|
| Status |
Public on Dec 18, 2019 |
| Title |
IEC-WT-control_1 |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: colon
genotype: wild type
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 |
| E-mail(s) |
yananzhang1031@hotmail.com
|
| 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 |
|
| Relations |
| BioSample |
SAMN10612978 |
| SRA |
SRX5162163 |
