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Sample GSM954706

Query DataSets for GSM954706

Status

Public on Feb 06, 2013

Title

DSM16992

Sample type

genomic

Source name

DSM16992

Organism

Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043

Characteristics

strain: DSM16992

Growth protocol

Each strain was grown in MRS over night and the DNA was extracted.

Extracted molecule

genomic DNA

Extraction protocol

Total DNA was isolated using phenol/chloroform extraction method. Briefly, cells pellet were resuspended in 10 ml of TES, lysozyme and mutanolysin and incubated for 2h at 37°C. Pellets were washed and resuspended in TE, 10% SDS, Proteinase K and CTAB/NaCl solution and incubatated for 2h. Then, washing with phenol/chloroform was performed following the Sambrook and Russell protocol. Finally, DNA was precipitated using EtOH 96% and resuspended in water.

Label

Cy5

Label protocol

DNA was labeled with Cy5-ULS using the Kreatech ULS array CGH Labeling kit (Kreatech Diagnostics) according to the supplier’s instructions.

Hybridization protocol

Hybridization of labeled test DNA to these microarrays was performed according to CombiMatrix protocols (http://www.combimatrix.com/support_docs.htm).

Scan protocol

Fluorescence scanning was performed employing a MicroArray scanner (InnoScan 700).

Data processing

Signal intensities for each spot were determined using Microarray Imager 5.8 software (CombiMatrix). Signal background was calculated as the mean of negative controls plus two times the SD. A global quantile normalization was performed, and log2 ratios among the reference sample (Bifidobacteriaadolescentis ATCC15703) and the other samples analyzed were calculated. The distribution of the log2-transformed ratios for each hybridization reaction was calculated separately. Log2-ratio data of Sample over reference is linked to the Series record.

Submission date

Jul 02, 2012

Last update date

Feb 06, 2013

Contact name

Marco Ventura

E-mail(s)

[email protected]

Phone

+390521905666

Organization name

University of Parma

Department

Dept. Life Sciences

Lab

Probiogenomics Lab.

Street address

Viale delle Scienze 11/A

City

Parma

ZIP/Postal code

43124

Country

Italy

Platform ID

GPL15738

Series (2)

GSE39047	Genomic diversity of Bifidobacterium pseudocatenulatum group
GSE39050	Genomic diversity of Bifidobacterium adolescentis and pseudocatenulatum group

Data table header descriptions
ID_REF
VALUE	Normalized signal intensity.

Data table
ID_REF	VALUE
PSEUDOCATENULATUM_orf00050_348_35_S	484.8
PSEUDOCATENULATUM_orf00050_649_35_X3	1703.45
PSEUDOCATENULATUM_orf00067_561_35_S	1422.75
PSEUDOCATENULATUM_orf00067_3_40_S	3527.8
PSEUDOCATENULATUM_orf00081_243_35_S	330.25
PSEUDOCATENULATUM_orf00082_659_35_S	677.5
PSEUDOCATENULATUM_orf00082_345_35_S	228.45
PSEUDOCATENULATUM_orf00091_71_36_X2	247.35
PSEUDOCATENULATUM_orf00092_923_35_S	310.65
PSEUDOCATENULATUM_orf00092_582_40_S	611.35
PSEUDOCATENULATUM_orf00092_265_37_S	154.7
PSEUDOCATENULATUM_orf00102_1560_37_S	358.65
PSEUDOCATENULATUM_orf00102_1254_36_S	519.05
PSEUDOCATENULATUM_orf00102_811_35_S	361.95
PSEUDOCATENULATUM_orf00102_446_38_S	387.1
PSEUDOCATENULATUM_orf00102_143_35_S	431.95
PSEUDOCATENULATUM_orf00155_864_35_S	1032.35
PSEUDOCATENULATUM_orf00155_91_40_S	1513.65
PSEUDOCATENULATUM_orf00181_1192_40_X2	1688.25
PSEUDOCATENULATUM_orf00181_39_36_X2	1708.45

Total number of rows: 5266

Table truncated, full table size 221 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM954706_DSM16992_raw_data.txt.gz	285.1 Kb	(ftp)(http)	TXT
Processed data included within Sample table
Processed data are available on Series record