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| |
brain
(0) |
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blood
(0) |
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connective
(1) |
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reproductive
(0) |
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muscular
(0) |
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digestive
(24) |
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liver
(0) |
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lung
(0) |
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urinary
(0) |
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endo/exo-crine
(0) |
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embryo
(0) |
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adult aerial structure
(0) |
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young aerial structure
(0) |
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root
(0) |
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meristem/growing tissue
(0) |
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flower/sexual organ
(0) |
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seed/fruit/grain
(0) |
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pooled
(0) |
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unclassified
(32) |
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all
(57) |
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| 1 |
GSM242040 |
HT3 delta PsbP |
218 |
Washington University in Saint Louis |
2007-11-09 |
[Other] Global proteomic characterization of photosystem II complexes from Synechocystis sp. PCC 6803 (GPL6115) |
protein |
Synechocystis sp. PCC 6803
 |
unclassified |
source_name:HT3 delta PsbP mutant HT3 wild type title:HT3 delta PsbP description:PSII Preparation: PSII was isolated from HT3, deltaPsbV HT3, deltaPsbQ HT3, and deltaPsbP HT3 strains as described previously . HT3 indicates the 6-His tagged CP47 used to affinity purify the complex . The final eluate from a Ni-NTA Agarose (Qiagen, Inc., Valencia, CA) column was suspended in 50 mM MES-NaOH pH 6.0, 10 mM CaCl2, 25% glycerol with 0.04% dodecyl maltoside. Chlorophyll concentrations were determined by methanol extraction and absorbance at 652 and 665 nm in a DW2000 spectrophotometer (SLM-Aminco, Urbana, IL) . AMT Peptide Identification: PSII preparations of approximately 1 mg protein were sent to Pacific Northwest National Laboratory (PNNL) for protein identification. The PSII samples were denatured by addition of equal volumes of 7 M urea, 2 M thiourea, and 1% CHAPS in 50 mM ammonium bicarbonate, pH 7.8 and then reduced with DTT to a final concentration of 5mM. CaCl2 was added to a final concentration of 1 mM. Samples were digested by the addition of sequencing grade modified trypsin (Promega, Madison, WI), using a ratio of 1:100 (wt/wt) protease to protein sample and incubated 4 hours at 37oC. Digests were desalted using Supelco Superclean SCX tubes (St. Louis, MO) with a Supelco vacuum manifold. The pH of each digestion was adjusted to 3.5 by addition of dilute formic acid. The SCX resin was conditioned with acetonitrile followed by 0.5 column volume (cv) 1M sodium formate. The column was washed with 2 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5 and the resin was re-equilibrated with 1 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptide mixtures were loaded onto the resin and washed with 3 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptides were eluted with 1 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5, followed by 0.5 cv of 100% acetonitrile. Eluted peptides were concentrated via Speedvac (ThermoSavant, San Jose, CA) to protein concentrations of 1.0 mg/mL, as determined by BCA assay (Pierce, Rockford, IL). Peptides were putatively identified using a capillary LC system, of a pair of model 100mL 100DM syringe pumps (Teledyne-Isco, Lincoln, NE), a series D controller (Teledyne-Isco, Lincoln, NE) and an in-house manufactured mixer, capillary column selector, and sample loop. Separations were achieved using a 5000 psi reversed-phase in-house packed capillary (150 um i.d., 360 um o.d., 60 cm long; Polymicro Technologies, Phoenix, AZ) by using an exponential gradient of 2 mobile-phase solvents consisting of 0.2% acetic acid and 0.05% trifluroacetic acid (TFA) in water and 0.1% TFA in 90% acetonitrile. Flow through the capillary HPLC column was ?1.8 uL/min when equilibrated to 100% mobile-phase 0.2% acetic acid and 0.05% TFA. For each HPLC sample, 10 ug was infused into a LCQ conventional ion trap MS (ThermoFinnigan, San Jose, CA) operating in a data dependent MS/MS mode over a 400 to 2000 m/Z range. For each cycle, the 3 most abundant ions from MC analysis were selected for MS/MS analysis by using a collision energy setting of 45%. Dynamic exclusion was used to discriminate against previously analyzed ions. The collision induced dissociation spectra from the conventional ion trap mass spectrophotometer were analyzed using SEQUEST and the genome sequence of Synechocystis 6803. PMT identifications were made based on a SEQUEST cross correlation (Xcorr) score ? 