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Sequencing Runs



Illumina

Run Date Sequence Facility CASAVA Pipeline v. Lane# Lane Name Flowcell Layout Number of Clusters (raw) Number of Clusters (PF) % Clusters Retained # of Reads People Project Source Comments
3/10/2015 Berkeley 1.8 2 EXP016 H2JJ5BCXX 50 SR ? ? ? ? Han Genomic Arabidopsis
3/10/2015 Berkeley 1.8 1 EXP015 H2JJ5BCXX 50 SR ? ? ? ? Han Genomic Arabidopsis
2/26/15 Berkeley 1.8 2 LCHT1213 C6AU3ACXX 100 PE ? ? ? ? Teerapong Capture Rice Genomic
1/30/15 Berkeley 1.8 2 LCHT52 H27FTBCXX 100 PE ? ? ? ? Helen TILLING Amplicons T26
1/23/15 Berkeley 1.8 1 LCHT51 H27FTBCXX 100 PE ? ? ? ? Helen TILLING Amplicons T26
1/28/15 Berkeley 1.8 7 LCCW060 C5TTWACXX 50 SR ? ? ? ? Isabelle Genomic Poplar
1/23/15 Berkeley 1.8 5 LCCW061 C5VMVACXX 100 PE ? ? ? ? Isabelle Genomic Poplar
12/23/14 Berkeley 1.8 6 LCHT017_2 C618KACXX 100 PE ? ? ? ? Helen Capture Pep Genomic
12/23/14 Berkeley 1.8 5 LCHT017_1 C618KACXX 100 PE ? ? ? ? Helen Capture Pep Genomic
12/12/14 Berkeley 1.8 4 LCCW006 C5YRKACXX 100 PE ? ? ? ? Isabelle Capture Flax Genomic
12/12/14 Berkeley 1.8 3 LCCW005 C5YRKACXX 100 PE ? ? ? ? Isabelle Capture Flax Genomic
12/12/14 Berkeley 1.8 2 LCCW004 C5YRKACXX 100 PE ? ? ? ? Isabelle Capture Flax Genomic
12/12/14 Berkeley 1.8 1 LCCW003 C5YRKACXX 100 PE ? ? ? ? Isabelle Capture Flax Genomic
11/26/14 Berkeley 1.8 8 LCCW002 C5NGRACXX 100 PE ? ? ? ? Isabelle Capture Flax Genomic
11/26/14 Berkeley 1.8 7 LCCW001 C5NGRACXX 100 PE ? ? ? ? Isabelle Capture Flax Genomic
11/12/14 Berkeley 1.8 5 LCNS001_re C59AVACXX 100 PE ? ? ? ? Terrapong Genomic Rice
11/04/14 Berkeley 1.8 2 LCJG002 C5CVCACXX 50 SR ? ? ? ? Isabelle RESCAN SynxNat Genomic
11/04/14 Berkeley 1.8 1 LCJG001 C5CVCACXX 50 SR ? ? ? ? Isabelle RESCAN SynxNat Genomic
10/27/14 Berkeley 1.8 6 LCCW010 C5ETNACXX 50 SR ? ? ? ? Isabelle Pop23 Poplar Genomic
10/17/14 Berkeley 1.8 5 LCCW009 C5ETNACXX 100 PE ? ? ? ? Isabelle Pop22 Poplar Genomic
10/17/14 Berkeley 1.8 4 LCCW008 C5ETNACXX 50 SR ? ? ? ? Isabelle Pop21 Poplar Genomic
10/17/14 Berkeley 1.8 3 LCCW007 C5ETNACXX 50 SR ? ? ? ? Isabelle Pop20 Poplar Genomic
10/17/14 Berkeley 1.8 2 LCJG004 C5ETNACXX 50 SR ? ? ? ? Isabelle RESCAN SynxNat Genomic
