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Sample GSM7657367 Query DataSets for GSM7657367
Status Public on Oct 25, 2023
Title Foxn1-Cre (+)/Ikzf1fl/fl 42
Sample type SRA
 
Source name thymus
Organism Mus musculus
Characteristics tissue: thymus
cell type: Thymic tuft cells
genotype: KO
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
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
 
Submission date Jul 21, 2023
Last update date Oct 25, 2023
Contact name Jun Hyung Sin
E-mail(s) junhyung.sin@ucsf.edu
Phone 4242419276
Organization name University of California, San Francisco
Department Pediatrics
Lab Waterfield
Street address 513 Parnassus Ave S-1076
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
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
Relations
BioSample SAMN36678924
SRA SRX21126180

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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