2.0, regardless of charge or mass. Using the same LC conditions, 5 ug of each sample analyzed in the ion trap was then analyzed in duplicate or triplicate by FTICR-MS. The FTICR mass spectrometers use ESI interfaced with an electrodynamic ion funnel assembly coupled to a radio frequency quadropole for collisional ion focusing and highly efficient ion accumulation and transport to a cylindrical FTICR for cell analysis . The resultant FTICR data was processed using the PRISM Data Analysis system, a series of software tools developed in-house. First the MS data was de-isotoped, giving the monoisotopic mass, charge, and intensity of the major peaks in each mass spectrum. Following this, the data was examined in a two-dimensional fashion to find groups of mass spectral peaks that were observed in sequential spectra. Each group, known as a unique mass class (UMC), has a median mass, central normalized elution time (NET), and abundance estimate, computed by summing the intensities of the MS peaks that compromise the UMC. The identity of each UMC was determined by comparing the mass and NET of each UMC with the mass and NET’s of the 4423 PMT’s in the Synechocystis 6803 AMT database (generated using the peptides observed from 23 LC/MS/MS). Search tolerances were ± 6 ppm for the mass and ±5% of the total run time for the elution time. |
| 2 |
GSM242041 |
HT3 delta PsbQ |
218 |
Washington University in Saint Louis |
2007-11-09 |
[Other] Global proteomic characterization of photosystem II complexes from Synechocystis sp. PCC 6803 (GPL6115) |
protein |
Synechocystis sp. PCC 6803
|
unclassified |
source_name:HT3 delta PsbQ HT3 wild type title:HT3 delta PsbQ description:PSII Preparation: PSII was isolated from HT3, deltaPsbV HT3, deltaPsbQ HT3, and deltaPsbP HT3 strains as described previously . HT3 indicates the 6-His tagged CP47 used to affinity purify the complex . The final eluate from a Ni-NTA Agarose (Qiagen, Inc., Valencia, CA) column was suspended in 50 mM MES-NaOH pH 6.0, 10 mM CaCl2, 25% glycerol with 0.04% dodecyl maltoside. Chlorophyll concentrations were determined by methanol extraction and absorbance at 652 and 665 nm in a DW2000 spectrophotometer (SLM-Aminco, Urbana, IL) . AMT Peptide Identification: PSII preparations of approximately 1 mg protein were sent to Pacific Northwest National Laboratory (PNNL) for protein identification. The PSII samples were denatured by addition of equal volumes of 7 M urea, 2 M thiourea, and 1% CHAPS in 50 mM ammonium bicarbonate, pH 7.8 and then reduced with DTT to a final concentration of 5mM. CaCl2 was added to a final concentration of 1 mM. Samples were digested by the addition of sequencing grade modified trypsin (Promega, Madison, WI), using a ratio of 1:100 (wt/wt) protease to protein sample and incubated 4 hours at 37oC. Digests were desalted using Supelco Superclean SCX tubes (St. Louis, MO) with a Supelco vacuum manifold. The pH of each digestion was adjusted to 3.5 by addition of dilute formic acid. The SCX resin was conditioned with acetonitrile followed by 0.5 column volume (cv) 1M sodium formate. The column was washed with 2 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5 and the resin was re-equilibrated with 1 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptide mixtures were loaded onto the resin and washed with 3 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptides were eluted with 1 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5, followed by 0.5 cv of 100% acetonitrile. Eluted peptides were concentrated via Speedvac (ThermoSavant, San Jose, CA) to protein concentrations of 1.0 mg/mL, as determined by BCA assay (Pierce, Rockford, IL). Peptides were putatively identified using a capillary LC system, of a pair of model 100mL 100DM syringe pumps (Teledyne-Isco, Lincoln, NE), a series D controller (Teledyne-Isco, Lincoln, NE) and an in-house manufactured mixer, capillary column selector, and sample loop. Separations were achieved using a 5000 psi reversed-phase in-house packed capillary (150 um i.d., 360 um o.d., 60 cm long; Polymicro Technologies, Phoenix, AZ) by using an exponential gradient of 2 mobile-phase solvents consisting of 0.2% acetic acid and 0.05% trifluroacetic acid (TFA) in water and 0.1% TFA in 90% acetonitrile. Flow through the capillary HPLC column was ?1.8 uL/min when equilibrated to 100% mobile-phase 0.2% acetic acid and 0.05% TFA. For each HPLC sample, 10 ug was infused into a LCQ conventional ion trap MS (ThermoFinnigan, San Jose, CA) operating in a data dependent MS/MS mode over a 400 to 2000 m/Z range. For each cycle, the 3 most abundant ions from MC analysis were selected for MS/MS analysis by using a collision energy setting of 45%. Dynamic exclusion was used to discriminate against previously analyzed ions. The collision induced dissociation spectra from the conventional ion trap mass spectrophotometer were analyzed using SEQUEST and the genome sequence of Synechocystis 6803. PMT identifications were made based on a SEQUEST cross correlation (Xcorr) score ? 