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| Status |
Public on Oct 25, 2023 |
| Title |
IKZF_1 |
| Sample type |
SRA |
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| Source name |
Thymus
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| Organism |
Mus musculus |
| Characteristics |
tissue: Thymus
cell type: medullary thymic epithelial cell
genotype: Foxn1-Cre(+) Ikaros+/fl
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Freshly sorted EPCAM+Ly51- mTECs were collected in 0.04% BSA in PBS, then lysed following the Chromium Single Cell ATAC Reagent Kit from 10X Genomics
Per UCSF Genomics Core
Using chromium single cell ATAC workflow (from 10X Genomics) nuclei were transposed and then encapsulated and barcoded. Libraries were sequenced using NovaSeq 6000 (Illumina)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Fragment files were created from FASTQ files using 10X Cell Ranger and were transformed into ArrowFiles in R using the ArchR package
Gene annotation was performed with the mm10 genome and doublets were removed using the filterDoublets function in ArchR
Iterative LSI-based dimensional reduction was performed with 4 iterations and after clustering and marker features analysis, clusters containing low number of variable features were removed from further analysis
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| Submission date |
Jul 24, 2023 |
| Last update date |
Oct 25, 2023 |
| Contact name |
Jun Hyung Sin |
| E-mail(s) |
junhyung.sin@ucsf.edu
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| Phone |
4242419276
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| Organization name |
University of California, San Francisco
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| Department |
Pediatrics
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| Lab |
Waterfield
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| Street address |
513 Parnassus Ave S-1076
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE238149 |
Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance [Ikaros scATAC-seq] |
| GSE238150 |
Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance |
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| Relations |
| BioSample |
SAMN36698917 |
| SRA |
SRX21144999 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7659473_filtered_tf_bc_matrix_WT.tar.gz |
47.9 Kb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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