Yale Center for Genome Analysis Shared Resource

Transcript

• 00:00Is Frances Lopez. And as
• 00:01Tania mentioned, I'll be talking
• 00:03about the Yale Center for
• 00:04Genome Analysis.
• 00:06And I'm gonna start directly
• 00:08with,
• 00:10what I oops. What I
• 00:11consider the most important slide,
• 00:13which is the summary of
• 00:14the things we do or
• 00:15we offer at the at
• 00:16the genome center. As a
• 00:18genome center, you can imagine,
• 00:20we offer any kind of
• 00:21solutions regarding next generation sequencing,
• 00:23but we also work with
• 00:24the,
• 00:25microarrays just for genotyping and
• 00:28transcriptomics.
• 00:30We also keep up with
• 00:31the cutting edge technologies
• 00:33in single cell and in
• 00:34special omics,
• 00:36for including multi omics profiling
• 00:38and transcriptomics.
• 00:41We provide bioinformatics
• 00:43support,
• 00:43free of charge
• 00:45and, grant support too. And
• 00:47I like to think about
• 00:48this bioinformatics support being end
• 00:50to end, so from experimental
• 00:52design to publication
• 00:55support.
• 00:56We also keep,
• 00:57doing r and d, offering
• 00:59new services, as much as
• 01:00we can. And often, this
• 01:01is through collaboration with the
• 01:03Arkansas Center Investigations.
• 01:06And one thing that is
• 01:07often forgotten is we offer
• 01:09consultation,
• 01:10and that is always free.
• 01:12So don't hesitate to contact
• 01:13us if you have,
• 01:16you know, if you have
• 01:17questions about the experimental design
• 01:19or what type of platform
• 01:21would be better for your
• 01:22needs to answer your questions.
• 01:27Just a brief introduction to
• 01:28the center. The center was
• 01:29established in two thousand nine.
• 01:31The director is doctor Zreken
• 01:33Manet.
• 01:34We are also at West
• 01:35Campus. You can find us
• 01:36at eight hundred thirty West
• 01:38Campus Drive.
• 01:39We have a bigger space
• 01:41of lot, and it's really
• 01:42beautiful.
• 01:43There are thirty five people
• 01:45working in there, including the
• 01:46bioinformaticians.
• 01:47If if you have the
• 01:48chance, we invite you to
• 01:49stop by and give a
• 01:51look, and we'll show you
• 01:52around.
• 01:54We also have,
• 01:56a computer HPC,
• 01:58a space dedicated only to
• 02:00the data that we produce.
• 02:01And
• 02:02so if you sequence with
• 02:03us, you would have you
• 02:04would have access to the
• 02:06high performance computing dedicated space,
• 02:08storage,
• 02:09and compute power for your
• 02:11analysis.
• 02:15We provide a a quite
• 02:16a big range of sequencing
• 02:18machines.
• 02:19Our main workforce
• 02:20is the NovaSeq x plus,
• 02:21the IlluminaSeq
• 02:22x plus, but we also
• 02:23offer,
• 02:25other alternative, including the LMAN
• 02:27Bioscience,
• 02:28the ABT.
• 02:29If you if you need,
• 02:30longer reads with, more higher
• 02:32acuity compared with,
• 02:35the Illumina machines, we also
• 02:37provide the,
• 02:38long read, you know, the
• 02:40third generation of sequencers,
• 02:43that that provide real time
• 02:44sequencing
• 02:45and kilobases of, reads, like
• 02:48the back bio and the
• 02:49nano nano pore meaning.
• 02:53So we can use,
• 02:55we off we use those
• 02:56machines with different,
• 02:58services. Here, I'm just listing
• 03:00probably, the most popular ones,
• 03:02but it goes from DNA
• 03:03sequencing, whole exome sequencing, whole
• 03:05genome sequencing,
• 03:07including FFPE tissues,
• 03:09for transcriptomics,
• 03:11epigenetics,
• 03:12ataxic,
• 03:15methylation sequencing.
• 03:16And, also, we work with
• 03:17different type of samples, including
• 03:19cell free DNA or even,
• 03:21dark blood spots.
• 03:25In the past ten years,
• 03:26as you probably know, single
• 03:28cell platforms are be becoming
• 03:30really popular.
• 03:31We we offer different alternative,
• 03:34including
• 03:36including,
• 03:37the single cell that
• 03:39we recently incorporated.
• 03:41But ten x has still
• 03:42been the most popular one.
• 03:43But don't forget, we also
• 03:45offer probably what could be
• 03:46alternative
• 03:48alternative options,
• 03:49could be cheaper like parts
• 03:51bioscience
• 03:52or the Illumina single cell,
• 03:55kits.
