Noi/NOTES/2012-5-25: Difference between revisions
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'''Program'''<br> | '''Program'''<br> | ||
98C 30s -> (98C 10s -> 58C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x15 -> 72C 3min | 98C 30s -> (98C 10s -> 58C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x15 -> 72C 3min | ||
[[File:2012_05_25_testqPCR_SR.png| 500px]] | |||
* Form the qPCR of tested samples, I could observe amplification in every samples except NTC, so I can continue amplify all samples and barcode with index primers. | * Form the qPCR of tested samples, I could observe amplification in every samples except NTC, so I can continue amplify all samples and barcode with index primers. | ||
* I have to aliquot AmpR3.3Indx primer due to the evaporation of the old plate storing at 4C. In the future I might store at -20C | * I have to aliquot AmpR3.3Indx primer due to the evaporation of the old plate storing at 4C. In the future I might store at -20C | ||
=== Plate layout and barcoded primer === | === Plate layout and barcoded primer === | ||
{| {{table}} border = 1 | {| {{table}} border = 1 | ||
| align="center" style="background:#f0f0f0;"| | | align="center" style="background:#f0f0f0;"|A1 | ||
| align="center" style="background:#f0f0f0;"| | | align="center" style="background:#f0f0f0;"|A2 | ||
| align="center" style="background:#f0f0f0;"| | | align="center" style="background:#f0f0f0;"|A3 | ||
| align="center" style="background:#f0f0f0;"| | | align="center" style="background:#f0f0f0;"|A4 | ||
| align="center" style="background:#f0f0f0;"| | | align="center" style="background:#f0f0f0;"|A5 | ||
| align="center" style="background:#f0f0f0;"| | | align="center" style="background:#f0f0f0;"|A6 | ||
| align="center" style="background:#f0f0f0;"| | | align="center" style="background:#f0f0f0;"|A7 | ||
| align="center" style="background:#f0f0f0;"| | | align="center" style="background:#f0f0f0;"|A8 | ||
|- | |- | ||
| AmpR6.3.Ind1||AmpR6.3.Ind9||AmpR6.3.Ind17||AmpR6.3.Ind25||AmpR6.3.Ind33||AmpR6.3.Ind41||AmpR6.3.Ind49||AmpR6.3.Ind57 | | AmpR6.3.Ind1||AmpR6.3.Ind9||AmpR6.3.Ind17||AmpR6.3.Ind25||AmpR6.3.Ind33||AmpR6.3.Ind41||AmpR6.3.Ind49||AmpR6.3.Ind57 | ||
|- | |- | ||
| B1||B2||B3||B4||B5||B6||B7||B8 | | B1||B2||B3||B4||B5||B6||B7||B8 | ||
|- | |- | ||
| AmpR6.3.Ind2||AmpR6.3.Ind10||AmpR6.3.Ind18||AmpR6.3.Ind26||AmpR6.3.Ind34||AmpR6.3.Ind42||AmpR6.3.Ind50||AmpR6.3.Ind58 | | AmpR6.3.Ind2||AmpR6.3.Ind10||AmpR6.3.Ind18||AmpR6.3.Ind26||AmpR6.3.Ind34||AmpR6.3.Ind42||AmpR6.3.Ind50||AmpR6.3.Ind58 | ||
|- | |- | ||
| C1||C2||C3||C4||C5||C6||C7||C8 | | C1||C2||C3||C4||C5||C6||C7||C8 | ||
|- | |- | ||
| AmpR6.3.Ind3||AmpR6.3.Ind11||AmpR6.3.Ind19||AmpR6.3.Ind27||AmpR6.3.Ind35||AmpR6.3.Ind43||AmpR6.3.Ind51||AmpR6.3.Ind59 | | AmpR6.3.Ind3||AmpR6.3.Ind11||AmpR6.3.Ind19||AmpR6.3.Ind27||AmpR6.3.Ind35||AmpR6.3.Ind43||AmpR6.3.Ind51||AmpR6.3.Ind59 | ||
|- | |- | ||
| D1||D2||D3||D4||D5||D6||D7||D8 | | D1||D2||D3||D4||D5||D6||D7||D8 | ||
|- | |- | ||
| AmpR6.3.Ind4||AmpR6.3.Ind12||AmpR6.3.Ind20||AmpR6.3.Ind28||AmpR6.3.Ind36||AmpR6.3.Ind44||AmpR6.3.Ind52||AmpR6.3.Ind60 | | AmpR6.3.Ind4||AmpR6.3.Ind12||AmpR6.3.Ind20||AmpR6.3.Ind28||AmpR6.3.Ind36||AmpR6.3.Ind44||AmpR6.3.Ind52||AmpR6.3.Ind60 | ||
