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Sample GSM3520240 Query DataSets for GSM3520240
Status Public on Dec 18, 2019
Title wt_dss_lif_LPLs
Sample type RNA
 
Source name lamina propria lymphocytes, day 10
Organism Mus musculus
Characteristics cell type: lamina propria lymphocytes (LPLs)
strain: C57BL6
genotype: wild type
treatment: DSS and LIF
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 15.050597
DarkCorner 3.509932
A_55_P1989846 6.398057
A_55_P1991598 4.0360837
A_55_P2022211 5.6095195
A_55_P1980764 2.5396378
A_55_P1964375 3.9368882
A_51_P128876 11.555387
A_55_P2121042 7.6324773
A_52_P219230 2.5396378
A_51_P207591 4.8296795
A_55_P2131920 3.6857543
A_55_P2404223 3.5797694
A_55_P2101944 16.280529
A_52_P358860 2.5396378
A_51_P119031 8.3438425
A_51_P309854 3.5793567
A_51_P343900 4.5982647
A_51_P234359 7.4492097
A_51_P487813 4.9601607

Total number of rows: 39485

Table truncated, full table size 900 Kbytes.




Supplementary file Size Download File type/resource
GSM3520240_wt_dss_lif.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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