• 03:58And as I mentioned, we
• 03:59like to keep up with
• 04:00the cutting edge technologies, including
• 04:02the special omics technologies.
• 04:05We like to divide it
• 04:06into big categories. The ones
• 04:08are image based platforms
• 04:10that give you a subcellular
• 04:11resolution.
• 04:12The problem is only based
• 04:13for human and mouse, but
• 04:15we also offer, sequencing based
• 04:17platforms
• 04:18on organism agnostics, including the
• 04:20Curio
• 04:21and the ten x and
• 04:24HD. And we also offer
• 04:25platforms for special,
• 04:27epigenetics.
• 04:32And even more recently, we
• 04:34have incorporated,
• 04:35proteomics in our services.
• 04:38We have two main ones,
• 04:39which is the all in
• 04:40reveal
• 04:41that allows you to measure
• 04:42over a thousand,
• 04:44proteins.
• 04:45And this is based on,
• 04:47immunoassays
• 04:48and the readouts that we
• 04:49use in next generation sequencing.
• 04:51And in the future, we're
• 04:52applying to incorporate a new,
• 04:54equipment, which is the Allyn
• 04:56signature
• 04:57that would allow us to
• 04:58offer more,
• 04:59panels for, protein analysis using
• 05:01the ALYN technology.
• 05:03We also offer the Bruker
• 05:04IsoSpark,
• 05:06which is an ELISA based
• 05:08immunoassays,
• 05:10to profile the cytokines.
• 05:15We've been working hard also
• 05:16to facilitate the access,
• 05:20and tracking of the samples.
• 05:21We created
• 05:23an iLab portal,
• 05:25where users can create accounts
• 05:27and track their samples through
• 05:28the process of sequencing.
• 05:31So if you you have
• 05:32the first time contacting us,
• 05:34you need to contact Chris
• 05:35Castaldi
• 05:36to create an account in
• 05:37iLab. And after that, if
• 05:39you need to send us
• 05:40the samples, we have different
• 05:41methods. You can come directly
• 05:43to the genome center or
• 05:44you can ship it to
• 05:45the genome center, but we
• 05:46also have two drop off
• 05:47locations
• 05:49in George, George Street, three
• 05:50hundred George Street and Tuck
• 05:53Building.
• 05:55And as I mentioned,
• 05:57we also provide,
• 05:58bioinformatics services.
• 06:00And in this case, it's
• 06:01me, the contact person.
• 06:03I like to divide the
• 06:04bioinformatics service in three big
• 06:06areas. Of course, the main
• 06:07one is
• 06:08to provide free data analysis
• 06:10services,
• 06:11from design to publication,
• 06:15support.
• 06:17We also provide training.
• 06:19We do workshops
• 06:20and seminars through the year.
• 06:23And, again oops.
• 06:26One thing that it's often
• 06:27forgotten
• 06:28is that,
• 06:29we also facilitate
• 06:32access to the technologies through
• 06:34pipelines. So we create pipelines
• 06:36that are accessible,
• 06:37in Macquarie,
• 06:39our HPC.
• 06:42And if any of those
• 06:43needs, they don't ended up
• 06:45following or they don't fit,
• 06:46your needs, we also have
• 06:47a bioinformatics teams that we
• 06:48can find other alternatives for
• 06:50you.
• 06:54Everything that I mentioned in
• 06:56this presentation is also available
• 06:58in our website. We try
• 06:59to keep it updated
• 07:00as much as we can,
• 07:02and you also have pricing
• 07:03in there about all the,
• 07:04services that we provide.
• 07:06And please don't hesitate to
• 07:07contact us at y c
• 07:08e a, IDL dot e
• 07:10d u. We have people
• 07:11monitoring that address.
• 07:13But if you have specific
• 07:14questions,
• 07:15for specific areas,
• 07:17probably this is the most
• 07:18important people that you need
• 07:19to know about it.
• 07:20We have.
• 07:22We have questions about genomics
• 07:24or any kind of the
• 07:25long read sequencing technologies.
• 07:28Irena can help you with,
• 07:29whole genomes and whole sequencing
• 07:31captures,
• 07:33ChIP seq or FFPP,
• 07:36sample manipulations.
• 07:38Chris Castaldi can help you
• 07:39with, as I mentioned, with
• 07:40the AI live accounts, but
• 07:42also with the transcriptomic.
• 07:44And myself,
• 07:46I'm the contact person for
• 07:47any kind of bioinformatic names,
• 07:49you may
• 07:50have. And that's it.