Illumina HiSeq 2500 sequencing; Ileal transcription profiles of NOD mice in Short-term Restoration experiment (Cecal microbiota transfer rescues the antibiotic-induced acceleration of type 1 diabetes  and alteration of intestinal gene expression)
Ileal transcription profiles of NOD mice in Short-term Restoration experiment (Cecal microbiota transfer rescues the antibiotic-induced acceleration of type 1 diabetes  and alteration of intestinal gene expression)
STR_1PAT5_s
Male NOD mice at P42 were sacrificed and ileum tissue were collected into RNAlater and then frozen at -80C until RNA extraction In the short term restoration experiment: the dams and their litters were randomly assigned to control, 1PAT antibiotic, and single dose cecal microbiota transfer groups. At postnatal (P) day 23, the pups were weaned and housed to separate males and females. All mice received acidified drinking water supplied by the facility routinely except for the periods when some litters were receiving antibiotic treatment.  In the short term restoration experiment: the dams and their litters were randomly assigned to control, 1PAT antibiotic, and single dose cecal microbiota transfer groups. 1. control: drinking water with no antibiotic all the time; 2. 1PAT(antibiotic): drinking water with 333mg/L tylosin during P5-P10. 3. Cecal microbiota transfer (single dose): drinking water with 333mg/L tylosin during P5-P10, and then inoculated 50 ul donor cecal microbiota donor material by gavage. All mice were wean at P23 and on P42, male mice were sacrificed and ileum tissue were collected for RNA extraction and RNAseq analysis. RNA was extracted using the Qiagen miRNAeasy kit (Qiagen, Valencia CA) using the standard protocol. Ribosomal RNA was removed using the Ribo-Zero rRNA depletion kit (Illumina, San Diego CA). The TruSeq RNA sample preparation kit (Illumina, San Diego, CA) was used to prepare cDNA libraries from RNA samples.