10/17/14 Berkeley 1.8 1 LCJG003 C5ETNACXX 50 SR ? ? ? ? Isabelle RESCAN SynxNat Genomic
10/17/14 Berkeley 1.8 7 LCHT003 C5A6YACXX 100 PE ? ? ? ? Isabelle Capture Flax Genomic
10/17/14 Berkeley 1.8 6 LCHT002 C5A6YACXX 100 PE ? ? ? ? Isabelle Capture Flax Genomic
10/17/14 Berkeley 1.8 5 LCHT001 C5A6YACXX 100 PE ? ? ? ? HT11 (Thailand) Capture Rice Genomic
10/17/14 Berkeley 1.8 4 LCSI001 C5CK1ACXX 50 SR ? ? ? ? Soichi RNA-Seq Arabidopsis thaliana
10/16/14 Berkeley 1.8 2 LCHT042 HARU1ADXX 100 PE ? ? ? ? Helen TILLING Amplicons Holla (TILL4)
10/16/14 Berkeley 1.8 1 LCHT041 HARU1ADXX 100 PE ? ? ? ? Helen TILLING Amplicons Holla (TILL4)
8/1/14 Berkeley 1.8 1 LCHT032 C4WHAACXX 50 SR ? ? ? ? Art & Yui Arabidopsis RNA-Seq
6/9/14 DNA Core 1.8 1 IMH15 M01533 (Miseq) 150 PE ? ? ? ? Isabelle Incode testing RESCAN
Alfred Lettuce cDNA contigs
Takashi Persimmon Methylation contigs
7/24/14 Berkeley 1.8 8 LCHT034 C4WHHACXX 50 SR ? ? ? ? Art & Yui Arabidopsis RNA-Seq
7/24/14 Berkeley 1.8 7 LCHT033 C4WHHACXX 50 SR ? ? ? ? Art & Yui Arabidopsis RNA-Seq
7/24/14 Berkeley 1.8 6 LCHT031 C4WHHACXX 50 SR ? ? ? ? Art & Yui Rice RNA-Seq
7/24/14 Berkeley 1.8 5 LCHT030 C4WHHACXX 50 SR ? ? ? ? Art & Yui Rice RNA-Seq
6/4/14 Berkeley 1.8 4 LCHT027_2 C3W25ACXX 100 PE ? ? ? ? Isabelle Capture 2 Flax Genomic Sequenced 2x
6/4/14 Berkeley 1.8 3 LCHT027_1 C3W25ACXX 100 PE ? ? ? ? Isabelle Capture 2 Flax Genomic
6/4/14 Berkeley 1.8 2 LCHT026 C3W25ACXX 100 PE ? ? ? ? Art Capture 7 Rice Genomic
6/4/14 Berkeley 1.8 1 LCHT025_2 C3W25ACXX 100 PE ? ? ? ? Art Capture 4/5 Rice Genomic Sequenced 2x
5/30/14 Berkeley 1.8 2 LCHT023 C4D4LACXX 50 SR ? ? ? ? Isabelle IFG-MZ-4_Pop19 Poplar Genomic
5/30/14 Berkeley 1.8 7 LCHT021 C4BC7ACXX 50 SR ? ? ? ? Isabelle IFG-MZ-3_Pop18 Poplar Genomic
5/30/14 Berkeley 1.8 6 LCHT022 C4BC7ACXX 50 SR ? ? ? ? Isabelle IFG-MZ-2_Pop17 Poplar Genomic
5/23/14 Berkeley 1.8 7 LCHT025_1 C3WBPACXX 100 PE ? ? ? ? Art Capture 4/5 Rice Genomic
5/23/14 Berkeley 1.8 6 LCHT024_1 C3WBPACXX 100 PE ? ? ? ? Art Capture 3/6 Rice Genomic sequenced 2x
5/23/14 Berkeley 1.8 5 LCHT024_1 C3WBPACXX 100 PE ? ? ? ? Art Capture 3/6 Rice Genomic
5/17/14 DNA Core 1.8 8 Pop16 BC3016ACXX 50 SR ? ? ? ? Isabelle IFG-MZ-1_Pop16 Poplar Genomic
