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Sample GSM767801

Query DataSets for GSM767801

Status

Public on Nov 01, 2011

Title

Mismatch_6

Sample type

RNA

Source name

Replecate_6

Organism

Homo sapiens

Characteristics

sample type: reference total RNA

Extracted molecule

total RNA

Extraction protocol

All RNAs are provided by Takara Co. Ltd. We extracted them accroding to their manuals.

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 8x15k Oligo Microarrays (027004) 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

Data processing

The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 030829_D_F_20101021) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

Submission date

Jul 27, 2011

Last update date

Nov 01, 2011

Contact name

Jun Sese

E-mail(s)

sese.jun@aist.go.jp

Organization name

National Institute of Advanced Industrial Science and Technology

Street address

2-4-7 Aomi

City

Koto

State/province

Tokyo

ZIP/Postal code

135-0064

Country

Japan

Platform ID

GPL13976

Series (2)

GSE30981	Gene expression levels with various artificial mutations -- with mismatch
GSE31202	Gene expression levels with various artificial mutations and inter-species array

Data table header descriptions
ID_REF
VALUE	Log2 normalized signal intensity

Data table
ID_REF	VALUE
A_23_P100001_2460_1MM_9_DL	9.276732071
A_23_P100074_1220_2DP_53G_29C_NM	10.3595025
A_23_P100074_1220_ORG_NM	10.79117022
A_23_P100189_240_3MM_5_DL	18.14122954
A_23_P100220_3358_1MM_4_IN	10.64969539
A_23_P100240_2757_1MM_8_IN	15.17521348
A_23_P10025_2874_3MM_2_IN	8.560630133
A_23_P100315_1317_1MM_1_DL	12.79811878
A_23_P100341_1326_2MM-2BS_4_MM	13.56088091
A_23_P100392_816_1MM_7_MM	9.816284018
A_23_P100408_1248_1MM_7_IN	4.346910099
A_23_P100478_733_ORG_1_NM	10.74274732
A_23_P100478_733_ORG_2_NM	10.61496653
A_23_P100486_630_2MM_4_IN	12.981993
A_23_P100499_433_2MM-2BS_7_MM	8.598266934
A_23_P100576_320_1MM_9_DL	12.14279473
A_23_P100583_2402_3MM_3_MM	4.779114183
A_23_P100642_1003_2MM_3_DL	7.543485057
A_23_P100660_1342_1MM_4_DL	13.89020252
A_23_P100704_2927_2MM_3_IN	9.478516848

Total number of rows: 8268

Table truncated, full table size 316 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM767801_withmismatch_2_2.txt.gz	510.4 Kb	(ftp)(http)	TXT
Processed data included within Sample table