Horejsh #AGBT19 Promega founded in '78; 1500 employees in 16 countries; 4K products. Expanding sequencing products, long read seq
4:37pm March 1st 2019 via Twitter Web Client
Douglas Horejsh (Promega) #ABRF19 “A collaborative solution provider for genome biology and sequencing workflows”
4:36pm March 1st 2019 via Twitter Web Client
Shaffer #AGBT19 Recent ref comparing miRNA library methods https://t.co/ifOUQWRm3U
4:35pm March 1st 2019 via Twitter Web Client
Shaffer #AGBT19 miRNA: As low as 1ng without adapter dimers, the bane of other methods, without gel-based cleanup.
4:32pm March 1st 2019 via Twitter Web Client
Shaffer #AGBT19 UPX: individual RT reactions, each well has ID, pooled into 1 tube. 96 becomes 1 library.
4:30pm March 1st 2019 via Twitter Web Client
Shaffer #AGBT19 FastSelect blocks cDNA synthesis of unwanted RNAs. Shows 1% rRNA vs 6-10% for RiboZero.
4:28pm March 1st 2019 via Twitter Web Client
Shaffer #AGBT19 rRNA depletion takes 29-37 steps and 2+ hours. Their FastSelect. 20 min, 1 step, >99% rRNA removal,… https://t.co/jLZ3LUB
4:27pm March 1st 2019 via Twitter Web Client
Shaffer #AGBT19 Portfolio - QIAseq for both DNA and RNA. Focus today - FastSelect for rRNA depletion; QIAseq UPX (u… https://t.co/zASEf4Z03M
4:26pm March 1st 2019 via Twitter Web Client
Jonathan Shaffer (QIAGEN) #AGBT19 “Next generation QIAseq: Sequence what matters using kits with enhanced throughpu… https://t.co/oDdPoFvRIq
4:25pm March 1st 2019 via Twitter Web Client
Lowman #AGBT19 Distribution of AE in 55 individuals by haplotype group: group 2 had zero AE's, carrying fewest unique alleles of all groups.
4:24pm March 1st 2019 via Twitter Web Client
Lowman #AGBT19 Study 3: OmniSeq Carl Morrison, TRBV polymorphism, 55 individuals with AE to CTLA-4 or PD1 Rx. Prepr… https://t.co/tqnN0Wusd7
4:22pm March 1st 2019 via Twitter Web Client
Lowman #AGBT19 Study 2: Fong lab UCSF, evaluate TCR converence and clonal expansion as predictive biomarkers. CTLA-… https://t.co/NMz7AhVJUN
4:20pm March 1st 2019 via Twitter Web Client
Lowman #AGBT19 Looked at responders and non-resp and TCR sequence, nice correlation.
4:19pm March 1st 2019 via Twitter Web Client
Lowman #AGBT19 ID in aa, but distinct CDR3 NT junctions. Dendritic cell vaccination elicits anti-cancer responses in ICB resistant pts.
4:18pm March 1st 2019 via Twitter Web Client
Lowman #AGBT19 3 studies from SITC. Study 1: TCR convergence, with Storkus of U Pitt, manuscript in prep. Repertoir… https://t.co/HPHZ5gFMAU
4:16pm March 1st 2019 via Twitter Web Client
Lowman #AGBT19 Oncomine has variety of analyses - Spectratyping plots, allele-ID, clonotyping, clone sizes per variable gene.
4:14pm March 1st 2019 via Twitter Web Client
Lowman #AGBT19 All similar workflow; AmpliSeq HD, Ion Chef, GeneStudio 5S, Reporter. Illustrates CDR1/2/3. LR is 32… https://t.co/Wu1ae5ZsyU
4:13pm March 1st 2019 via Twitter Web Client
Lowman #AGBT19 Broad line of I-O assays using AmpliSeq. Targeted AmpliSeq: TCR Beta - LR, - SR, Immune Response. SR… https://t.co/nTWlEMKIzy
4:11pm March 1st 2019 via Twitter Web Client
Geoffrey Lowman (Thermo Fisher Scientific) #AGBT19 “Emerging next-generation sequencing solutions for T-cell receptor repertoire analysis”
4:10pm March 1st 2019 via Twitter Web Client
Badgett #AGBT19 >5K publications, ~5 new papers/day. ~1650 publications in 2018 alone.
3:52pm March 1st 2019 via Twitter Web Client
Badgett #AGBT19 CLR ave yield 67.4 Gb, 27 SMRT cells, 20.5kb ave RL. CCS: ave yield 250.4 Gb, 31 SMRT cells, 62.5 kb ave RL.
Badgett #AGBT19 Pre-release chemistry. Second Quarter release. Hudson Alpha: assembly 721MB Contig N50 11.9MB colle… https://t.co/aHGZFkPtPZ
3:51pm March 1st 2019 via Twitter Web Client
Badgett #AGBT19 CLR (continuous long reads) - range from 80GB-100GB with similar readlengths. Early-access with th… https://t.co/pnsUezikvL
3:50pm March 1st 2019 via Twitter Web Client
Badgett #AGBT19 Performance of Sequel II 8M new ZMW’s. https://t.co/wUWULwBVqm
3:49pm March 1st 2019 via Hootsuite Inc.
Badgett #AGBT19 Sequel II: an 8x higher increase in yield. Reduced project time, lower cost, equivalent performance. 8M ZMW.