5/7/14 DNA Core 1.8 2 IMH14 AH7UCAADXX 50 SR ? ? ? ? Takashi small RNA MP & FP developing buds Rapid Mode
5/7/14 DNA Core 1.8 1 IFG03 AH7UCAADXX 50 SR ? ? ? ? Isabelle Genomic Poplar Genomic Rapid Mode
5/1/14 Berkeley 1.8 1 LCHT010 H9B2GADXX 100 PE ? ? 97.26 146,462,470 Helen T23-Lane2 mix PCR Rapid Mode
5/1/14 Berkeley 1.8 1 LCHT009 H9B2GADXX 100 PE ? ? 97.01 149,876,715 Helen T23-Lane1 mix PCR Rapid Mode
4/30/14 DNA Core 1.8 8 IFG01 BC306TACXX 50 SR ? ? ? ? Isabelle Genomic poplar genomic
4/5/14 DNA Core 1.8 1 IMH13 AC3YNGACXX 100 PE ? ? ? ? Isabelle Genomic Poplar Re-Sequence of previous lane
Takashi Capture Arabidopsis
Soichi Capture Arabidopsis
Michelle Mixed Amplicons Arabidopsis
3/5/14 DNA Core 1.8 2 IMH13 AC2YJ3ACXX 100 PE ? ? ? ? Isabelle Genomic Poplar Same samples in IMH12
Takashi Capture Arabidopsis T-DNA
Soichi Capture Arabidopsis T-DNA
Michelle Mixed Amplicons Arabidopsis Britt Lab
2/22/14 DNA Core 1.8 3 BK1 AC1DLYACXX 50 SR ? ? ? ? Brad RNA-seq Arabidopsis
1/?/14 BGI Sac 1.7 6 Pop14 FCC308AACXX 50SR ? ? ? ? Isabelle Genomic Poplar
1/?/14 BGI Sac 1.7 5 Art2_3 FCC3L9AACXX 100 PE ? ? ? ? Art Capture Rice
1/?/14 BGI Sac 1.7 4 Art2_3 FCC3L9AACXX 100 PE ? ? ? ? Art Capture Rice
1/?/14 BGI Sac 1.7 7 Z201 FCC2UFRACXX 100 PE ? ? ? ? Matt RNA-seq Poplar
1/?/14 BGI Sac 1.7 3 Z203 FCC2UJ5ACXX 100 PE ? ? ? ? Matt RNA-seq Poplar
1/?/14 BGI Sac 1.7 2 Z202 FCC2UJ5ACXX 100 PE ? ? ? ? Matt RNA-seq Poplar
1/17/14 DNA Core 1.8 7 Pop15 BC2UFWACXX 50 SR ? ? ? ? Isabelle Genomic Poplar
12/18/13 DNA Core 1.8 2 LuzFlui-3x AH7R7CADXX 150 PE ? ? ? ? Henny Genomic Mouse Lane aka imh11 and contains re-sequencing of Fluidigm Pilot
Shamoni RNA-seq Luzula
Helen Fluidigm Rice
12/4/13 DNA Core 1.8 1 Pop 11 Rescan AH7T73ADXX 50 SE ? ? ? ? Isabelle RESCAN Poplar
11/?/13 BGI 1.7 8 Cassava-Sorghum Capture FCC2UG4ACXX 100 PE ? ? ? ? Isabelle Capture Cassava + Sorghum
7 Cassava-Sorghum Capture FCC2UG4ACXX 100 PE ? ? ? ? Isabelle Capture Cassava + Sorghum
10/21/13 Berkeley 1.8 6 Pop 13 C2APKACXX 50 SE ? ? ? ? Isabelle/Han Popar Poplar genomic
10/09/13 DNA Core 1.8 2 Pop 12 AH115FADXX 150 PE ? ? ? ? Isabelle Poplar Poplar genomic
9/21/13 Berkeley 1.8 2 LCKN003 C2DFPACXX 50 SE ? ? ? ? Gib RNA-seq Arabidopsis
