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Sample GSM1706650

Query DataSets for GSM1706650

Status

Public on Jun 10, 2015

Title

dcpA knockout rep1

Sample type

RNA

Source name

dcpA knockout rep1

Organism

Mycolicibacterium smegmatis MC2 155

Characteristics

genotype/variation: Strain impaired in c-di-GMP signalling

Extracted molecule

total RNA

Extraction protocol

Qiagen's RNeasy minikit (Cat7410 4)

Label

Cy3

Label protocol

Random hexamer method of labeling was done followed by T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis). Agilent’s Quick-Amp labeling Kit (p/n5190-0442) was used.

Hybridization protocol

Agilent’s In situ Hybridzation kit 5188-5242 was used for hybridization

Scan protocol

scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

Description

Gene expression after 48 hours for dcpA knockout strain

Data processing

Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Gene based analysis was performed)

Submission date

Jun 09, 2015

Last update date

Jun 10, 2015

Contact name

Dipankar Chatterji

E-mail(s)

[email protected]

Phone

+918022932836

Organization name

Indian Institute of Science

Department

Molecular Biphysics Unit

Lab

108

Street address

Malleshwaram

City

Bangalore

State/province

Karnataka

ZIP/Postal code

560012

Country

India

Platform ID

GPL20299

Series (1)

GSE69681

Gene expression analysis of rel knockout and dcpA knockout strains of Mycobacterium smegmatis MC2 155

Data table header descriptions
ID_REF
VALUE	Log base 2 normalized data

Data table
ID_REF	VALUE
GT_msm_specific_GE_000001	-1.767
GT_msm_specific_GE_000002	-0.597
GT_msm_specific_GE_000003	-1.223
GT_msm_specific_GE_000004	-0.214
GT_msm_specific_GE_000005	-1.278
GT_msm_specific_GE_000006	-0.864
GT_msm_specific_GE_000007	-0.947
GT_msm_specific_GE_000008	-1.448
GT_msm_specific_GE_000009	-0.514
GT_msm_specific_GE_000010	-1.339
GT_msm_specific_GE_000012	-1.188
GT_msm_specific_GE_000013	-0.495
GT_msm_specific_GE_000014	-1.514
GT_msm_specific_GE_000015	-0.777
GT_msm_specific_GE_000016	-2.617
GT_msm_specific_GE_000017	-0.665
GT_msm_specific_GE_000018	-1.292
GT_msm_specific_GE_000019	-0.448
GT_msm_specific_GE_000020	-0.240
GT_msm_specific_GE_000021	0.040

Total number of rows: 6898

Table truncated, full table size 220 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM1706650_delta_dcpA-1.txt.gz	3.0 Mb	(ftp)(http)	TXT
Processed data included within Sample table