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Ilian Atanassov, 06/22/2015 12:33 PM
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.
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 |
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 -----------------------------------------------------------------------------------------------------------------
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 |
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, 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, 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, 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, 40% input |