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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 25, 2023 |
| Title |
Foxn1-Cre (-)/Ikzf1fl/fl 41 |
| Sample type |
SRA |
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| Source name |
thymus
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| Organism |
Mus musculus |
| Characteristics |
tissue: thymus
cell type: Thymic tuft cells
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly sorted L1CAM+ thymic tuft cells were collected into SMART-seq lysis buffer (+RNA Inhibitor, 10X lysis buffer [Takara Biosciences], 5' SMART seq PRIMER III [Takara Biosciences], H20)
Per UCSF Genomics Core
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Aire-dependent genes and Fezf2-dependent genes were identified using previously published RNA-seq data.
Sequence alignment was performed using STAR (Version 2.7.9a) and mappings were restricted to those that were uniquely assigned to the mouse genome, and unique read alignments were used to quantify expression and aggregated on a per-gene basis using the Ensembl (GRCm39) annotation
Differentially expressed genes between expreimental groups were determined used DESeq2
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| Submission date |
Jul 21, 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 |
GPL21103 |
| Series (2) |
| GSE237988 |
Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance [Tuft cell RNA-seq] |
| GSE238150 |
Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance |
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| Relations |
| BioSample |
SAMN36678925 |
| SRA |
SRX21126179 |
| 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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