|- | |- | ||
| E1||E2||E3||E4||E5||E6||E7||E8 | | E1||E2||E3||E4||E5||E6||E7||E8 | ||
|- | |- | ||
| AmpR6.3.Ind5||AmpR6.3.Ind13||AmpR6.3.Ind21||AmpR6.3.Ind29||AmpR6.3.Ind37||AmpR6.3.Ind45||AmpR6.3.Ind53||AmpR6.3.Ind61 | | AmpR6.3.Ind5||AmpR6.3.Ind13||AmpR6.3.Ind21||AmpR6.3.Ind29||AmpR6.3.Ind37||AmpR6.3.Ind45||AmpR6.3.Ind53||AmpR6.3.Ind61 | ||
|- | |- | ||
| F1||F2||F3||F4||F5||F6||F7||F8 | | F1||F2||F3||F4||F5||F6||F7||F8 | ||
|- | |- | ||
| AmpR6.3.Ind6||AmpR6.3.Ind14||AmpR6.3.Ind22||AmpR6.3.Ind30||AmpR6.3.Ind38||AmpR6.3.Ind46||AmpR6.3.Ind54||AmpR6.3.Ind62 | | AmpR6.3.Ind6||AmpR6.3.Ind14||AmpR6.3.Ind22||AmpR6.3.Ind30||AmpR6.3.Ind38||AmpR6.3.Ind46||AmpR6.3.Ind54||AmpR6.3.Ind62 | ||
|- | |- | ||
| G1||G2||G3||G4||G5||G6||G7|| | | G1||G2||G3||G4||G5||G6||G7|| | ||
|- | |- | ||
| AmpR6.3.Ind7||AmpR6.3.Ind15||AmpR6.3.Ind23||AmpR6.3.Ind31||AmpR6.3.Ind39||AmpR6.3.Ind47||AmpR6.3.Ind55|| | | AmpR6.3.Ind7||AmpR6.3.Ind15||AmpR6.3.Ind23||AmpR6.3.Ind31||AmpR6.3.Ind39||AmpR6.3.Ind47||AmpR6.3.Ind55|| | ||
|- | |- | ||
| H1||H2||H3||H4||H5||H6||H7|| | | H1||H2||H3||H4||H5||H6||H7|| | ||
|- | |- | ||
| AmpR6.3.Ind8||AmpR6.3.Ind16||AmpR6.3.Ind24||AmpR6.3.Ind32||AmpR6.3.Ind40||AmpR6.3.Ind48||AmpR6.3.Ind56|| | | AmpR6.3.Ind8||AmpR6.3.Ind16||AmpR6.3.Ind24||AmpR6.3.Ind32||AmpR6.3.Ind40||AmpR6.3.Ind48||AmpR6.3.Ind56|| | ||
|} | |} | ||
* Note: There are total 70 reactions (A1-H9, no samples in well ID G8 and H8 and A10-H12) | * Note: There are total 70 reactions (A1-H9, no samples in well ID G8 and H8 and A10-H12) | ||
Line 89: | Line 86: | ||
'''Program'''<br> | '''Program'''<br> | ||
98C 30s -> (98C 10s -> 58C 30s -> 72C 30s)x8 -> (98C 10s -> 72C 30s)x14 -> 72C 3min | 98C 30s -> (98C 10s -> 58C 30s -> 72C 30s)x8 -> (98C 10s -> 72C 30s)x14 -> 72C 3min | ||
* I performed qPCR | * I performed qPCR in duplicate with the same condition and stopped at the same cycle | ||
[[File:2012_05_25_qPCR_SR_plate1.png| 500px]] [[File:2012_05_25_qPCR_SR_plate2.png| 500px]] | [[File:2012_05_25_qPCR_SR_plate1.png| 500px]] [[File:2012_05_25_qPCR_SR_plate2.png| 500px]] | ||
* Since A9-H9 reactions shoot up earlier than other samples, I took out 60ul at cycles 20 | * Since A9-H9 reactions shoot up earlier than other samples, I took out 60ul at cycles 20 | ||
Line 248: | Line 245: | ||
* Resuspended with H2O, total volume 60ul | * Resuspended with H2O, total volume 60ul | ||
* Quantified concentration by Qubit dsDNA assay by Alan (based on size 375bp): 83.18nM or 14.4ng/ul | * Quantified concentration by Qubit dsDNA assay by Alan (based on size 375bp): 83.18nM or 14.4ng/ul | ||
[[File:ZhangLab_2 2012-05-30 17hr 20min_PQ_NP_BSPP_SR_Ind1-60_May21_2012.jpg| | * Concentration by PAGE quantification is 33.5ng/ul | ||
* '''Library IDs: NP-BSPP-SR_Ind1-60_May21,2012''', sequenced by | [[File:ZhangLab_2 2012-05-30 17hr 20min_PQ_NP_BSPP_SR_Ind1-60_May21_2012.jpg| 180px]] | ||
* '''Library IDs: NP-BSPP-SR_Ind1-60_May21,2012''', sequenced on '''HiseqMay29''' run at BioGem (Lane: 4-8) | |||
** '''Note: Mapping was performed by Dinh'''. | |||
** '''Raw reads: /media/SeqStore2/120531_SN100_DD/NP_BSPP''' | |||
* The rest of libraries (Ind61,62,65-72) were pooled in another library, '''NP_BSPP_SR_HV_Ind61.62.65-80_May31,2012:''' continued on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-31 | |||
