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Sample GSM4159453 Query DataSets for GSM4159453
Status Public on Oct 13, 2020
Title GF1
Sample type RNA
 
Source name mouse plasma sample,germ-free mice
Organism Mus musculus
Characteristics sample type: plasma
gender: male
Treatment protocol Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 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 Human 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%).
Description germ-free mice
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 Nov 13, 2019
Last update date Oct 13, 2020
Contact name X XX
Organization name university
Street address Road 89
City X
ZIP/Postal code 11
Country China
 
Platform ID GPL19980
Series (2)
GSE140339 Gut microbiota regulates tumor via circRNA/miRNA networks II
GSE140887 Gut microbiota regulates tumor via circRNA/miRNA networks

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASCRMP000001 8.361312313
ASCRMP000002 5.249785374
ASCRMP000003 5.59517756
ASCRMP000004 5.019475161
ASCRMP000006 9.501534745
ASCRMP000007 7.087333647
ASCRMP000009 8.227758955
ASCRMP000013 11.8172051
ASCRMP000014 5.391218372
ASCRMP000016 5.334509769
ASCRMP000020 6.36995561
ASCRMP000021 8.557031932
ASCRMP000022 7.134953434
ASCRMP000023 5.589358728
ASCRMP000025 7.283362859
ASCRMP000026 5.751052272
ASCRMP000030 5.15250499
ASCRMP000032 7.675428801
ASCRMP000033 5.223291648
ASCRMP000035 8.602980178

Total number of rows: 992

Table truncated, full table size 24 Kbytes.




Supplementary file Size Download File type/resource
GSM4159453_GF1.txt.gz 703.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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