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Sample GSM3520241 Query DataSets for GSM3520241
Status Public on Dec 18, 2019
Title ko_dss_LPLs
Sample type RNA
 
Source name lamina propria lymphocytes, day 10
Organism Mus musculus
Characteristics cell type: lamina propria lymphocytes (LPLs)
strain: C57BL6
genotype: Stat4-/-
treatment: DSS
Treatment protocol Freshly isolated LPLs from mice on day 10 after exposure to mock water, dextran sulfate sodium (DSS) solution, or DSS solution and LIF-treatment were were collected and stored in TRIzol reagent at -80℃ fridge.
Extracted molecule total RNA
Extraction protocol RNA were prepared with TRIzol reagent. Breifly, add 1ml of TRIzol per 1*10^6 cells, which were solubilized for 5 min at room temperature (RT). Then, add 0.2ml of coloroform per ml of TRIzol, mix vigorously for 15 sec, and stand the mixture for 2-3 min at RT, following by a centrifuge at 13,000rpm for 15 min at 4℃. Transfer the upper clear phase to a panel of fresh tubes. Add 0.5ml of isopropanol per each milliliter of the clear phase, mix vigorously, and stand the mixture for 10 min, following by a centrifuge at 13,000rpm for 10 min at 4℃. Decant the supernatant. Resuspend the pellet immediately with 1ml of 75% ethanol, following by a centrifuge at 13,000rpm for 5 min at 4℃. Decant the supernatant, and remove any remaining liquid. Resolve the RNA with RNase-free water, and store it at -80℃.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Dec 18, 2018
Last update date Dec 21, 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 GPL11202
Series (2)
GSE124078 STAT4 activation by leukemia inhibitory factor confers a therapeutic effect on intestinal inflammation [array]
GSE124079 STAT4 activation by leukemia inhibitory factor confers a therapeutic effect on intestinal inflammation

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 16.866302
DarkCorner 2.8901505
A_55_P1989846 5.263714
A_55_P1991598 5.0848417
A_55_P2022211 6.2759995
A_55_P1980764 3.1302826
A_55_P1964375 3.0243487
A_51_P128876 10.43248
A_55_P2121042 8.821427
A_52_P219230 2.4111457
A_51_P207591 3.924762
A_55_P2131920 2.4111457
A_55_P2404223 3.1201434
A_55_P2101944 15.824715
A_52_P358860 3.6288288
A_51_P119031 5.860466
A_51_P309854 2.4111457
A_51_P343900 6.5125284
A_51_P234359 6.840724
A_51_P487813 4.140956

Total number of rows: 39485

Table truncated, full table size 899 Kbytes.




Supplementary file Size Download File type/resource
GSM3520241_ko_dss.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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