* Update: Library IDs: '''NP_BSPP_SR_HV_Ind61.62.65-80_May31,2012''', sequenced on '''HiSeqJun7''' run at Biogem ('''Lane: 8''') | |||
== Sample indexes == | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Sample IDs''' | |||
| align="center" style="background:#f0f0f0;"|'''Lab IDs''' | |||
| align="center" style="background:#f0f0f0;"|'''Well IDs''' | |||
| align="center" style="background:#f0f0f0;"|'''IndX''' | |||
|- | |||
| '''Cell pellet or gDNA samples from Sergio'''|||||| | |||
|- | |||
| HUES2 p41||Ap15-1||A1||AmpR6.3.Ind1 | |||
|- | |||
| ASThiPS4F1 p12||Ap15-2||B1||AmpR6.3.Ind2 | |||
|- | |||
| ASThiPS4F2 p12||Ap15-3||C1||AmpR6.3.Ind3 | |||
|- | |||
| HUES6 p39 Control TeSR||Ap15-4||D1||AmpR6.3.Ind4 | |||
|- | |||
| HUES6 p39 ACTIVIN||Ap15-5||E1||AmpR6.3.Ind5 | |||
|- | |||
| HUES6 p39 BMP-4||Ap15-6||F1||AmpR6.3.Ind6 | |||
|- | |||
| HUES9 p39 Control TeSR||Ap15-7||G1||AmpR6.3.Ind7 | |||
|- | |||
| HUES9 p39 ACTIVIN||Ap15-8||H1||AmpR6.3.Ind8 | |||
|- | |||
| HUES9 p39 BMP-4||Ap15-9||A2||AmpR6.3.Ind9 | |||
|- | |||
| HUES3 p36 Control TeSR||Ap15-10||B2||AmpR6.3.Ind10 | |||
|- | |||
| HUES3 p36 ACTIVIN||Ap15-11||C2||AmpR6.3.Ind11 | |||
|- | |||
| HUES3 p36 BMP-4||Ap15-12||D2||AmpR6.3.Ind12 | |||
|- | |||
| H1 p54 Control TeSR||Ap15-13||E2||AmpR6.3.Ind13 | |||
|- | |||
| H1 p54 ACTIVIN||Ap15-14||F2||AmpR6.3.Ind14 | |||
|- | |||
| ASThiPS4F5 p16 Control TeSR||Ap15-15||G2||AmpR6.3.Ind15 | |||
|- | |||
| ASThiPS4F5 p16 ACTIVIN ||Ap15-16||H2||AmpR6.3.Ind16 | |||
|- | |||
| ASThiPS4F4 p36 Control TeSR||Ap15-17||A3||AmpR6.3.Ind17 | |||
|- | |||
| ASThiPS4F4 p36 ACTIVIN||Ap15-18||B3||AmpR6.3.Ind18 | |||
|- | |||
| ASThiPS4F4 p36 BMP-4||Ap15-19||C3||AmpR6.3.Ind19 | |||
|- | |||
| Huv-iPS4F6 p23 ACTIVIN||Ma15-1||D3||AmpR6.3.Ind20 | |||
|- | |||
| H1 p48||Ma15-2||E3||AmpR6.3.Ind21 | |||
|- | |||
| H9 p47 ||Ma15-3||F3||AmpR6.3.Ind22 | |||
|- | |||
| HUES3 p33||Ma15-4||G3||AmpR6.3.Ind23 | |||
|- | |||
| HUES6 p26||Ma15-5||H3||AmpR6.3.Ind24 | |||
|- | |||
| HUES8 p35||Ma15-6||A4||AmpR6.3.Ind25 | |||
|- | |||
| HUES9 p36||Ma15-7||B4||AmpR6.3.Ind26 | |||
|- | |||
| ASThiPS4F3 p24 (derived from Astrocytes)||Ma15-8||C4||AmpR6.3.Ind27 | |||
|- | |||
| ASThiPS4F4 p16 (derived from Astrocytes)||Ma15-9||D4||AmpR6.3.Ind28 | |||
|- | |||
| FiPS4F2 p32 (derived from IMR90 fibroblasts)||Ma15-10||E4||AmpR6.3.Ind29 | |||
|- | |||
| FiPS4F5 p29 (derived from IMR90 fibroblasts)||Ma15-11||F4||AmpR6.3.Ind30 | |||
|- | |||
| KiPS4FA p54 (derived from keratinocytes)||Ma15-12||G4||AmpR6.3.Ind31 | |||
|- | |||
| Huv-iPS4F6 p23 (derived from HUVECs)||Ma15-13||H4||AmpR6.3.Ind32 | |||
|- | |||
| IMR90 p6||Ma15-14||A5||AmpR6.3.Ind33 | |||
|- | |||
| Keratinocytes p3||Ma15-15||B5||AmpR6.3.Ind34 | |||
|- | |||
| H1 p47 Control||Ma15-16||C5||AmpR6.3.Ind35 | |||
|- | |||
| H1 p47 BMP-4||Ma15-17||D5||AmpR6.3.Ind36 | |||
|- | |||
| ASThiPS4F5 p12 Control||Ma15-18||E5||AmpR6.3.Ind37 | |||
|- | |||
| ASThiPS4F5 p12 BMP-4||Ma15-19||F5||AmpR6.3.Ind38 | |||
|- | |||
| Huv-iPS4F6 p23 Control||Ma15-20||G5||AmpR6.3.Ind39 | |||
|- | |||
| Huv-iPS4F6 p23 BMP-4||Ma15-21||H5||AmpR6.3.Ind40 | |||
|- | |||
