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Series GSE136727 Query DataSets for GSE136727
Status Public on Apr 22, 2020
Title mRNA transcriptome sequencing of colon tissues from Usp25+/+ and Usp25-/- mice treated with 2.5% DSS for 5 five days followed by two-day normal water
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Female Usp25+/+ and Usp25-/- 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). Total RNAs were prepared and the qualities of RNAs were determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently purified from 10 ug total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. The first strand cDNA 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 resulted 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 100 bp paired-end reads strategy (Novogene Co. Ltd, Beijing). Quality control of mRNA-seq data was performed by using Fatsqc and low-quality bases were trimmed by Cutadapt. All RNA-seq data were mapped to the mouse genome (mm9) by TopHat (version 2.1.1) and allow maximum 2 mismatch per read. Gene expression level was calculated by Cufflinks with default parameters and normalized by FPKM.
Overall design Two Usp25+/+ mice and two Usp25-/- mice were used.
Contributor(s) Wang X, Zhong B
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Submission date Sep 02, 2019
Last update date Apr 22, 2020
Contact name Pin-Ji Lei
Organization name Massachusetts General Hospital
Department Department of Radiation Oncology
Lab Edwin L. Steele Laboratories
Street address 100 Blossom Street
City Boston
State/province Massachusetts
ZIP/Postal code 02114
Country USA
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (4)
GSM4056800 WT-139
GSM4056801 WT-140
GSM4056802 KO-826
BioProject PRJNA563342
SRA SRP220360

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE136727_gene_fpkm.txt.gz 392.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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