9/21/13 Berkeley 1.8 1 LCKN002 C2DFPACXX 50 SE ? ? ? ? Gib RNA-seq Arabidopsis
9/17/13 Berkeley 1.8 3 LCKN001 C2DFYACXX 50 SE ? ? ? ? Gib RNA-seq Arabidopsis
9/17/13 Berkeley 1.8 2 LCKN000 C2DFYACXX 50 SE ? ? ? ? Takashi RNA-seq Persimmon Grapevine
9/12/13 DNA Core 1.8 2 T22 Final Library BH1164ADXX ? ? ? ? Helen TILLING Amplicons
9/11/13 DNA Core 1.8 1 Holla(P)Pilot RESCAN M02034 (Miseq) 150PE 500178 455635 91.1 ? Helen RESCAN HollaP Pilot
7/24/13 Berkeley 1.8 2 LCHT002 H0R3CADXX 150 PE ? ? ? ? Takashi RNA-seq Persimmon Rapid Mode
7/24/13 Berkeley 1.8 1 LCHT001 H0R3CADXX 150 PE ? ? ? ? Helen T21 HOLLA Rapid Mode
6/5/13 Berkeley 1.8 1 Sample_Flax1 H0R3KADXX 100 PE ? ? ? ? Nagu Flax Capture Rapid Mode
2 Sample_FLAX2 H0R3KADXX 100 PE ? ? ? ? Nagu Flax Capture Rapid Mode
Takashi Mixed Amplicons Rapid Mode (spike)
6/1/13 DNA Core 1.8 3 SynxNat Plate II Pop10 BD1KRWACXX 50 SE ? ? ? ? Isabelle SynxNat RESCAN
Poplar
5/25/13 DNA Core 1.8 8 SynxNat Plate1 BD1KEDACXX 50 SE ? ? ? ? Isabelle SynxNat RESCAN
5/17/13 DNA Core 1.8 8 Art Capture BC1N60ACXX 100 PE ? ? ? ? Art Rice Capture
3/21/13 DNA Core 1.8 3 Pop8 Final AD1GEAACXX 50SE ? ? ? ? Isabelle Poplar RESCAN
2/8/13 DNA Core 1.8 8 Pop9 Final BD1G2MACXX 50 SE 553/690.6 516.5/600.1 93.6 ? Isabelle Poplar Genomic
2/8/13 DNA Core 1.8 7 Pop7 Final A BD1G2MACXX 50 SE 753/690.6 578.6/600.1 78.8 ? Isabelle RESCAN Poplar Real Pop7
2/8/13 DNA Core 1.8 4 Spiked in PhiX (K4-4, K4-9,K4-12,K4-1) BD1G2MACXX 50 SE 706/690.6 548.0/600.1 77.7 ? Isabelle CHIP Rice
2/06/13 DNA Core 1.8 1 Pop7B Final AD1AM7ACXX 50 SE 576/779.8 536.5/683.6 93.3 148,337,266 Whan thaliana genomic Lane was mis-named
Han thaliana genomic
1/19/13 DNA Core 1.8 8 MFP-P3 (Takashi) BD1JBLACXX 100 PE 698/710.4 642.2/651.2 92.3 ? Takashi Persimmon Genomic
1/19/13 DNA Core 1.8 4 PhiX + K27 rice ChIP spike in BD1JBLACXX 100 PE 774/710.4 672.5/651.2 87.1 ? Isabelle Rice Chip
1/12/13 DNA Core 1.8 6 Pop6 AD123LACXX 50 SE 668/577.6 567.3/516.4 85.3 ? Isabelle Poplar RESCAN
12/29/12 DNA Core 1.8 8 Pop5b BC0KHWACXX 50 SE 670/755.9 615.7/678 92.1 ? Isabelle Poplar RESCAN Correct adapters
11/28/12 DNA Core 1.8 6 Pop5 AC0JV3ACXX 50 SE 671/733.5 613.3/645.7 91.5 ? Isabelle Poplar RESCAN used wrong adapters for poplar
