Jie:LabNotes/sample record/sample sent: Difference between revisions

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==Sample sent out==
==Sample sent out==
   20080812 to Yuan Gao: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2008-8-04]
   20080812 to Yuan Gao: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2008-8-4]
   IMB90_iPS: 120nM x 20ul
   IMB90_iPS: 120nM x 20ul
   Hybrid_1: 97nM x 20ul  
   Hybrid_1: 97nM x 20ul  
Line 7: Line 7:
     IMB90_iPS: 35ng/ul x 30ul
     IMB90_iPS: 35ng/ul x 30ul
     Hybrid_1: 36ng/ul x 30ul
     Hybrid_1: 36ng/ul x 30ul
  20080902 to Yuan Gao:
    Hybrid_1_Covaris_sequencing_Library: 27.8ng/ul (187nM) x 15ul. refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2008-8-26]
    BJ, 17.4ng/ul (117nM) x 15ul. refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2008-8-15]
    BJ_iPS_11, 18.6ng/ul (125nM) x 25ul
    BJ_iPS_12, 32.7ng/ul (220nM) x 25ul
    Hybrid_2, 28.3ng/ul (190nM) x 25ul
  20080915 to Bing Ren: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2008-9-12]
    No_1(BJ): 17.2ng/ul (104nM) x 15ul
    No_9(Hybrid_2): 18.6ng/ul (112nM) x 15ul
  20080917 to Yuan Gao: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2008-9-5]
    hFib2, 27.1ng/ul (164nM) x 30ul
    hFib2_iPS4, 22.2ng/ul (134nM) x 30ul
    HUES_63, 30.8ng/ul (186nM) x 30ul
    IMR90, 31.1ng/ul (189nM) x 30ul
  20080917 to Agencourt: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2008-9-4]
    Captured PCR_BJ (96-well plasmids)
    Sequencing library_BJ (96-well plasmids)
  20080924 to Yuan Gao:refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/ASE/2008-9-22]
    G2: 26.1ng/ul (132nM) x 15ul
    2B: 26.8ng/ul (140nM) x 15ul
    3B: 40.7ng/ul (213nM) x 15ul
    H1: 33.4ng/ul (175nM) x 15ul
    H2: 43.3ng/ul (227nM) x 15ul
  20091026 to Yuan Gao: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/ExonomeSeq/2009-1-19]
  short probe: 15.3ng/ul (36nM) x 15ul;
  long probe (high con.): 18.7ng/ul (30nM) x 15ul;
  20090206 to Kun: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-1-13] and [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-1-22]
  BJ:        75.4nM x 15ul;
  Hybrid_1:  87.6nM x 15ul;
  PGP1_F:      106nM x 15ul;
  HUES12:    74.9nM x 15ul;
  PGP1_iPS1:  90.3nM x 15ul;
  PGP1_L:    77.6nM x 15ul;
  PGP3_L:    80.9nM x 15ul;
  PGP9_L:    96.9nM x 15ul;
200905 to Yuan Gao: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-5-20]
  NA21070*1 100406 captured targets: 25.3ng/ul (96nM) x 15ul;
  NA21070*1 100406 normalized captured targets: 23.1ng/ul (87nM) x 15ul;
  PGP2_052909A: 111nM x 15ul;refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/ExonomeSeq/2009-5-29]
  PGP3_052909A: 126nM x 15ul.
20090608 to BioGem:  refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-5-29]
DF6-9-9_P16(4): 11nM x 10ul x 2 lanes;
foreskin: 15nM x 10ul x 1lane.
20090610 to Zhen Ye: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-6-4]
  NA21070*1_100406_97k 21.2nM x 14ul;
  DF6-9-9_P16(4)_30k 21.2nM x 14ul;
  foreskin_30k 21.2nM x 14ul;
20090615 to Yuan Gao: the following 3 samples are captured targets of mouse DNA.refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/AlanFung:LabNotes/Capturing/Ms_Meth/EoH;E4H;E24H/2009-6-9]
  E24H 6.56 ng/ul * 46uL (26nM)
  E4H 19.6 ng/ul * 40uL (40nM)
  EoH 43.53 ng/ul * 75uL (88nM)
20090618 to Zhen Ye: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/ASE/2009-6-10] 
  Hybrid_1: 4.3ng/ul (37nM) x 5ul
  BJ: 7.2ng/ul (62nM) x 5ul
  The above 2 samples for end-sequencing.
20090625 to Agencourt: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-6-22]
3 96-well plates containing the three blunt clones to Agencourt on 09-06-25.
one 96-well plate containing the clones from DMNT3B and MMP9 together with the forward and reverse primers to Agencourt on 09-06-25.
20090629 to Agencourt: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-6-22]
one 96-well palte containg the clones from LSP1 and MATN4 together with the forward and reverse primers to Agencourt on 09-06-29.
20090705 to Agencourt: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-7-1]
two 96-well plates for ASM validation for regions overlap r2 and SNP.
20090709 to Genewiz for fuzzl-methylated gene ASE validation: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-7-2]
20090713 to Genewiz for fuzzl-methylated gene ASE validation: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-7-2]
20090714 to Genewiz for genomic alleotype validatioon of GLIPR1L2 on GM12863,64,72~75:refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-7-14]
20090831 to Agencourt: refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/CpgSeq/2009-7-27]
Four plates for cell type and individual dependent ASM validation:
rs6061990_PGP3L_PGP9L_rs3746459_BJ;
MATN4_PGP1F_PGP1iPS_rs10846023_BJ;
DNMT3B_PGP3L_PGP9L_rs34206253_PGP1L;
rs8128908_PGP1L_PGP1F_rs34206253_PGP1F_MMP9_PGP1L