| H9 p43 mTeSR||SR-1||A6||AmpR6.3.Ind41 | |||
|- | |||
| H9 p43 ACTIVIN ||SR-2||B6||AmpR6.3.Ind42 | |||
|- | |||
| H9 p43 BMP4||SR-3||C6||AmpR6.3.Ind43 | |||
|- | |||
| HUV0iPS4F1 p19||SR-4||D6||AmpR6.3.Ind44 | |||
|- | |||
| HUV-hiPS4F1 p20 ACTIVIN||SR-5||E6||AmpR6.3.Ind45 | |||
|- | |||
| HUV-hiPS4F1 p20 BMP4||SR-6||F6||AmpR6.3.Ind46 | |||
|- | |||
| HUV-iPS4F3 F19||SR-7||G6||AmpR6.3.Ind47 | |||
|- | |||
| HUV-hiPS4F3 p20 ACTIVIN||SR-8||H6||AmpR6.3.Ind48 | |||
|- | |||
| HUV-hiPS4F3 p20 BMP4||SR-9||A7||AmpR6.3.Ind49 | |||
|- | |||
| aMSCs p7||SR-10||B7||AmpR6.3.Ind50 | |||
|- | |||
| MSCiPS #8 p14||SR-11||C7||AmpR6.3.Ind51 | |||
|- | |||
| MSCiPS #4 p14||SR-12||D7||AmpR6.3.Ind52 | |||
|- | |||
| hNiPS2F p23||SR-13||E7||AmpR6.3.Ind53 | |||
|- | |||
| hKiPS3F-7 p24||SR-14||F7||AmpR6.3.Ind54 | |||
|- | |||
| hNSC ||SR-15||G7||AmpR6.3.Ind55 | |||
|- | |||
| hFiPS4F-7 p9||SR-16||H7||AmpR6.3.Ind56 | |||
|- | |||
| HUVEC p2||SR-17||A8||AmpR6.3.Ind57 | |||
|- | |||
| hiPS AST4F-4 p9||SR-18||B8||AmpR6.3.Ind58 | |||
|- | |||
| KERAT MMTA ||SR-19||C8||AmpR6.3.Ind59 | |||
|- | |||
| KiPS4F #8||SR-20||D8||AmpR6.3.Ind60 | |||
|- | |||
| olf MSC ||SR-21||E8||AmpR6.3.Ind61 | |||
|- | |||
| KiPS||SR-22||F8||AmpR6.3.Ind62 | |||
|- | |||
| '''Old bis-cvt gDNA by Dinh (09/01/2010)'''|||||| | |||
|- | |||
| Astrocytes D10||SRB_1||A9||AmpR6.3.Ind65 | |||
|- | |||
| AstiPS4F4 D11||SRB_2||B9||AmpR6.3.Ind66 | |||
|- | |||
| AstiPS4F5 D9||SRB_3||C9||AmpR6.3.Ind67 | |||
|- | |||
| HUVEC D12||SRB_4||D9||AmpR6.3.Ind68 | |||
|- | |||
| HUViPS4F1 D13||SRB_5||E9||AmpR6.3.Ind69 | |||
|- | |||
| HUViPS4F3 D14||SRB_6||F9||AmpR6.3.Ind70 | |||
|- | |||
| HFF-XF D3||SRB_7||G9||AmpR6.3.Ind71 | |||
|- | |||
| hNSC D1||SRB_8||H9||AmpR6.3.Ind72 | |||
|- | |||
| '''gDNA samples from Harvard (ASM ASCM project)'''|||||| | |||
|- | |||
| GM gDNA 4-5-12||GM||||AmpR6.3.Ind73 | |||
|- | |||
| P10E3 gDNA 4-5-12||P10E3||||AmpR6.3.Ind74 | |||
|- | |||
| DF2 gDNA 4-5-12||DF2||||AmpR6.3.Ind75 | |||
|- | |||
| H0 gDNA 4-5-12||H0||||AmpR6.3.Ind76 | |||
|- | |||
| H7 gDNA 4-5-12||H7||||AmpR6.3.Ind77 | |||
|- | |||
| H14 gDNA 4-5-12||H14||||AmpR6.3.Ind78 | |||
|- | |||
| H16 gDNA 4-5-12||H16||||AmpR6.3.Ind79 | |||
|- | |||
| GM:H0:: 1:1||GM:H0 1:1||||AmpR6.3.Ind80 | |||
|} | |||
* continued on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-31 |
Latest revision as of 22:47, 18 June 2012
- [Link to calendar]
- Continued from: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-21#SLN_mix_solution
PCR Amplification with barcoded primers (AmpF6.4Sol and AmpR6.3 IndX No.1-72)[edit]
- I tested if the capture works well by performing qPCR of few samples in small volume 25ul, sample E1, F1, G1 and NTC
Captured template | 1 rxn | 4.2 rxn mix |
10uM AmpF6.4Sol | 0.5 | 2.1 |
10uM AmpR6.3Sol | 0.5 | 2.1 |
50x SYBG | 0.2 | 0.84 |
2x Phusion MM | 12.5 | 52.5 |
H2O | 8.8 | 36.96 |
- Aliquot 22.5ul to each tube and add 2.5ul of circularized DNA templates
Program
98C 30s -> (98C 10s -> 58C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x15 -> 72C 3min File:2012 05 25 testqPCR SR.png
- Form the qPCR of tested samples, I could observe amplification in every samples except NTC, so I can continue amplify all samples and barcode with index primers.
