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Series GSE126641 Query DataSets for GSE126641
Status Public on Jan 28, 2020
Title FAMIN is a multifunctional purine enzyme enabling the purine nucleotide cycle (Macrophage RNA Seq dataset)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary FAMIN (LACC1, C13orf31) loss-of-function causes systemic juvenile idiopathic arthritis and very early-onset inflammatory bowel disease, while a common I254V substitution results in hypomorphic function and increases susceptibility to Crohn’s disease and leprosy. In this study, we compare the mRNA transcriptional profiles of M0, M1 and M2-polarised bone marrow-derived macrophages from mice engineered at their endogenous locus to express human non-risk (Faminp.254I), risk (Faminp.254V) and monogenic (Faminp.284R) disease variants.
Overall design Bone marrow-derived macrophages were cultured from Faminp.254I (n=5), Faminp.254V (n=5) and Faminp.284R (n=5) mice, polarised to M0, M1 or M2 phenotype, and transcriptional profiles compared. Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, 74104) in accordance with the manufacturer's instructions. Strand-specific single-end sequencing libraries were prepared using TruSeq Stranded mRNA kit (Illumina Inc.). Eleven libraries were sequenced at a time in one lane on an Illumina HiSeq4000. FastQ files were quality-checked (FastQC) and any residual adaptor sequences were removed (Cutadapt). Reads were then aligned to the reference genome (mm10, UCSC) using STAR.
Contributor(s) Sewell GW, Haag LM, Cader M, Ebel J, Rosenstiel P, Kaser A
Citation(s) 31978345
Submission date Feb 15, 2019
Last update date Jan 28, 2020
Contact name Gavin Sewell
Organization name Cambridge Institute of Therapeutic Immunology and Infectious Disease
Department Jeffrey Cheah Biomedical Centre, University of Cambridge
Street address Puddicombe Way
City Cambridge
State/province Cambridgeshire
ZIP/Postal code CB2 0AW
Country United Kingdom
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (45)
GSM3610258 p254V_1_M0
GSM3610259 p254V_1_M1
GSM3610260 p254V_1_M2
BioProject PRJNA522787
SRA SRP186014

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Supplementary file Size Download File type/resource
GSE126641_Macrophage_RNA_Seq_Readcounts.txt.gz 1.2 Mb (ftp)(http) TXT
GSE126641_Macrophage_cpm.txt.gz 3.0 Mb (ftp)(http) TXT
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