2.0, regardless of charge or mass. Using the same LC conditions, 5 ug of each sample analyzed in the ion trap was then analyzed in duplicate or triplicate by FTICR-MS. The FTICR mass spectrometers use ESI interfaced with an electrodynamic ion funnel assembly coupled to a radio frequency quadropole for collisional ion focusing and highly efficient ion accumulation and transport to a cylindrical FTICR for cell analysis . The resultant FTICR data was processed using the PRISM Data Analysis system, a series of software tools developed in-house. First the MS data was de-isotoped, giving the monoisotopic mass, charge, and intensity of the major peaks in each mass spectrum. Following this, the data was examined in a two-dimensional fashion to find groups of mass spectral peaks that were observed in sequential spectra. Each group, known as a unique mass class (UMC), has a median mass, central normalized elution time (NET), and abundance estimate, computed by summing the intensities of the MS peaks that compromise the UMC. The identity of each UMC was determined by comparing the mass and NET of each UMC with the mass and NET’s of the 4423 PMT’s in the Synechocystis 6803 AMT database (generated using the peptides observed from 23 LC/MS/MS). Search tolerances were ± 6 ppm for the mass and ±5% of the total run time for the elution time. |
| 3 |
GSM242042 |
HT3 delta PsbV |
218 |
Washington University in Saint Louis |
2007-11-09 |
[Other] Global proteomic characterization of photosystem II complexes from Synechocystis sp. PCC 6803 (GPL6115) |
protein |
Synechocystis sp. PCC 6803
|
unclassified |
source_name:HT3 delta PsbV HT3 wild type title:HT3 delta PsbV description:PSII Preparation: PSII was isolated from HT3, deltaPsbV HT3, deltaPsbQ HT3, and deltaPsbP HT3 strains as described previously . HT3 indicates the 6-His tagged CP47 used to affinity purify the complex . The final eluate from a Ni-NTA Agarose (Qiagen, Inc., Valencia, CA) column was suspended in 50 mM MES-NaOH pH 6.0, 10 mM CaCl2, 25% glycerol with 0.04% dodecyl maltoside. Chlorophyll concentrations were determined by methanol extraction and absorbance at 652 and 665 nm in a DW2000 spectrophotometer (SLM-Aminco, Urbana, IL) . AMT Peptide Identification: PSII preparations of approximately 1 mg protein were sent to Pacific Northwest National Laboratory (PNNL) for protein identification. The PSII samples were denatured by addition of equal volumes of 7 M urea, 2 M thiourea, and 1% CHAPS in 50 mM ammonium bicarbonate, pH 7.8 and then reduced with DTT to a final concentration of 5mM. CaCl2 was added to a final concentration of 1 mM. Samples were digested by the addition of sequencing grade modified trypsin (Promega, Madison, WI), using a ratio of 1:100 (wt/wt) protease to protein sample and incubated 4 hours at 37oC. Digests were desalted using Supelco Superclean SCX tubes (St. Louis, MO) with a Supelco vacuum manifold. The pH of each digestion was adjusted to 3.5 by addition of dilute formic acid. The SCX resin was conditioned with acetonitrile followed by 0.5 column volume (cv) 1M sodium formate. The column was washed with 2 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5 and the resin was re-equilibrated with 1 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptide mixtures were loaded onto the resin and washed with 3 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptides were eluted with 1 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5, followed by 0.5 cv of 100% acetonitrile. Eluted peptides were concentrated via Speedvac (ThermoSavant, San Jose, CA) to protein concentrations of 1.0 mg/mL, as determined by BCA assay (Pierce, Rockford, IL). Peptides were putatively identified using a capillary LC system, of a pair of model 100mL 100DM syringe pumps (Teledyne-Isco, Lincoln, NE), a series D controller (Teledyne-Isco, Lincoln, NE) and an in-house manufactured mixer, capillary column selector, and sample loop. Separations were achieved using a 5000 psi reversed-phase in-house packed capillary (150 um i.d., 360 um o.d., 60 cm long; Polymicro Technologies, Phoenix, AZ) by using an exponential gradient of 2 mobile-phase solvents consisting of 0.2% acetic acid and 0.05% trifluroacetic acid (TFA) in water and 0.1% TFA in 90% acetonitrile. Flow through the capillary HPLC column was ?1.8 uL/min when equilibrated to 100% mobile-phase 0.2% acetic acid and 0.05% TFA. For each HPLC sample, 10 ug was infused into a LCQ conventional ion trap MS (ThermoFinnigan, San Jose, CA) operating in a data dependent MS/MS mode over a 400 to 2000 m/Z range. For each cycle, the 3 most abundant ions from MC analysis were selected for MS/MS analysis by using a collision energy setting of 45%. Dynamic exclusion was used to discriminate against previously analyzed ions. The collision induced dissociation spectra from the conventional ion trap mass spectrophotometer were analyzed using SEQUEST and the genome sequence of Synechocystis 6803. PMT identifications were made based on a SEQUEST cross correlation (Xcorr) score ? 2.0, regardless of charge or mass. Using the same LC conditions, 5 ug of each sample analyzed in the ion trap was then analyzed in duplicate or triplicate by FTICR-MS. The FTICR mass spectrometers use ESI interfaced with an electrodynamic ion funnel assembly coupled to a radio frequency quadropole for collisional ion focusing and highly efficient ion accumulation and transport to a cylindrical FTICR for cell analysis . The resultant FTICR data was processed using the PRISM Data Analysis system, a series of software tools developed in-house. First the MS data was de-isotoped, giving the monoisotopic mass, charge, and intensity of the major peaks in each mass spectrum. Following this, the data was examined in a two-dimensional fashion to find groups of mass spectral peaks that were observed in sequential spectra. Each group, known as a unique mass class (UMC), has a median mass, central normalized elution time (NET), and abundance estimate, computed by summing the intensities of the MS peaks that compromise the UMC. The identity of each UMC was determined by comparing the mass and NET of each UMC with the mass and NET’s of the 4423 PMT’s in the Synechocystis 6803 AMT database (generated using the peptides observed from 23 LC/MS/MS). Search tolerances were ± 6 ppm for the mass and ±5% of the total run time for the elution time. |
| 4 |
GSM226339 |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 74, rep1 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Typhimurium
 |
intestine |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 74, rep1 |
| 5 |
GSM226340 |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 74, rep2 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Typhimurium
|
intestine |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 74, rep2 |
| 6 |
GSM226341 |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 12023, rep1 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Typhimurium
|
intestine |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 12023, rep1 |
| 7 |
GSM226342 |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 12023, rep2 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Typhimurium
|
intestine |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 12023, rep2 |
| 8 |
GSM226343 |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 204, rep1 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Typhimurium
|
intestine |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 204, rep1 |
| 9 |
GSM226344 |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 204, rep2 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Typhimurium
|
intestine |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 204, rep2 |
| 10 |
GSM226345 |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 227, rep1 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Typhimurium
|
intestine |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 227, rep1 |
| 11 |
GSM226346 |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 227, rep2 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Typhimurium
|
intestine |
Salmonella enterica subsp. enterica serovar Typhimurium, strain 227, rep2 |
| 12 |
GSM226359 |
Salmonella enterica subsp. enterica serovar Pullorum, strain 10704, rep1 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Pullorum
 |
intestine |
Salmonella enterica subsp. enterica serovar Pullorum, strain 10704, rep1 |
| 13 |
GSM226360 |
Salmonella enterica subsp. enterica serovar Pullorum, strain 10704, rep2 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Pullorum
|
intestine |
Salmonella enterica subsp. enterica serovar Pullorum, strain 10704, rep2 |
| 14 |
GSM226361 |
Salmonella enterica subsp. enterica serovar Pullorum, strain B52, rep1 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Pullorum
|
intestine |
Salmonella enterica subsp. enterica serovar Pullorum, strain B52, rep1 |
| 15 |
GSM226362 |
Salmonella enterica subsp. enterica serovar Pullorum, strain B52, rep2 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Pullorum
|
intestine |
Salmonella enterica subsp. enterica serovar Pullorum, strain B52, rep2 |
| 16 |
GSM226347 |
Salmonella enterica subsp. enterica serovar Enteritidis, strain 12694, rep1 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Enteritidis
 |
intestine |
Salmonella enterica subsp. enterica serovar Enteritidis, strain 12694, rep1 |
| 17 |
GSM226348 |
Salmonella enterica subsp. enterica serovar Enteritidis, strain 12694, rep2 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Enteritidis
|
intestine |
Salmonella enterica subsp. enterica serovar Enteritidis, strain 12694, rep2 |
| 18 |
GSM226349 |
Salmonella enterica subsp. enterica serovar Enteritidis, strain 97, rep1 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Enteritidis
|
intestine |
Salmonella enterica subsp. enterica serovar Enteritidis, strain 97, rep1 |
| 19 |
GSM226350 |
Salmonella enterica subsp. enterica serovar Enteritidis, strain 97, rep2 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Enteritidis
|
intestine |
Salmonella enterica subsp. enterica serovar Enteritidis, strain 97, rep2 |
| 20 |
GSM226351 |
Salmonella enterica subsp. enterica serovar Dublin, strain 12709, rep1 |
20 |
Health Protection Agency |
2007-08-31 |
[Other] Identification of protein variations in closely related Salmonella serovars (GPL5794) |
protein |
Salmonella enterica subsp. enterica serovar Dublin
 |
intestine |
Salmonella enterica subsp. enterica serovar Dublin, strain 12709, rep1 |
|
|
|