organism: Mus musculus
description: Protocols: MedLNs, mesLNs, spleens, lungs, or siLP were taken from infected mice, 3, 5, 7, 10 or 30 days after infection as well as from uninfected mice. At each time point, cells were isolated from medLNs and mesLNs, by smashing the tissue through 70μm cell strainer. Lungs were incubated in collagenase D (0.72mg/ml, Amersham, Bucks, UK) for 30min, smashed through 70μm cell strainer, and suspended in RBC lysis buffer (eBioscience Ltd). Spleens were smashed through 70μm cell strainer, and suspended in RBC lysis buffer. siLP cells were isolated from colonic tissue as previously described38. In brief, siLP cells were released by digestion of the tissue with RPMI/4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) supplemented with 60 μg/ml DNaseI (Sigma), and 400 ng/ml of Liberase (Roche Applied Science, Burgess Hill, UK). Isolated cells were stained with conjugated antibodies for sorting. For RT-qPCR and bulk RNA-seq experiments, single cells were sorted into lysis buffer and was stored in -80°C. Cells were spun down and lysed in RLT plus buffer. RNA was then extracted using SPRI beads Smartseq2 was used to generate and amplify cDNA. Nextera XT was used to generate the libraries
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2019-07-25T04:02:53Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-07-12T14:36:50Z
attributes.tag: External Id
attributes.value: SAMEA5771425
attributes.tag: INSDC center name
attributes.value: Sanger Institute
attributes.tag: INSDC first public
attributes.value: 2019-07-25T04:02:53Z
attributes.tag: INSDC last update
attributes.value: 2019-07-12T14:36:50Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8003:37_new_gut_15
attributes.tag: age
attributes.value: 8 to 12
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell type
attributes.value: CD4 T cell
attributes.tag: cohort
attributes.value: newko
attributes.tag: common name
attributes.value: house mouse
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: individual
attributes.value: 15
attributes.tag: organism part
attributes.value: gut
attributes.tag: sample name
attributes.value: E-MTAB-8003:37_new_gut_15
attributes.tag: scientific_name
attributes.value: Mus musculus
attributes.tag: sex
attributes.value: not available