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Sample GSM3752411 Query DataSets for GSM3752411
Status Public on May 06, 2019
Title RAW264.7 cells_IR-61_repeat1
Sample type RNA
Source name RAW264.7 cells, IR-61, repeat1
Organism Mus musculus
Characteristics tissue: Abelson murine leukemia virus-induced tumor; ascites
cell line: RAW264.7
agent: IR-61
strain: BALB/c
gender: male
age: adult
Treatment protocol RAW264.7 cells was treated with vehicle control or IR-61 for 24h in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol RAW264.7 cells were treated with vehicle control or IR-61 for 24 h and then RNA was extracted, reverse transcription and analyzed.
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 ( Agilent p/n G2565BA) 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 Gene expression after 24h in IR-61-treated RAW264.7 cells
Data processing The scanned images were analyzed with Feature Extraction Software (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 May 05, 2019
Last update date May 06, 2019
Contact name Yawei Wang
Organization name Third Millitary Medical University
Street address 30 gaotanyan center street
City Chongqing
ZIP/Postal code 400038
Country China
Platform ID GPL11202
Series (1)
GSE130718 Determinaton the effect of IR-61 on macrophage gene expression

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 11.9539995
DarkCorner 2.3236887
A_55_P1989846 13.687694
A_55_P1991598 5.1441774
A_55_P2022211 11.918337
A_55_P1980764 6.843553
A_55_P1964375 12.866759
A_51_P128876 13.981011
A_55_P2121042 5.4096727
A_52_P219230 8.348347
A_51_P207591 7.010499
A_55_P2131920 9.666331
A_55_P2404223 7.765725
A_55_P2101944 15.36599
A_52_P358860 7.828247
A_51_P119031 11.126018
A_51_P309854 2.3534846
A_51_P343900 12.270455
A_51_P234359 6.2572103
A_51_P487813 14.0858

Total number of rows: 39485

Table truncated, full table size 895 Kbytes.

Supplementary file Size Download File type/resource
GSM3752411_IR-61_002.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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