Takashi SynxNat TRD Amplicon
11/28/12 DNA Core 1.8 5 Pop4 Rescan AC0JV3ACXX 50 SE 663/733.5 613.6/645.7 92.8 ? Isabelle Poplar Rescan Dual Index Test
11/28/12 DNA Core 1.8 4 PhiX plus Spike-In: K4-8 & K4-14 AC0JV3ACXX 100 PE 690/733.5 613.9/645.7 89.2 ? Isabelle Rice Chip
11/28/12 DNA Core 1.8 1 IN-Pool AC0JV3ACXX 50 SE 627/733.5 524/645.7 83.7 ? Isabelle Chip Rice
11/14/12 DNA Core 1.8 3 Tom Tai UN AC1730ACXX 100 PE 771/730.3 700.6/648.5 91.2 ? Nagu Tai Capture rice genomic
11/10/12 DNA Core 1.8 7 ChIP K4/K27 Pool#2 AC0JRMACXX 50SE 618/ 430.2/ 69.3 ? Isabelle Chip Rice Redo of IMH7
11/10/12 DNA Core 1.8 6 HOLLA AC0JRMACXX 50SE 598/ 512.3/ 87 144,121,527 Nagu Rescan HOLLA
09/27/12 DNA Core 1.8 1 Fluidigm Pool 1-48 M00384_0072_MS2001121-300V2 150 PE 275 259 94.37 ? Helen Fluidigm Rice
09/25/12 DNA Core 1.8 8 Pop3 BC0T5UACXX 50SE 711/690 512.1/540 73.6 ? Isabelle Rescan Poplar
09/25/12 DNA Core 1.8 3 IMH7 BC0T5UACXX 50SE 696/690 533.3/540 76.6 ? Isabelle Chip Rice
09/25/12 DNA Core 1.8 2 LC Mix 6b BC0T5UACXX 50SE 768/690 553.8/540 73.1 ? Brad RNA-Seq Arabidopsis
Whan RNA-seq Arabidopsis
09/25/12 DNA Core 1.8 1 LC Mix 6a BC0T5UACXX 50SE 711/690 556.9/540 73.2 ? Brad RNA-Seq Arabidopsis
Whan RNA-seq Arabidopsis
07/25/12 Berkeley 1.8 8 2012July_LCMIX5 D1242ACXX 100PE 3501190/? 3311743/? 94.81 504,171,465 Nagu Capture 5 + Controls Rice genomic
Diana Thaliana Hybrids Amplicons Mix
Mital ? Amplicons Custom Barcodes
Kumitaa ? Amplicons Custom Barcodes
07/20/12 BGI Sac 1.7 2 MP1-10 FCD0M49ACXX 100 PE 2134675/? 2020224/? 94.8 193,941,510 Takashi Genomic Library Persimmon Genomic
07/03/12 Berkeley 1.8 8 LCHT001 c0v3dacxx 100PE 3042110/4179792 2870195/3796810 94.62 292,042,634 Helen TILLING 20 PCR Fragments Old Style Barcodes
07/02/12 BGI Sac 1.7 3 FP1 FCC0EGWACXX 100 PE 2113165/? 2036738/? 96.5 195,530,000 Takashi Genomic Library Persimmon Genomic
07/01/12 Berkeley 1.8 2 LCHT002_2 c0vfvacxx 50SE 3751856/3441770 3083019/2972194 83.27 180,089,108 Nagu Holla Rescan Holla genomic SphI
07/01/12 Berkeley 1.8 1 LCHT002_1 c0vfvacxx 50SE 3805267/3441770 3088644/2972194 82.30 182,652,824 Nagu Holla Rescan Holla genomic SphI
06/25/12 DNA Core 1.8 1 HEL1 120625_M00384_0049_AMS0005375 150 PE ? ? ? 14,749,246 Helen HOLLA test mixed pcr product bioo adaptor
Takashi synxnat mixed pcr product Staggered adaptors
Whan RNAseq arabidopsis RNA bioo adaptor
05/30/12 BGI HK 1.7 3 Ndiana FCC0U06ACXX 100 PE ? ? ? 283,660,000 Nagu Capture 4? rice genomic
Diana DB13-DB16 arabidopsis RNA
05/09/12 BGI HK 1.7 8 IMH5 CSZSE012044196 50 SE ? ? ? 129,100,000 Nagu RESCAN HOLLA
Ravi Aneuploids thaliana genomic
Isabelle Chip rice K27 Pol2 input
Whan RNA-seq thaliana RNA
05/09/12 BGI HK 1.7 4 Gib CSZSE012044195 50 SE ? ? ? 118,540,000 Gib RNA seq arabidopsis RNA
05/04/12 BGI HK 1.7 2 Ivalu FCD0VHAACXX 100 PE ? ? ? 239,260,000 Ivalu TILLING RESCAN brassica genomic
03/06/12 DNA Core 1.8 5 Sample_T18_2 BD0MCCACXX 100 PE 360/582 345.9/489.8 96.4 191,251,416 Helen T18 mix PCR
02/28/12 DNA Core 1.8 1 Sample_T19_Pool BD0HEGACXX 50 SE 524/593.5 458.7/509.9 88 126,805,522 Nagu RESCAN Tomato H1706
Helen T19 H1706 and Clamy PCR
02/22/12 DNA Core 1.8 7 Sample_T18_1 AC0E96ACXX 100 PE 665/495.9 604.3/460.7 91.2 334,107,520 Helen T18 mix PCR
02/22/12 DNA Core 1.8 3 Sample_IMH4 AC0E96ACXX 100 PE 481/495.9 429.1/460.7 89.6 ? Isabelle RESCAN cassava genomic
Ivalu TILLING RESCAN brassica genomic
Nagu Capture 3 Rice capture
01/09/12 DNA Core 1.8 6 Capture1 AC0EBFACXX 100 PE 592/494 532.4/453.7 90.3 294,385,832 Nagu Capture 1 rice genomic
12/15/11 BGI Sac 1.7 6 Rice Redo HWI-ST1135_0053 100 PE ? ? ? 156,490,030 Isabelle Heterosis Rice mRNA seq
12/15/11 BGI Sac 1.7 5 Rice Redo HWI-ST1135_0053 100 PE ? ? ? 128,262,776 Isabelle Heterosis Rice mRNA seq
12/10/11 DNA Core 1.8 3 Capture 2 AC0CVFACXX 100 PE 524/400.8 485.9/357.6 93.1 ? Nagu Capture 2 rice genomic
12/09/11 DNA Core 1.8 1 Monster (IMH3) BD0BU8ACXX 100 PE 582/521.6 493.2/468.6 85.2 272,689,574 Helen T18 test mix genomic
Han Aneuploidy thaliana genomic
Isabelle RESCAN cassava
Ivalu TILLING RESCAN brassica genomic
Nagu Key, Track, Capture R4-R8 rice genomic



Pac Bio

Run Date Sequence Facility Lane# Lane Name Layout People Project Source Comments
05/06/14 DNA Core 4 BAC80, Mag, 150k, 180min, P4C2 180 bp Isabelle Persimmon Persimmon Male Bac Library
05/06/14 DNA Core 3 BAC26, Mag, 150k, 180min, P4C2 180 bp Isabelle Persimmon Persimmon Male Bac Library
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