3:48pm March 1st 2019 via Twitter Web Client
Badgett #AGBT19 SMRTbell Express Template Prep Kit 2.0: 4h workflow, 500bp to >30 kb. single-tube, additive workflo… https://t.co/I59Ooyl
3:46pm March 1st 2019 via Twitter Web Client
Badgett #AGBT19 pbsv 1.0 calling indels. Now >20bp in size with 2.0, also finding inversions and translocations.
3:45pm March 1st 2019 via Twitter Web Client
Badgett #AGBT19 ASHG 2018 workshop recording https://t.co/k780KH2JaF Iso-Seq 3 recovers 20% more reads.
3:43pm March 1st 2019 via Twitter Web Client
Badgett #AGBT19 CCS now up to 20kb. Example: ave RL of 84kb, throughput per SMRT cell to 50Gb, ave readlength up to… https://t.co/tPFoKJoYeG
3:39pm March 1st 2019 via Twitter Web Client
Badgett #AGBT19 Sequel System 6.0 >20kb long reads. Consensus QV45, and short-read polishing hurts quality. Interme… https://t.co/iCLXcg2
3:38pm March 1st 2019 via Twitter Web Client
Marty Badgett (PacBio) #AGBT19 The Sequel II System the next evolution of SMRT sequencing
3:35pm March 1st 2019 via Twitter Web Client
Kothandaraman #AGBT19 Offer solutions for PGD, PGS, Inh disorders and oncology. RNA kits for small RNA, transcripto… https://t.co/dlzNmSQ9oG
3:29pm March 1st 2019 via Twitter Web Client
Kothandaraman #AGBT19 Moving the magnet, not the liquid. chemagic 360, prime, prime junior systems.
3:24pm March 1st 2019 via Twitter Web Client
Kothandaraman #AGBT19 % of time - 75% / 10% / 15% is the hands-on time for sample prep / sequencing / data analysis.
3:21pm March 1st 2019 via Twitter Web Client
Arvind Kothandaraman (Perkin Elmer) #AGBT19 Sample prep simplified. Starts with three images: fire, wheel, electron… https://t.co/4mxNHlUcwG
3:19pm March 1st 2019 via Twitter Web Client
Corcoran #AGBT19 Alissa Align and Call, also Alissa Interpret to classify and curate variants.
3:15pm March 1st 2019 via Twitter Web Client
Corcoran #AGBT19 Lasergen: SBS platform, with a key tech is a lightning terminator. Linker of dye to nt, is also te… https://t.co/zPHHaBpN60
Corcoran #AGBT19 Femto pulse - first pulsed-field parallel CE instrument, 12 samples in 1h. New: 4150 TapeStatoin,… https://t.co/lxcFaaON0w
3:14pm March 1st 2019 via Twitter Web Client
Corcoran #AGBT19 AATI now has a high sensitivity femto pulse, as well as the fragment analyzer 288 samples/run.
3:12pm March 1st 2019 via Twitter Web Client
Corcoran #AGBT19 Adv over mechanical shearing is minimize sample loss via sample transfer. Enrichment: all-in-one c… https://t.co/UFoVWp9oYf
3:06pm March 1st 2019 via Twitter Web Client
Corcoran #AGBT19 New Seq tech (in grey) - Lightning Terminator. Sample prep: Oct 18 SureSelect XT HS enzymatic shea… https://t.co/3XttzNIeCW
3:03pm March 1st 2019 via Twitter Web Client
Corcoran #AGBT19 Agilent '05 aCGH, '09 SureSelect; '12 SureFISH and Dako; '19 Advanced Analytics, Lasergen and Genohm.
3:01pm March 1st 2019 via Twitter Web Client
Kevin Corcoran (Agilent) #AGBT19 New developments in NGS from Agilent.
3:00pm March 1st 2019 via Twitter Web Client
Ishii #AGBT19 CpG methylation over ATAC-Seq peaks - violin plots across six types of methods looks very good for EM-Seq.
2:58pm March 1st 2019 via Twitter Web Client
Ishii #AGBT19 Fragment distribution of size across samples https://t.co/TDLPfHKmBV
2:52pm March 1st 2019 via Hootsuite Inc.
Ishii #AGBT19 Picard metrics on HiSeq-X; nine busy bar plots. Accel, SPLAT. Shows 99% conversion rate. Dupl rates d… https://t.co/noEZHvN1oU
2:49pm March 1st 2019 via Twitter Web Client
Ishii #AGBT19 EM-Seq - TET2/Oxidation Enhancer, add glucosyl group. Then made into ssDNA, and treated to APOBEC (de… https://t.co/oT88dlH7NQ
2:46pm March 1st 2019 via Twitter Web Client
Ishii #ABRF19 Illustration of methods - contrast to EM-Seq https://t.co/ZmW6E11QH8
2:45pm March 1st 2019 via Hootsuite Inc.
@00livier Yes the GeoMx from Nanostring is designed around FFPE. They have a service program now, system launches a… https://t.co/Owt2QqO1DC
2:42pm March 1st 2019 via Hootsuite Inc. in reply to 00livier
Ishii #AGBT19 Epigenetics is reversible, established early, DNMT 3a/3b are de novo, CpG context, often in islands around promoter regions.
2:40pm March 1st 2019 via Twitter Web Client