- I have to aliquot AmpR3.3Indx primer due to the evaporation of the old plate storing at 4C. In the future I might store at -20C
Plate layout and barcoded primer[edit]
A1 | A2 | A3 | A4 | A5 | A6 | A7 | A8 |
AmpR6.3.Ind1 | AmpR6.3.Ind9 | AmpR6.3.Ind17 | AmpR6.3.Ind25 | AmpR6.3.Ind33 | AmpR6.3.Ind41 | AmpR6.3.Ind49 | AmpR6.3.Ind57 |
B1 | B2 | B3 | B4 | B5 | B6 | B7 | B8 |
AmpR6.3.Ind2 | AmpR6.3.Ind10 | AmpR6.3.Ind18 | AmpR6.3.Ind26 | AmpR6.3.Ind34 | AmpR6.3.Ind42 | AmpR6.3.Ind50 | AmpR6.3.Ind58 |
C1 | C2 | C3 | C4 | C5 | C6 | C7 | C8 |
AmpR6.3.Ind3 | AmpR6.3.Ind11 | AmpR6.3.Ind19 | AmpR6.3.Ind27 | AmpR6.3.Ind35 | AmpR6.3.Ind43 | AmpR6.3.Ind51 | AmpR6.3.Ind59 |
D1 | D2 | D3 | D4 | D5 | D6 | D7 | D8 |
AmpR6.3.Ind4 | AmpR6.3.Ind12 | AmpR6.3.Ind20 | AmpR6.3.Ind28 | AmpR6.3.Ind36 | AmpR6.3.Ind44 | AmpR6.3.Ind52 | AmpR6.3.Ind60 |
E1 | E2 | E3 | E4 | E5 | E6 | E7 | E8 |
AmpR6.3.Ind5 | AmpR6.3.Ind13 | AmpR6.3.Ind21 | AmpR6.3.Ind29 | AmpR6.3.Ind37 | AmpR6.3.Ind45 | AmpR6.3.Ind53 | AmpR6.3.Ind61 |
F1 | F2 | F3 | F4 | F5 | F6 | F7 | F8 |
AmpR6.3.Ind6 | AmpR6.3.Ind14 | AmpR6.3.Ind22 | AmpR6.3.Ind30 | AmpR6.3.Ind38 | AmpR6.3.Ind46 | AmpR6.3.Ind54 | AmpR6.3.Ind62 |
G1 | G2 | G3 | G4 | G5 | G6 | G7 | |
AmpR6.3.Ind7 | AmpR6.3.Ind15 | AmpR6.3.Ind23 | AmpR6.3.Ind31 | AmpR6.3.Ind39 | AmpR6.3.Ind47 | AmpR6.3.Ind55 | |
H1 | H2 | H3 | H4 | H5 | H6 | H7 | |
AmpR6.3.Ind8 | AmpR6.3.Ind16 | AmpR6.3.Ind24 | AmpR6.3.Ind32 | AmpR6.3.Ind40 | AmpR6.3.Ind48 | AmpR6.3.Ind56 |
- Note: There are total 70 reactions (A1-H9, no samples in well ID G8 and H8 and A10-H12)
Components | 1x rxn | 71 rxn mix |
Captured template | 10.00 | 0.00 |
10uM AmpF6.4Sol | 2.00 | 142.00 |
10uM AmpR6.3Indx (X=1-72) | 2.00 | 0.00 |
2x Kapa SYBR MM | 50.00 | 3550.00 |
H2O | 36.00 | 2,556.00 |
Total | 100.00 | 6,248.00 |
- Aliquot 88ul, add 2ul of 10uM AmpR6.3Indx and 10ul of circularized DNA template
Program
98C 30s -> (98C 10s -> 58C 30s -> 72C 30s)x8 -> (98C 10s -> 72C 30s)x14 -> 72C 3min
- I performed qPCR in duplicate with the same condition and stopped at the same cycle
File:2012 05 25 qPCR SR plate1.png File:2012 05 25 qPCR SR plate2.png
- Since A9-H9 reactions shoot up earlier than other samples, I took out 60ul at cycles 20
- Took 60ul of PCR product from plate1 and 2 (total volume 120ul) - Purified with 0.8 vol of AmPure beads - Eluted with 60ul EB buffer - Performed PAGE quantification by loading sample 1ul
Well ID | conc. (ng/ul) | Total amount in 60ul (ng) | Volume for 60ng (ul) | Well ID |
A1 | 13.66 | 819.34 | 4.39 | A1 |
B1 | 11.97 | 718.02 | 5.01 | B1 |
C1 | 12.50 | 750.04 | 4.80 | C1 |
D1 | 11.37 | 682.37 | 5.28 | D1 |
E1 | 9.32 | 559.04 | 6.44 | E1 |
F1 | 11.67 | 699.95 | 5.14 | F1 |
G1 | 12.32 | 739.22 | 4.87 | G1 |
H1 | 13.97 | 838.08 | 4.30 | H1 |
