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Sample GSM375574 Query DataSets for GSM375574
Status Public on Jun 01, 2009
Title udder_healthy_24h_REP1_1
Sample type RNA
 
Source name mammary gland tissue, healthy, external control
Organism Bos taurus
Characteristics tissue: udder
infection: uninfected
time: 24h
Treatment protocol E. coli 1303 was isolated from clinical cases; Inoculum Dose: Bovine mastitis isolate E. coli 1303 belongs to the major E. coli phylogenetic group A (E. coli collection of reference strains, ECOR-A). According to a multiplex PCR-based screening for virulence-associated genes of pathogenic E. coli, this strain does not represent an extraintestinal or intestinal pathogenic E. coli isolate. Only the genes coding for type 1 fimbriae, F17 fimbriae, antigen 43, the ferric citrate siderophore system and the EAST1 toxin could be detected. Bacteria were kept cryo-conserved (Mikrobank-system CryobankTM, Mast Diagnostika, Reinfeld, Germany) for subsequent infections. Bacteria were plated on Columbia sheep blood agar and incubated (37°C) for 24h. A few colonies were transferred to a tube of brain-heart infusion broth (Oxoid, Wesel, Germany) and incubated for 6h (37°C); then a 100-μl sample was transferred to a tube of trypticase soy broth (9.9ml, Oxoid, Wesel, Germany). Serial dilutions were made after 18h to prepare the desired inoculum dose of 500CFU/2ml 0.9% sterile, pyrogen free saline. The inoculum dose was plated for control and ranged from 421-613CFU/2ml. Inoculum was administered intracisternally in one quarter through the teat canal. Cows were slaughtered after 24h. Samples from untreated quarters from healthy cows served as controls.
Growth protocol 10 healthy, primiparous, midlactating German Holstein Frisian cows; no history of clinical mastitis; quarter milk samples less than 50,000 somatic cells/ml and free of mastitis pathogens; oestrus synchronized with Cloprostenol (Prostaglandin-F2alpha-analogue, Selectavet,Weyarn), before trial cows were entirely milked out with 20 I.U. Oxytocin i.v. (Veyx-Pharma, Schwarzenborn).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from bovine mammary gland tissue with the Trizol method according to the manufacturers protocol
Label biotin
Label protocol total RNA was transcribed and labeled with Ambion Kit MessageAmp II Biotin Enhanced according to the manufacturers protocol
 
Hybridization protocol fragmented cRNA was hybridized to Affymetrix GeneChip Bovine Genome Arrays and washed and stained with Affymetrix Wash&Stain Kit on an Affymetrix Fluidics Station 450
Scan protocol Affymetrix GeneChip Scanner 3000
Description Udder tissue; healthy untreated animal
Data processing RMA Normalization
 
Submission date Feb 26, 2009
Last update date Jun 30, 2009
Contact name Stefan Krebs
E-mail(s) krebs-st@lmb.uni-muenchen.de
Phone 0049-89-2180 76715
Organization name Ludwig-Maximilian University
Department Gene Center
Lab Lafuga Genomics
Street address Feodor-Lynen-Str. 25
City Munich
ZIP/Postal code 81377
Country Germany
 
Platform ID GPL2112
Series (2)
GSE15020 Transcriptome analysis of bovine mammary gland tissue treated with E. coli for 24 hours
GSE15025 E. coli infection induces distinct local and systemic transcriptome responses in the mammary gland

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 9.414697645
AFFX-BioB-5_at 9.137896199
AFFX-BioB-M_at 9.419721036
AFFX-BioC-3_at 10.88524766
AFFX-BioC-5_at 10.23312853
AFFX-BioDn-3_at 12.57799527
AFFX-BioDn-5_at 11.27049188
AFFX-Bt_Cyph_3_at 11.48798821
AFFX-Bt_Cyph_5_at 9.95207052
AFFX-Bt_Cyph_M_at 10.81288568
AFFX-Bt_eIF-4E_3_at 10.08026147
AFFX-Bt_eIF-4E_5_at 6.106752494
AFFX-Bt_eIF-4E_M_at 7.616343294
AFFX-Bt_GST_3_at 8.936545814
AFFX-Bt_GST_5_at 8.754555664
AFFX-Bt_GST_M_at 8.374210723
AFFX-Bt_Lacphor_5_s_at 14.44470344
AFFX-Bt_Lacphor_M_s_at 14.53920978
AFFX-Bt-A00196-1_s_at 4.970437842
AFFX-Bt-AB076373-1_at 3.211080956

Total number of rows: 24128

Table truncated, full table size 676 Kbytes.




Supplementary file Size Download File type/resource
GSM375574.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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