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Sample GSM307408

Query DataSets for GSM307408

Status

Public on Nov 01, 2008

Title

Patient 14

Sample type

RNA

Source Name

Influenza A H1N1

Organism(s)

Influenza A virus

Characteristics

County 1 M 0
Human isolate
Nasopharyngeal swab

Extracted molecule

total RNA

Extraction protocol

Nasopharyngeal swabs were submitted to the laboratory in viral transport media and total nucleic acid was extracted from the viral transport media with Qiagen RNeasy columns following manufacturers protocol

Label

Biotin

Label protocol

Two ul of total RNA was reverse-transcribed and amplified using Invitrogen's One Tube RT PCR kit with Platinum Taq and SuperScript III in the presence of biotin-14-dCTP (Invitrogen) And CombiMatrix' Influenza A primer sets (pool 1(H1+H3) and pool 2(NA))

Hybridization protocol

CombiMatrix 12K ECD microarrays, design 5200, were prehybridized for 10 min at 45C and hybridized for 1 hr at 45C with sample in 2x hybridization buffer (CombiMatrix). Arrays were washed 1x with 3xSSPE with Tween 20, 2x with 2xPBS with Tween 20 and then blocked with 5x PBS/Casein (BioFX) for 5 min at RT. Arrays were labeled with Streptavidin-HRP (Sigma) for 30 min at RT and then washed 2x with 2x PBST, 2x with pH4 buffer (BioFX), and 1x with TMB substrate (BioFX). TMB was added to the array which was scanned with CombiMatrix' ElectraSense scanner and data were analyzed with CombiMatrix Influenza analysis software.

Scan protocol

Arrays were scanned with CombiMatrix' ElectraSense scanner

Description

Nasopharyngeal swabs were submitted to the laboratory in viral transport media for immediate culture. Influenza was identified by DFA testing and the H group subtyped by a haemagglutination assay with antisera provided by the CDC. Total nucleic acid was extracted from the viral transport media and the presence of influenza A RNA was confirmed and the H group typed by real time RT-PCR

Data processing

The raw probe signal intensity data for each subtype and each subgroup were averaged to make a subtype and subgroup call (CombiMatrix Influenza Analysis software)

Submission date

Jul 24, 2008

Contact name

Michael Joseph Lodes

E-mail(s)

mlodes@combimatrix.com

Phone

425-493-2272

Fax

425-493-2010

Organization name

CombiMatrix Corp

Department

Assay Development

Street address

6500 Harbour Heights Pkwy, Suite 303

City

Mukilteo

State/province

Washington

ZIP/Postal code

98275

Country

USA

Platform ID

GPL7090

Series (1)

GSE12226

The Detection and Subtyping of Seasonal Influenza A H1N1 Isolates Using a Microarray

Data table header descriptions
ID_REF
VALUE	raw probe signal intensity

Data table
ID_REF	VALUE
9bee3d49b45c164a890ed3ca25693fbd	3363.603159
9885bd8c4e0119d925674cb4649ec1ce	6767.798973
cab2ad2bb2ead3e95711f9e1f3ee0b9a	6332.14657
5117cfedf1a3e2bde37979ff8663bccb	7343.379001
ce7204169c97164bec383d6872eaace0	3580.678628
9576abedb2697ea34a8bf204e903bfde	7302.940682
bf92c6a80bc98ceef0f834c42ff7b228	3005.873535
35e800a8b5aace8fb0eae6ff1a2372d1	4074.591094
1552085fd94cca7deb0ec0d8334470dd	2597.906542
e4de0ceea4701f780f21030421a03e49	5852.37568
30a8fd697e4f5055deab9444e85de03f	3512.19985
399e22ca0a96ef2623d868663bfd8cbf	3072.172946
65125ea49caef35746887281bd3abb4e	8210.049736
62b5df84a32931587f6cd5b91db0caad	6609.193844
59f40d651251b8f7297d2caae09a30f9	1940.836588
2580102156785c377ad8b4024f8897f2	6576.746022
f2020b481b482baf2dc09fafc669f39a	5946.214839
3686696b4f780a5deff58ea331e98564	3173.034709
bb4e54529a6142d9f7f082011aac6098	2696.217679
d23c02489aa8ab7f09e5b4f39d9fb465	4525.740878

Total number of rows: 12020

Table truncated, full table size 526 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM307408.txt.gz	777.9 Kb	(ftp)(http)	TXT
Raw data provided as supplementary file
Processed data included within Sample table