GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3520237 Query DataSets for GSM3520237
Status Public on Dec 18, 2019
Title IEC-S4-KO-control_1
Sample type SRA
Source name Intestinal epithelial cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: colon
genotype: Stat4-/-
treatment: control
cell type: intestinal epithelial cell (IEC)
Treatment protocol IECs were treated with 20ng/ml of LIF at different time points.
Growth protocol IECs were isolated from colon of wild type (WT) and Stat4-/- mice, and plated on Matrigel-coated 12-well plates in F12/DMEM medium, supplemented with 5% FBS, insulin mix, 100U/ml of both penicillin and streptomycin. The IECs were allowed to attach for 24 hours, at which time all unattached material was removed and the cells were supplied with fresh culture medium as described above.
Extracted molecule total RNA
Extraction protocol IECs were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description IECs.GeneExpression.FPKM.xlsx
Data processing Bowtie2 was used to map clean reads to reference gene. Bowtie2 parameters forPE reads:-q--phred64--sensitive--dpad0--gbar99999999--mp1,1--np1--score-minL,0,-0.1-I1-X1000--no-mixed--no-discordant -p 16-k 200 Bowtie2 parameters forSE reads:-q--phred64--sensitive--dpad0--gbar99999999--mp1,1--np1--score-minL,0,-0.1-p16-k 200
HISAT was used to map clean reads to reference genome.HISAT parameters forPE reads:-p8--phred64--sensitive--no-discordant--no-mixed-I1-X1000 HISTAparameters forSE reads:-p8--phred64--sensitive-I1-X 1000
FPKM method is used in calculated expression level.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs
Submission date Dec 18, 2018
Last update date Dec 18, 2019
Contact name Yanan S Zhang
Phone 86-18817575525
Organization name Soochow University
Department Institutes of Biology and Medical Sciences
Lab Institutes of Biology and Medical Sciences
Street address 199 Renai Road
City Suzhou
State/province Jiangsu
ZIP/Postal code 215123
Country China
Platform ID GPL17021
Series (2)
GSE124077 STAT4 activation by leukemia inhibitory factor confers a therapeutic effect on intestinal inflammation [RNA-Seq]
GSE124079 STAT4 activation by leukemia inhibitory factor confers a therapeutic effect on intestinal inflammation
BioSample SAMN10612976
SRA SRX5162165

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap