Wiki » History » Version 28
Version 27 (Ilian Atanassov, 06/22/2015 12:29 PM) → Version 28/29 (Ilian Atanassov, 06/22/2015 12:33 PM)
h1. Worm - RBP samples
Desired amounts:
* 100 ug protein amount for digestion
* 8-10 ug peptide amount for LC-MS/MS analysis
"X" indicates that the substance was added, "NA" that no information is available.
The excess columns show how much sample material was not used for analysis and is in a -80deg freezer.
The "Protein concentration [ug/ul]" shows the protein concentration in the aliquot from the sample preparation (also RNA measurement would be done on them).
Concentrations were measured using 280nm abs assay of a nanodrop instrument.
h2. N2
|*Sample name*|*Worm culture*|*Protein concentration before RNAse treatment [ug/ul]*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|
|NA|850 T|NA|Zisong|07/2014|1|No|NA|NA|4.6|NA|140729Li_QX1_Chang_N2_1400ng_01.raw
140729Li_QX1_Chang_N2_1400ng_02.raw
140729Li_QX1_Chang_N2_1400ng_03.raw|30/07/2014|3|X|X|NA|2390
2363
2353||
|1a|500 T|2|Puneet|22/01/2015|1|No|2000|1700|32|20|NA|NA|NA|X|X||NA||
|1b|200 T|2|Puneet|22/01/2015|1|No|900|720|26|13|NA|NA|NA|X|X||NA||
|1c|100 T|1|Puneet|22/01/2015|1|No|300|180|16|6|NA|NA|NA|X|X||NA||
|1d|50 T|0.6|Puneet|22/01/2015|1|No|100|0|17|7|NA|NA|NA|X|X||NA||
|2|500 T|2|Puneet|22/01/2015|1|Yes|2000|1800|36|23|NA|NA|NA||X|X|NA||
|3|200 T|2|Puneet|22/01/2015|1|Yes|850|680|18|7|NA|NA|NA|X||NA|NA|vhl-1 mutant|
h2. P6662
|*Sample name*|*Worm culture*|*Protein concentration [ug/ul]*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples name*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|
|NA|650 T|NA|Zisong|07/2014|1|No|NA|NA|4.2|NA|140729Li_QX1_Chang_PS6662_1250ng_01.raw
140729Li_QX1_Chang_PS6662_1250ng_02.raw
140729Li_QX1_Chang_PS6662_1250ng_03.raw|31/07/2014|3|X|X|NA|2226
2199
2173||
*------------------------------------------------------------------------------------------- Analysis in June 2015 -----------------------------------------------------------------------------------------------------------------*
h2. N2
|*Sample name*|*Worm culture*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|
|NA|500 T|NA|Rene,
Puneet,
Francesca|06/2015|1|Yes|NA|NA|2.5|0|150609Li_Dieterich_N2minusCL|10/06/2015|1|X|||872||
|NA|500 T|NA|Rene,
Puneet,
Francesca|06/2015|1|No|NA|NA|4.5|0|150609Li_Dieterich_N2PlusCL.raw|10/06/2015|1|X|X||1186||
|NA|500 T|NA|Rene,
Puneet,
Francesca|06/2015|2|Yes|NA|NA|2.5|0|||1|X|||||
|NA|500 T|NA|Rene,
Puneet,
Francesca|06/2015|2|No|NA|NA|4.5|0|||1|X|X||||
h2. IMCD
|*Sample name*|*Cell culture*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|
|NA|NA|Rene,
Francesca|06/2015|1|Yes|NA|NA|60.4|0|150610Li_Dieterich_IMCD_Norm_minusCL_4ul.raw|11/06/2015|1|X|||728|Normoxia, Francesca|06/2015|1|Yes|NA|NA|60.4|0|150610Li_Dieterich_IMCD_Norm_minusCL_4ul.raw|11/06/2015|1|X|||872|Normoxia, 40% input|
|NA|NA|Rene,
Francesca|06/2015|1|No|NA|NA|55.3|0|150610Li_Dieterich_IMCD_Norm_PlusCL_4ul.raw|12/06/2015|1|X|X||759|Normoxia, Francesca|06/2015|1|No|NA|NA|55.3|0|150610Li_Dieterich_IMCD_Norm_PlusCL_4ul.raw|12/06/2015|1|X|X||1186|Normoxia, 40% input|
|NA|NA|Rene,
Francesca|06/2015|1|Yes|NA|NA|50|0|150610Li_Dieterich_IMCD_Hyp_minusCL_4ul.raw|12/06/2015|1|X|||728|Hypoxia, Francesca|06/2015|1|Yes|NA|NA|50|0|150610Li_Dieterich_IMCD_Hyp_minusCL_4ul.raw|12/06/2015|1|X||||Hypoxia, 40% input|
|NA|NA|Rene,
Francesca|06/2015|1|No|NA|NA|54|0|150610Li_Dieterich_IMCD_Hyp_PlusCL_4ul.raw|12/06/2015|1|X|X||786|Hypoxia, Francesca|06/2015|1|No|NA|NA|54|0|150610Li_Dieterich_IMCD_Hyp_PlusCL_4ul.raw|12/06/2015|1|X|X|||Hypoxia, 40% input|
Desired amounts:
* 100 ug protein amount for digestion
* 8-10 ug peptide amount for LC-MS/MS analysis
"X" indicates that the substance was added, "NA" that no information is available.
The excess columns show how much sample material was not used for analysis and is in a -80deg freezer.
The "Protein concentration [ug/ul]" shows the protein concentration in the aliquot from the sample preparation (also RNA measurement would be done on them).
Concentrations were measured using 280nm abs assay of a nanodrop instrument.
h2. N2
|*Sample name*|*Worm culture*|*Protein concentration before RNAse treatment [ug/ul]*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|
|NA|850 T|NA|Zisong|07/2014|1|No|NA|NA|4.6|NA|140729Li_QX1_Chang_N2_1400ng_01.raw
140729Li_QX1_Chang_N2_1400ng_02.raw
140729Li_QX1_Chang_N2_1400ng_03.raw|30/07/2014|3|X|X|NA|2390
2363
2353||
|1a|500 T|2|Puneet|22/01/2015|1|No|2000|1700|32|20|NA|NA|NA|X|X||NA||
|1b|200 T|2|Puneet|22/01/2015|1|No|900|720|26|13|NA|NA|NA|X|X||NA||
|1c|100 T|1|Puneet|22/01/2015|1|No|300|180|16|6|NA|NA|NA|X|X||NA||
|1d|50 T|0.6|Puneet|22/01/2015|1|No|100|0|17|7|NA|NA|NA|X|X||NA||
|2|500 T|2|Puneet|22/01/2015|1|Yes|2000|1800|36|23|NA|NA|NA||X|X|NA||
|3|200 T|2|Puneet|22/01/2015|1|Yes|850|680|18|7|NA|NA|NA|X||NA|NA|vhl-1 mutant|
h2. P6662
|*Sample name*|*Worm culture*|*Protein concentration [ug/ul]*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples name*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|
|NA|650 T|NA|Zisong|07/2014|1|No|NA|NA|4.2|NA|140729Li_QX1_Chang_PS6662_1250ng_01.raw
140729Li_QX1_Chang_PS6662_1250ng_02.raw
140729Li_QX1_Chang_PS6662_1250ng_03.raw|31/07/2014|3|X|X|NA|2226
2199
2173||
*------------------------------------------------------------------------------------------- Analysis in June 2015 -----------------------------------------------------------------------------------------------------------------*
h2. N2
|*Sample name*|*Worm culture*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|
|NA|500 T|NA|Rene,
Puneet,
Francesca|06/2015|1|Yes|NA|NA|2.5|0|150609Li_Dieterich_N2minusCL|10/06/2015|1|X|||872||
|NA|500 T|NA|Rene,
Puneet,
Francesca|06/2015|1|No|NA|NA|4.5|0|150609Li_Dieterich_N2PlusCL.raw|10/06/2015|1|X|X||1186||
|NA|500 T|NA|Rene,
Puneet,
Francesca|06/2015|2|Yes|NA|NA|2.5|0|||1|X|||||
|NA|500 T|NA|Rene,
Puneet,
Francesca|06/2015|2|No|NA|NA|4.5|0|||1|X|X||||
h2. IMCD
|*Sample name*|*Cell culture*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|
|NA|NA|Rene,
Francesca|06/2015|1|Yes|NA|NA|60.4|0|150610Li_Dieterich_IMCD_Norm_minusCL_4ul.raw|11/06/2015|1|X|||728|Normoxia, Francesca|06/2015|1|Yes|NA|NA|60.4|0|150610Li_Dieterich_IMCD_Norm_minusCL_4ul.raw|11/06/2015|1|X|||872|Normoxia, 40% input|
|NA|NA|Rene,
Francesca|06/2015|1|No|NA|NA|55.3|0|150610Li_Dieterich_IMCD_Norm_PlusCL_4ul.raw|12/06/2015|1|X|X||759|Normoxia, Francesca|06/2015|1|No|NA|NA|55.3|0|150610Li_Dieterich_IMCD_Norm_PlusCL_4ul.raw|12/06/2015|1|X|X||1186|Normoxia, 40% input|
|NA|NA|Rene,
Francesca|06/2015|1|Yes|NA|NA|50|0|150610Li_Dieterich_IMCD_Hyp_minusCL_4ul.raw|12/06/2015|1|X|||728|Hypoxia, Francesca|06/2015|1|Yes|NA|NA|50|0|150610Li_Dieterich_IMCD_Hyp_minusCL_4ul.raw|12/06/2015|1|X||||Hypoxia, 40% input|
|NA|NA|Rene,
Francesca|06/2015|1|No|NA|NA|54|0|150610Li_Dieterich_IMCD_Hyp_PlusCL_4ul.raw|12/06/2015|1|X|X||786|Hypoxia, Francesca|06/2015|1|No|NA|NA|54|0|150610Li_Dieterich_IMCD_Hyp_PlusCL_4ul.raw|12/06/2015|1|X|X|||Hypoxia, 40% input|