RNA-Seq Analysis of Mouse IMCD3 Cells

The methodology and data described below were generated by Chan SC, Zhang Y, Shao A, Avdulov S, Herrera J, Aboudehen K, Pontoglio M, and Igarashi P at the University of Minnesota (USA) and Institut National de la Santé et de la Recherche Médicale (France). These data are being hosted by the Epithelial Systems Biology Laboratory at the National Heart Lung and Blood Institute as a part of the Kidney Systems Biology Project. Website created by Jevin Z. Clark.

Methods:

mIMCD3 cells culture condition for RNA-sequencing: The authors used RNA-sequencing analysis of wild-type and HNF-1ߖdeficient mIMCD3 cells. Here, only the wild type data are presented. mIMCD3 WT cells were seeded at 5x10⁵cells per well in 6-well tissue culture plate. Cells were maintained in 4ml DMEM, low glucose with 10% FBS and antibiotics (100U/ml penicillin and 100mg/ml streptomycin) at 37 ℃, 5% CO2 incubator until 80-90% confluent. Cells were replenished with 4ml DMEM medium, low glucose with 10% FBS and antibiotics (100U/ml penicillin and 100mg/ml streptomycin) for another 24hrs at 37 ℃, 5% CO2 incubator. Cells were fully confluent for total RNA harvesting.

RNA Seq Method:TruSeq stranded mRNA libraries were generated from each sample and sequenced in a 50 bp paired-end run on a HiSeq 2500 instrument using v4 chemistry by the University of Minnesota Genomics Center. Raw paired-end RNA-sequencing (RNA-seq) reads in fastq format were analyzed using gopher-pipeline software. Raw data were downloaded from National Center for Biotechnology Information Gene Expression Omnibus (accession number GSE97770) and used to calculate TPM (transcripts per million). Briefly, the 50 bp paired-end reads were mapped to mouse Ensembl genome (Mus_musculus.GRCm38.v94) using STAR/2.5.4a. TPM values were calculated with RSEM/1.3.0 (--strandedness reverse). Transcripts with the top 8000 mean TPM values are reported here.

Reference:
Chan SC, Zhang Y, Shao A, Avdulov S, Herrera J, Aboudehen K, Pontoglio M, Igarashi P. Mechanism of Fibrosis in HNF1B-Related Autosomal Dominant Tubulointerstitial Kidney Disease. J Am Soc Nephrol. 2018 Aug 10. pii: ASN.2018040437. doi: 10.1681/ASN.2018040437. PubMed PMID:30097458.

Download data

**NOTE: In the Raw Average WT Counts column "--" signifies an annotation discrepancy between the two data sets.