SINGLE CELL GENOMICS
SINGLE CELL GENOMICS

The ability to analyze independently or concomitantly the expression of genes and the accessibility profile of the genomic DNA at the single-cell level has now enabled deeper insights into cell function. Analyzing the molecular features of thousands of animal and plant cells in the same workflow also provides information regarding gene function, regulatory networks, and their regulation in response to stress or during cell differentiation.

Services

Located in the Beadle Center (N305/N326), the Single Cell Genomics Core Facility provides to animal and plant scientists the following services using the 10x Genomics Chromium System:

  • Single-cell/nucleus RNA-seq technology to analyze gene expression at the single-cell level.
  • Single-nucleus ATAC-seq technology to analyze profiles of chromatin accessibility at the single-cell level.
  • Single-nucleus Multiome ATAC + Gene Expression technology to concomitantly analyze gene expression and chromatin accessibility at the single-cell level.

The SCG core facility will also provide access to highly sensitive technologies to quantify and estimate the quality of nucleotidic samples:

  • Qubit technology, Invitrogen
  • Bioanalyzer technology, Agilent

Hours: Monday-Friday 9:00 am-5:00 pm or by appointment

Service Fees

ServiceInternal UsersExternal Academic UsersIndustry Users
single-cell RNA-seq 1 sample $1,680 $2,240 $2,800
(per sample) 2 to 4 samples $1,528 $1,910 $2,388
>5 samples $1,376 $1,720 $2,150
single-cell ATAC-seq 1 sample $1,650 $2,200 $2,640
(per sample) 2 to 4 samples $1,425 $1,900 $2,280
>5 samples $1,290 $1,720 $2,064
single-cell Multiome-seq 1 sample $2,730 $3,640 $4,368
(per sample) 2 to 4 samples $2,445 $3,260 $3,912
>5 samples $2,287.50 $3,050 $3,660
Isolation of plant nuclei 1 to 4 samples $150 $150 $150
Bioanalyzer DNA chip 1 to 11 samples $54 $72 $86.40
Bioanalyzer RNA chip 1 to 11 samples $48.80 $65 $78
Qubit per sample $3 $4 $6

Instruments

10x Genomics Chromium System
Qubit technology, Invitrogen
Bioanalyzer technology, Agilent
Coming soon: GridION, Oxford Nanopore Technologies

Policies

Cancellations/Missed Appointments – Users who have scheduled time may cancel up to 24 hours in advance of their start time. If users do not show up for a scheduled appointment or cancel within 24 hours of the appointment, they will be billed $100.

Late Arrivals – The billing time will start at the beginning of the scheduled appointment. Users will be billed $30 per hour of delay

Radioactive Materials – Radiolabeled samples are not permitted in the Core Facility.

Acknowledgments – Please acknowledge the Single Cell Genomics Core Facility in any grant application or publication in which equipment and/or staff expertise was provided. Also, please send the Core Facility Director a copy of accepted publications containing data generated in the facility.

Biosafety – To decrease possible infection risk to Core Facility staff and lab users, we require that all samples be described before analysis so appropriate handling and containment can be implemented.

Personnel

Director: Marc Libault, PhD
N305 Beadle Center
Phone: 402-472-4530
Email: mlibault2@unl.edu

Research Manager: Sandra Thibivilliers
N304 Beadle Center
Phone: 402-472-4512
Email: sthibivilliers2@unl.edu

Publications

  • Isolation of Plant Root Nuclei for Single Cell RNA Sequencing. Thibivilliers S, Anderson D, Libault M. Curr Protoc Plant Biol. 2020 Dec;5(4):e20120. doi: 10.1002/cppb.20120.
  • Isolating and Cryo-Preserving Pig Skin Cells for Single Cell RNA Sequencing Study. Li Han, Carlos P Jara, Ou Wang, Sandra Thibivilliers, Rafał K. Wóycicki, Mark A. Carlson, William H. Velander, Eliana P. Araújo, Marc Libault, Chi Zhang, Yuguo Lei bioRxiv 2021.01.31.429035. doi: https://doi.org/10.1101/2021.01.31.429035
  • Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level. Farmer A, Thibivilliers S, Ryu KH, Schiefelbein J, Libault M. Mol Plant. 2021 Mar 1;14(3):372-383. doi: 10.1016/j.molp.2021.01.001.
  • Plant Single-Cell Multiomics: Cracking the Molecular Profiles of Plant Cells. Thibivilliers S, Libault M. Trends Plant Sci. 2021 Jun;26(6):662-663. doi: 10.1016/j.tplants.2021.03.001.
  • Enhancing Our Understanding of Plant Cell-to-Cell Interactions Using Single-Cell Omics. Thibivilliers S, Libault M. Front Plant Sci. 2021 Aug 5;12:696811. doi: 10.3389/fpls.2021.696811. eCollection 2021.
  • Vision, challenges and opportunities for a Plant Cell Atlas. Plant Cell Atlas Consortium, Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JA, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY. Elife. 2021 Sep 7;10:e66877. doi: 10.7554/eLife.66877.
  • Isolation of Plant Nuclei Compatible with Micro-fluidic Single-nucleus ATAC-sequencing. Thibivilliers S, Anderson D, Libault M. Bio-Protocol, in press
  • Biological and Cellular Functions of the Microdomain-Associated FWL/CNR Protein Family in Plants. Thibivilliers S, Farmer A, Libault M. Plants (Basel). 2020 Mar 19;9(3):377. doi: 10.3390/plants9030377.

Advisory Committee

Facility Advisory Group
The mission of the Facility Advisory Group is to provide guidance and feedback to the facility regarding the most effective use of its resources to meet research demands.

Member list coming soon.

Contact the Director

Director: Marc Libault, PhD
N305 Beadle Center

Telephone Number:
402-472-4530
Email: mlibault2@unl.edu