GEO DataSets

(Submitter supplied) Analysis of Clostridium difficile (Cd) from the cecal contents of germ-free mice or Bacteroides thetaiotaomicron (Bt)-monocolonized mice on a standard, polysaccharide rich diet or polysaccharide deficient diet 5 days after infection. Results identify genes that are involved in the Cd response to diet, in vivo colonization and in interactions with Bt.

Organism:

Bacteroides fragilis NCTC 9343; Clostridioides difficile 630; Bacteroides thetaiotaomicron; Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL19121

20 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bacteroides fragilis NCTC 9343; Bacteroides fragilis 638R

Type:

Expression profiling by array

Platforms:

GPL15188 GPL15187

6 Samples

Download data: CALLS, PAIR

(Submitter supplied) Genome expression study of Bacteroides fragilis ATCC25285 strain containing the EcfO gene constitutively expressed from plasmid pFD340

Organism:

Bacteroides fragilis NCTC 9343

Type:

Expression profiling by array

Platform:

GPL15187

2 Samples

Download data: CALLS, PAIR

(Submitter supplied) The factors that govern the retention and abundance of specific microbial lineages within a developing intestinal microbiota remain poorly defined. Human milk oligosaccharides consumed by nursing infnats pass undigested to the distal gut where they may be consumed by microbes. We investigated the transcriptional response of Bacterides fragilis, a prominent gut resident, to the presence of HMOs.

Organism:

Bacteroides fragilis NCTC 9343

Type:

Expression profiling by array

Platform:

GPL14584

4 Samples

Download data: CEL

(Submitter supplied) Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp mutant strain and a Bacteroides fragilis NCTC 9343 delta-lfg mutant strain, each as compared to the wild-type strain. The mutations engineered into these strains interfere with B. fragilis protein glycosylation.

Organism:

Bacteroides fragilis NCTC 9343

Type:

Expression profiling by array

Platform:

GPL7163

9 Samples

Download data: CALLS, PAIR

(Submitter supplied) Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 double mutant compared to the wild-type strain. Keywords: expression analysis

Organism:

Bacteroides fragilis NCTC 9343

Type:

Expression profiling by array

Platform:

GPL6805

6 Samples

Download data: CALLS, FTR, PAIR, TIFF, TXT

(Submitter supplied) Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH triple mutant, compared to the wild-type strain. The mutations engineered into this strain render it acapsular. The mutants analyzed in this study are further described in Coyne, M. J., M. Chatzidaki-Livanis, L. C. Paoletti, and L. E. Comstock. 2008. Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis. more...

Organism:

Bacteroides fragilis NCTC 9343

Type:

Expression profiling by array

Platform:

GPL6805

6 Samples

Download data: CALLS, FTR, PAIR, TIFF

(Submitter supplied) The idea was to examine the role of OxyR in control of the oxidative stress response of B. fragilis when exposed to either atmospheric oxygen, 5% oxygen atmosphere, or hydrogen peroxide Keywords: stress response

Organism:

Bacteroides fragilis; Bacteroides fragilis NCTC 9343

Type:

Expression profiling by array

Platform:

GPL3596

27 Samples

Download data

(Submitter supplied) The GPL14584 contains reads for B. fragilis and this platform contains reads for C. difficile strain 630 in addition to B. fragilis. Protocol: see manufacturer's web site

Organism:

Bacteroides fragilis NCTC 9343; Clostridioides difficile 630

1 Series

20 Samples

Download data: TXT

(Submitter supplied) The GPL19121 contains reads for C. difficile strain 630 in addition to B. fragilis. Protocol: see manufacturer's web site

Organism:

Bacteroides fragilis NCTC 9343

1 Series

4 Samples

Download data: CDF, CSV

(Submitter supplied) 2006-07-27_TI272559_60mer Catalog design for Bacteroides fragilis NCTC 9343 (ATCC 25285) covering NC_003228, NC_006873.Probes selected for 4231/4231 sequences. Median number of probes/sequence is 18 with an average of 18.00. Each probe will be replicated 5 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content. more...

Organism:

Bacteroides fragilis NCTC 9343

2 Series

2 Samples

Download data: NDF, NGD

(Submitter supplied) Roche NimbleGen design name 2006-07-27_TI272559_60mer, design ID 4433. Catalog design for 4,231 genes from Bacteroides fragilis NCTC 9343 and associated plasmid pBF9343 with eighteen 60-mer probes per gene. Each probe is replicated 5 times and the probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content. The Platform data table reflects a condensed representation of the expression array's replicate features. The .ndf and .ngd files are linked below as supplementary files. Protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See http://www.nimblegen.com/

Organism:

Bacteroides fragilis NCTC 9343

1 Series

9 Samples

Download data: NDF, NGD

(Submitter supplied) NimbleGen design name 2005-08-12_B_fragilis_24mer, NimbleGen design ID 2451. A 1:2 expression design for 4,302 genes from Bacteroides fragilis NCTC 9343 and associated plasmid pBF9343 with fourteen 24-mer probe pairs (PM/MM) per gene. Each probe is replicated 3 times. The design includes random GC and other control probes. The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. more...

Organism:

Bacteroides fragilis NCTC 9343

2 Series

12 Samples

Download data: NDF, NGD

(Submitter supplied) Bacteroides fragilis NCTC9343 sequence using annotation supplied to us by EBI through the client. Each probe replicated 2x on chip. Selected 18 probe-pairs per target for 5165 target genes. This included probe pairs for putative "small" RNAs and ribosomal RNAs that will not be published. probes were 24 mer This means, 18 perfect match 24mers paired with 18 24mers containing two mismatches.

Organism:

Bacteroides fragilis NCTC 9343

1 Series

27 Samples

Download data: TXT