MRNA transcriptome sequencing of colitis from Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice after administered DSS and of colorectal tumors from Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice after AOM/DSS colorectal tumor model treatment

ABSTRACT: Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice were administered 2.5% DSS dissolved in sterile water for 5 days, followed by regular water for 2 days. The colons were flushed with PBS to clear feces and slit open longitudinally. The distal colon tissues (0.5 cm in length, about 0.5 cm away from the anus) were washed in PBS and homogenized in 2 ml TRIzol (Invitrogen). Colorectal tumors from Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice were AOM/DSS colorectal tumor model. The colorectal tumors were flushed with PBS to clear feces and homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently purified from 10μg total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. First-strand complementary DNA was synthesized with NEBNext RNA First-Strand Synthesis Module. NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first-strand cDNA. The resulting double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 150-bp paired-end reads strategy (Novogene). Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev). All RNA-seq data were mapped to the mouse genome (Mus_musculus_Ensemble_94) by Hisat2 (v.2.0.5) and allowed a maximum of two mismatches per read. Gene expression level was calculated by FeatureCounts (v.2.0.0) with default parameters and normalized by FPKM (Fragments Per Kilobase of exon model per Million mapped fragments).

ORGANISM(S): Mus musculus

PROVIDER: GSE166277 | GEO | 2021/02/06

REPOSITORIES: GEO