A2 | 14.19 | 851.55 | 4.23 | A2 |
B2 | 13.07 | 784.08 | 4.59 | B2 |
C2 | 14.71 | 882.63 | 4.08 | C2 |
D2 | 14.17 | 850.27 | 4.23 | D2 |
E2 | 17.12 | 1026.97 | 3.51 | E2 |
F2 | 16.72 | 1003.03 | 3.59 | F2 |
G2 | 17.42 | 1045.27 | 3.44 | G2 |
H2* | 15.41 | 924.62 | 3.89 | H2* |
A3 | 14.31 | 858.62 | 4.19 | A3 |
B3 | 16.01 | 960.41 | 3.75 | B3 |
C3 | 15.83 | 949.64 | 3.79 | C3 |
D3 | 10.69 | 641.17 | 5.61 | D3 |
E3 | 6.92 | 415.03 | 8.67 | E3 |
F3 | 12.93 | 775.83 | 4.64 | F3 |
G3 | 12.04 | 722.32 | 4.98 | G3 |
H3 | 12.10 | 726.03 | 4.96 | H3 |
A4 | 16.39 | 983.11 | 3.66 | A4 |
B4 | 15.02 | 901.02 | 4.00 | B4 |
C4 | 12.66 | 759.53 | 4.74 | C4 |
D4 | 9.03 | 541.89 | 6.64 | D4 |
E4 | 16.28 | 976.88 | 3.69 | E4 |
F4 | 11.63 | 698.04 | 5.16 | F4 |
G4* | 8.79 | 527.68 | 6.82 | G4* |
H4 | 17.56 | 1053.63 | 3.42 | H4 |
A5* | 11.98 | 718.73 | 5.01 | A5* |
B5* | 12.10 | 726.10 | 4.96 | B5* |
C5 | 13.53 | 811.88 | 4.43 | C5 |
D5 | 14.28 | 856.59 | 4.20 | D5 |
E5 | 18.77 | 1125.92 | 3.20 | E5 |
F5 | 13.74 | 824.13 | 4.37 | F5 |
G5 | 15.84 | 950.23 | 3.79 | G5 |
H5 | 18.66 | 1119.88 | 3.21 | H5 |
A6 | 14.10 | 845.88 | 4.26 | A6 |
B6 | 15.23 | 913.85 | 3.94 | B6 |
C6 | 15.54 | 932.41 | 3.86 | C6 |
D6 | 14.23 | 853.91 | 4.22 | D6 |
E6 | 13.29 | 797.58 | 4.51 | E6 |
F6 | 13.74 | 824.66 | 4.37 | F6 |
G6 | 14.29 | 857.67 | 4.20 | G6 |
H6 | 13.94 | 836.22 | 4.31 | H6 |
A7 | 15.95 | 956.98 | 3.76 | A7 |
B7 | 14.68 | 880.72 | 4.09 | B7 |
C7 | 14.81 | 888.76 | 4.05 | C7 |
D7 | 15.94 | 956.39 | 3.76 | D7 |
E7* | 6.96 | 417.31 | 8.63 | E7* |
F7** | 4.17 | 250.11 | 14.39 | F7** |
G7 | 15.68 | 940.75 | 3.83 | G7 |
H7* | 13.03 | 781.77 | 4.60 | H7* |
A8 | 15.51 | 930.69 | 3.87 | A8 |
B8 | 14.18 | 850.94 | 4.23 | B8 |
C8* | 12.09 | 725.59 | 4.96 | C8* |
D8 | 11.08 | 664.88 | 5.41 | D8 |
E8** | 2.68 | 160.74 | E8** | |
F8** | 4.95 | 297.18 | F8** | |
A9 | 8.36 | 501.40 | A9 | |
B9 | 7.97 | 478.09 | B9 | |
C9 | 8.74 | 524.33 | C9 | |
D9 | 7.70 | 461.86 | D9 | |
E9 | 6.27 | 376.26 | E9 | |
F9 | 7.92 | 474.91 | F9 | |
G9 | 4.52 | 270.94 | G9 | |
H9 | 7.51 | 450.74 | H9 |
- Note: For the sequencing libraries, NP-BSPP-SR_Ind1-60_May21,2012, I combined samples in well ID A1-D8 (total 60 libraries)
- Performed PAGE size selection with 6% TBE 5-well gel (4 gels)
File:ZhangLab 2 2012-05-28 11hr 15min PAGE-SS-1.jpg File:ZhangLab 2 2012-05-28 11hr 17min PAGE-SS-2.jpg
- Resuspended with H2O, total volume 60ul
- Quantified concentration by Qubit dsDNA assay by Alan (based on size 375bp): 83.18nM or 14.4ng/ul
- Concentration by PAGE quantification is 33.5ng/ul
File:ZhangLab 2 2012-05-30 17hr 20min PQ NP BSPP SR Ind1-60 May21 2012.jpg
- Library IDs: NP-BSPP-SR_Ind1-60_May21,2012, sequenced on HiseqMay29 run at BioGem (Lane: 4-8)
- Note: Mapping was performed by Dinh.
