctrl_r2); HT3-CTTGCCGCATGTCAT (hnf4ctrl_r3); HT5-CTTTGTCTTTGTGAG (hnf4dtec_r1); HT6-TATGCTGCCACGGTA (hnf4dtec_r2); HT8-TATAGAACGCCAGGC (hnf4dtec_r3); HT9-TGCCTATGAAACAAG (hnf4dtec_r4)
library type: ADT oligo
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| Extracted molecule |
protein |
| Extraction protocol |
mTEC were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies, hashing with TotalSeq antibodies against H2-Kb, and flow sorting mTECs into DMEM/10%FCS.
Purified cells were sent to the Broad Institute Genomics Platform, which performed encapsulation and RNA and hash library preparation following 10X Genomics protocols (3' v3.1 chemistry)
scRNA-seq
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| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
7 samples (3 Hnf4ctrl, 4 Hnf4dTEC) were hashed together into a single 10X scRNA-seq run
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
metadata.txt
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| Data processing |
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as transcript-by-cell matrices using Cell Ranger (v6.1.0, 10X Genomics).
Hash-by-cell matrices were computed using CITE-seq-count (v1.4.3).
Cells with no or multiple hashes, high mitochondrial content, or lineage markers of contaminants (i.e., T, endothelial cells) were filtered out in Seurat (v4.0.2)
Assembly: mm10
Supplementary files format and content: The tsv files for barcodes, features and counts for gene expression and hash matrices, and txt files indicating retained cells with their hash assignment.
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| Submission date |
Feb 20, 2023 |
| Last update date |
Jun 26, 2023 |
| Contact name |
CBDM Lab |
| E-mail(s) |
cbdm@hms.harvard.edu
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| Phone |
617-432-7747
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| Organization name |
Harvard Medical School
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| Department |
Microbiology and Immunobiology
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| Lab |
CBDM
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE225660 |
Hnf4 controls gut and liver gene programs in the thymus [scRNAseq] |
| GSE225661 |
Hnf4 controls gut and liver gene programs in the thymus |
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| Relations |
| BioSample |
SAMN33385896 |
| SRA |
SRX19447531 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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