|
| Status |
Public on May 31, 2015 |
| Title |
LSP_ppGpp0_MINUS_R1_ChIP |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
SL1344 ΔrelAΔspoT (ppGpp0) strain grown to LSP (OD600 = 4.2) and ChIP-chip performed minus antibody.
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: SL1344
|
| Treatment protocol |
Minus antibody to beta subunit of RNA polymerase
|
| Growth protocol |
25 ml LB cultures in 250 ml flasks 37°C shaking @ 250 rpm
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
All cultures grown aerobically at 37°C with shaking at 250 rpm in LB to specified OD's. Crosslinking and immunoppt performed as described in Lucchini et al (2007) PLoS Pathog 2(8):e81.DOI:10.1371
|
| Label |
Cy5 dCTP
|
| Label protocol |
Labelling according to Erikkson et al., 2006 Inf & Immun, 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| |
|
| Channel 2 |
| Source name |
Genomic DNA from S. Typhimurium SL1344
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: SL1344
|
| Treatment protocol |
gDNA labelled with Cy5 dCTP
|
| Growth protocol |
25 ml LB cultures in 250 ml flasks 37°C shaking @ 250 rpm
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
All cultures grown aerobically at 37°C with shaking at 250 rpm in LB to specified OD's. Crosslinking and immunoppt performed as described in Lucchini et al (2007) PLoS Pathog 2(8):e81.DOI:10.1371
|
| Label |
Cy3 dCTP
|
| Label protocol |
Labelling according to Erikkson et al., 2006 Inf & Immun, 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| |
|
| |
| Hybridization protocol |
Hybridisation according to Erikkson et al., 2006 Inf & Immun, 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| Scan protocol |
GenePix 4000A at 5µm resolution
|
| Description |
Biol. Rep. 1 of 3
|
| Data processing |
Intensity ratio's of channel 1 (immunoppt labelled DNA fragments) divided by channel 2 (reference gDNA) signals calculated using GenePix 4000A
|
| |
|
| Submission date |
Nov 28, 2014 |
| Last update date |
May 31, 2015 |
| Contact name |
Arthur Thompson |
| E-mail(s) |
arthur.thompson@ifr.ac.uk
|
| Phone |
01603 255181
|
| Organization name |
Institute of Food Research
|
| Street address |
Colney Lane
|
| City |
Norwich |
| ZIP/Postal code |
NR4 7UA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19472 |
| Series (2) |
| GSE63711 |
RNA polymerase binding sites revealed by ChIP-chip in S. Typhimurium wild-type, ΔrelAΔspoT (ppGpp0), and ΔdksA strains at early stationary phase (ESP) and late stationary phase (LSP) |
| GSE63715 |
Transcriptional profiles of Salmonella Typhimurium 4/74 parent and relA spoT, rpoS and dksA strains during stationary phase, and RNA polymerase distribution as determined by chromatin immunoprecipitation in parent, relA spoT and dksA strains |
|