- Raw reads: /media/SeqStore2/120531_SN100_DD/NP_BSPP
- The rest of libraries (Ind61,62,65-72) were pooled in another library, NP_BSPP_SR_HV_Ind61.62.65-80_May31,2012: continued on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-31
- Update: Library IDs: NP_BSPP_SR_HV_Ind61.62.65-80_May31,2012, sequenced on HiSeqJun7 run at Biogem (Lane: 8)
Sample indexes[edit]
Sample IDs | Lab IDs | Well IDs | IndX |
Cell pellet or gDNA samples from Sergio | |||
HUES2 p41 | Ap15-1 | A1 | AmpR6.3.Ind1 |
ASThiPS4F1 p12 | Ap15-2 | B1 | AmpR6.3.Ind2 |
ASThiPS4F2 p12 | Ap15-3 | C1 | AmpR6.3.Ind3 |
HUES6 p39 Control TeSR | Ap15-4 | D1 | AmpR6.3.Ind4 |
HUES6 p39 ACTIVIN | Ap15-5 | E1 | AmpR6.3.Ind5 |
HUES6 p39 BMP-4 | Ap15-6 | F1 | AmpR6.3.Ind6 |
HUES9 p39 Control TeSR | Ap15-7 | G1 | AmpR6.3.Ind7 |
HUES9 p39 ACTIVIN | Ap15-8 | H1 | AmpR6.3.Ind8 |
HUES9 p39 BMP-4 | Ap15-9 | A2 | AmpR6.3.Ind9 |
HUES3 p36 Control TeSR | Ap15-10 | B2 | AmpR6.3.Ind10 |
HUES3 p36 ACTIVIN | Ap15-11 | C2 | AmpR6.3.Ind11 |
HUES3 p36 BMP-4 | Ap15-12 | D2 | AmpR6.3.Ind12 |
H1 p54 Control TeSR | Ap15-13 | E2 | AmpR6.3.Ind13 |
H1 p54 ACTIVIN | Ap15-14 | F2 | AmpR6.3.Ind14 |
ASThiPS4F5 p16 Control TeSR | Ap15-15 | G2 | AmpR6.3.Ind15 |
ASThiPS4F5 p16 ACTIVIN | Ap15-16 | H2 | AmpR6.3.Ind16 |
ASThiPS4F4 p36 Control TeSR | Ap15-17 | A3 | AmpR6.3.Ind17 |
ASThiPS4F4 p36 ACTIVIN | Ap15-18 | B3 | AmpR6.3.Ind18 |
ASThiPS4F4 p36 BMP-4 | Ap15-19 | C3 | AmpR6.3.Ind19 |
Huv-iPS4F6 p23 ACTIVIN | Ma15-1 | D3 | AmpR6.3.Ind20 |
H1 p48 | Ma15-2 | E3 | AmpR6.3.Ind21 |
H9 p47 | Ma15-3 | F3 | AmpR6.3.Ind22 |
HUES3 p33 | Ma15-4 | G3 | AmpR6.3.Ind23 |
HUES6 p26 | Ma15-5 | H3 | AmpR6.3.Ind24 |
HUES8 p35 | Ma15-6 | A4 | AmpR6.3.Ind25 |
HUES9 p36 | Ma15-7 | B4 | AmpR6.3.Ind26 |
ASThiPS4F3 p24 (derived from Astrocytes) | Ma15-8 | C4 | AmpR6.3.Ind27 |
ASThiPS4F4 p16 (derived from Astrocytes) | Ma15-9 | D4 | AmpR6.3.Ind28 |
FiPS4F2 p32 (derived from IMR90 fibroblasts) | Ma15-10 | E4 | AmpR6.3.Ind29 |
FiPS4F5 p29 (derived from IMR90 fibroblasts) | Ma15-11 | F4 | AmpR6.3.Ind30 |
KiPS4FA p54 (derived from keratinocytes) | Ma15-12 | G4 | AmpR6.3.Ind31 |
Huv-iPS4F6 p23 (derived from HUVECs) | Ma15-13 | H4 | AmpR6.3.Ind32 |