Latest revision as of 17:39, 31 August 2009

Sample sent out[edit]

 20080812 to Yuan Gao: refer to LabNotes on [1]
  IMB90_iPS: 120nM x 20ul
  Hybrid_1: 97nM x 20ul 
 20080813 to Covaris: refer to LabNotes on [2]
   IMB90_iPS: 35ng/ul x 30ul
   Hybrid_1: 36ng/ul x 30ul
 20080902 to Yuan Gao: 
   Hybrid_1_Covaris_sequencing_Library: 27.8ng/ul (187nM) x 15ul. refer to LabNotes on [3]
   BJ, 17.4ng/ul (117nM) x 15ul. refer to LabNotes on [4]
   BJ_iPS_11, 18.6ng/ul (125nM) x 25ul
   BJ_iPS_12, 32.7ng/ul (220nM) x 25ul
   Hybrid_2, 28.3ng/ul (190nM) x 25ul
 20080915 to Bing Ren: refer to LabNotes on [5]
   No_1(BJ): 17.2ng/ul (104nM) x 15ul
   No_9(Hybrid_2): 18.6ng/ul (112nM) x 15ul
 20080917 to Yuan Gao: refer to LabNotes on [6]
   hFib2, 27.1ng/ul (164nM) x 30ul
   hFib2_iPS4, 22.2ng/ul (134nM) x 30ul
   HUES_63, 30.8ng/ul (186nM) x 30ul
   IMR90, 31.1ng/ul (189nM) x 30ul
 20080917 to Agencourt: refer to LabNotes on [7]
   Captured PCR_BJ (96-well plasmids)
   Sequencing library_BJ (96-well plasmids)
 20080924 to Yuan Gao:refer to LabNotes on [8]
   G2: 26.1ng/ul (132nM) x 15ul
   2B: 26.8ng/ul (140nM) x 15ul
   3B: 40.7ng/ul (213nM) x 15ul
   H1: 33.4ng/ul (175nM) x 15ul
   H2: 43.3ng/ul (227nM) x 15ul
 20091026 to Yuan Gao: refer to LabNotes on [9]
 short probe: 15.3ng/ul (36nM) x 15ul;
 long probe (high con.): 18.7ng/ul (30nM) x 15ul;
 20090206 to Kun: refer to LabNotes on [10] and [11]
 BJ:         75.4nM x 15ul;
 Hybrid_1:   87.6nM x 15ul;
 PGP1_F:      106nM x 15ul;
 HUES12:     74.9nM x 15ul;
 PGP1_iPS1:  90.3nM x 15ul;
 PGP1_L:     77.6nM x 15ul;
 PGP3_L:     80.9nM x 15ul;
 PGP9_L:     96.9nM x 15ul;

200905 to Yuan Gao: refer to LabNotes on [12]

 NA21070*1 100406 captured targets: 25.3ng/ul (96nM) x 15ul;
 NA21070*1 100406 normalized captured targets: 23.1ng/ul (87nM) x 15ul;
 PGP2_052909A: 111nM x 15ul;refer to LabNotes on [13]
 PGP3_052909A: 126nM x 15ul.

20090608 to BioGem: refer to LabNotes on [14]

DF6-9-9_P16(4): 11nM x 10ul x 2 lanes;
foreskin: 15nM x 10ul x 1lane.

20090610 to Zhen Ye: refer to LabNotes on [15]

  NA21070*1_100406_97k 21.2nM x 14ul;
  DF6-9-9_P16(4)_30k 21.2nM x 14ul;
  foreskin_30k 21.2nM x 14ul;

20090615 to Yuan Gao: the following 3 samples are captured targets of mouse DNA.refer to LabNotes on [16]

 E24H 6.56 ng/ul * 46uL (26nM)
 E4H 19.6 ng/ul * 40uL	(40nM)
 EoH 43.53 ng/ul * 75uL (88nM)

20090618 to Zhen Ye: refer to LabNotes on [17]

 Hybrid_1: 4.3ng/ul (37nM) x 5ul
 BJ: 7.2ng/ul (62nM) x 5ul
 The above 2 samples for end-sequencing.

20090625 to Agencourt: refer to LabNotes on [18]

3 96-well plates containing the three blunt clones to Agencourt on 09-06-25.
one 96-well plate containing the clones from DMNT3B and MMP9 together with the forward and reverse primers to Agencourt on 09-06-25.

20090629 to Agencourt: refer to LabNotes on [19]

one 96-well palte containg the clones from LSP1 and MATN4 together with the forward and reverse primers to Agencourt on 09-06-29.

20090705 to Agencourt: refer to LabNotes on [20]

two 96-well plates for ASM validation for regions overlap r2 and SNP.

20090709 to Genewiz for fuzzl-methylated gene ASE validation: refer to LabNotes on [21]

20090713 to Genewiz for fuzzl-methylated gene ASE validation: refer to LabNotes on [22]

20090714 to Genewiz for genomic alleotype validatioon of GLIPR1L2 on GM12863,64,72~75:refer to LabNotes on [23]

20090831 to Agencourt: refer to LabNotes on [24]

Four plates for cell type and individual dependent ASM validation:
rs6061990_PGP3L_PGP9L_rs3746459_BJ;
MATN4_PGP1F_PGP1iPS_rs10846023_BJ;
DNMT3B_PGP3L_PGP9L_rs34206253_PGP1L;
rs8128908_PGP1L_PGP1F_rs34206253_PGP1F_MMP9_PGP1L