IMR90 p6 | Ma15-14 | A5 | AmpR6.3.Ind33 |
Keratinocytes p3 | Ma15-15 | B5 | AmpR6.3.Ind34 |
H1 p47 Control | Ma15-16 | C5 | AmpR6.3.Ind35 |
H1 p47 BMP-4 | Ma15-17 | D5 | AmpR6.3.Ind36 |
ASThiPS4F5 p12 Control | Ma15-18 | E5 | AmpR6.3.Ind37 |
ASThiPS4F5 p12 BMP-4 | Ma15-19 | F5 | AmpR6.3.Ind38 |
Huv-iPS4F6 p23 Control | Ma15-20 | G5 | AmpR6.3.Ind39 |
Huv-iPS4F6 p23 BMP-4 | Ma15-21 | H5 | AmpR6.3.Ind40 |
H9 p43 mTeSR | SR-1 | A6 | AmpR6.3.Ind41 |
H9 p43 ACTIVIN | SR-2 | B6 | AmpR6.3.Ind42 |
H9 p43 BMP4 | SR-3 | C6 | AmpR6.3.Ind43 |
HUV0iPS4F1 p19 | SR-4 | D6 | AmpR6.3.Ind44 |
HUV-hiPS4F1 p20 ACTIVIN | SR-5 | E6 | AmpR6.3.Ind45 |
HUV-hiPS4F1 p20 BMP4 | SR-6 | F6 | AmpR6.3.Ind46 |
HUV-iPS4F3 F19 | SR-7 | G6 | AmpR6.3.Ind47 |
HUV-hiPS4F3 p20 ACTIVIN | SR-8 | H6 | AmpR6.3.Ind48 |
HUV-hiPS4F3 p20 BMP4 | SR-9 | A7 | AmpR6.3.Ind49 |
aMSCs p7 | SR-10 | B7 | AmpR6.3.Ind50 |
MSCiPS #8 p14 | SR-11 | C7 | AmpR6.3.Ind51 |
MSCiPS #4 p14 | SR-12 | D7 | AmpR6.3.Ind52 |
hNiPS2F p23 | SR-13 | E7 | AmpR6.3.Ind53 |
hKiPS3F-7 p24 | SR-14 | F7 | AmpR6.3.Ind54 |
hNSC | SR-15 | G7 | AmpR6.3.Ind55 |
hFiPS4F-7 p9 | SR-16 | H7 | AmpR6.3.Ind56 |
HUVEC p2 | SR-17 | A8 | AmpR6.3.Ind57 |
hiPS AST4F-4 p9 | SR-18 | B8 | AmpR6.3.Ind58 |
KERAT MMTA | SR-19 | C8 | AmpR6.3.Ind59 |
KiPS4F #8 | SR-20 | D8 | AmpR6.3.Ind60 |
olf MSC | SR-21 | E8 | AmpR6.3.Ind61 |
KiPS | SR-22 | F8 | AmpR6.3.Ind62 |
Old bis-cvt gDNA by Dinh (09/01/2010) | |||
Astrocytes D10 | SRB_1 | A9 | AmpR6.3.Ind65 |
AstiPS4F4 D11 | SRB_2 | B9 | AmpR6.3.Ind66 |
AstiPS4F5 D9 | SRB_3 | C9 | AmpR6.3.Ind67 |
HUVEC D12 | SRB_4 | D9 | AmpR6.3.Ind68 |
HUViPS4F1 D13 | SRB_5 | E9 | AmpR6.3.Ind69 |
HUViPS4F3 D14 | SRB_6 | F9 | AmpR6.3.Ind70 |
HFF-XF D3 | SRB_7 | G9 | AmpR6.3.Ind71 |
hNSC D1 | SRB_8 | H9 | AmpR6.3.Ind72 |
gDNA samples from Harvard (ASM ASCM project) | |||
GM gDNA 4-5-12 | GM | AmpR6.3.Ind73 | |
P10E3 gDNA 4-5-12 | P10E3 | AmpR6.3.Ind74 | |
DF2 gDNA 4-5-12 | DF2 | AmpR6.3.Ind75 | |
H0 gDNA 4-5-12 | H0 | AmpR6.3.Ind76 | |
H7 gDNA 4-5-12 | H7 | AmpR6.3.Ind77 | |
H14 gDNA 4-5-12 | H14 | AmpR6.3.Ind78 | |
H16 gDNA 4-5-12 | H16 | AmpR6.3.Ind79 | |
GM:H0:: 1:1 | GM:H0 1:1 | AmpR6.3.Ind80 |