LSU Genomics Facility (College of Science) Survey

L S U G e n o m i c s F a c i l i t y ( C o l l e g e o f S c i e n c e ) S u r v e y 1 of 5 To select a box, double-click it, choose ‘Checked’ 4) In 2015, do you expect to need any under Default value, and click ‘OK’... or, just highlight Sanger-Sequencing services? the appropriate text with color.

1) To which services does your lab need Yes (continuing with #5) access (at LSU or elsewhere)? Maybe (continuing with #5) Sanger-Sequencing (e.g., BigDye). No (skipping to #14) NGS (Next Generation Sequencing). Questions 5-13: Sanger-Sequencing. A DNA Sequencing facility generates read qPCR (ABI ViiA7; ABI Prism 7500). data by capillary electrophoresis of BigDye

DNA shearing (Diagenode Bioruptor) reactions, performs basecalling, and delivers P32 or Fluorescent imaging (Typhoon) the data (i.e., sequence text files and DNA/RNA/Protein fluorescent chromatograms). Clients submit samples to the facility as either: quantitation (Qubit 2.0). (a) ‘DNA Templates’ ; or as, DNA/RNA/Protein fluorescent (b) ‘Sequenced DNA’. quantitation/sizing (Bioanalyzer). DNA size-selection (Invitrogen E-gel). 5) Do you ever use the following options? Sample concentration (SpeedVac).  (5-a) I submit DNA templates to the facility, None of the above (SKIP to #28). which performs the BigDye sequencing reactions, electrophoresis, and 2) Did you know that the LSU Genomics basecalling...... Yes No Facility (GF, in A628 of LSA) provides: (If ‘yes’, answer Question #6).  all services in #1 above: Yes No  (5-b) I submit cleaned BigDye sequencing  free use of SpeedVac, Typhoon, qPCR reactions; then, the facility performs ONLY platforms, & Bioruptor. Yes No the capillary electrophoresis and the basecalling...... Yes No  online reservations through its

Genomics_Schedule•It for self-service (If ‘yes’, answer Question #7). instruments...... Yes No 6) Option 5-a: When submitting DNA  the GF website regarding supplies, templates, staff-run services, & technical support, a) you typically receive the data after how (Science Aid Center, documents, and many work (business) days? website links)...... Yes No 1; 2; 3; 4; 5+ days. 3) Did you know that the Genomics Facility b) what facility options exist for sequencing provides benefits to users by: difficult templates ? (e.g., GC-rich or AT-rich  stocking supplies for NGS work, qPCR, templates, or microsatellites) different volumes of BigDye. & Sanger-Sequencing? Yes No o  having no shipping charges for higher denaturation temp (e.g., 98 C). LifeTechnologies?...... Yes No more cycles.  obtaining major supply discounts due to Other: . . ordering in bulk?..... Yes No c) the facility’s base reimbursement rate (i.e., for standard sequencing) is ___?

Survey return methods: (a) Send electronic copies to [email protected]; (b) Drop off paper copies at either A628 Life Science Annex or put in Scott Herke’s mailbox in 202 LSB. L S U G e n o m i c s F a c i l i t y ( C o l l e g e o f S c i e n c e ) S u r v e y 2 of 5 I do not know the cost. Option 5-a (submit DNA Templates). ~$2.50/well (~$240/96-well plate) Option 5-b (BigDye Seq. reactions). ~$2.25/well (~$216/96-well plate) Free training. ~$2.00/well (~$192/96-well plate) Free technical support. ~$1.75/well (~$168/96-well plate) 9) ~$1.50/well (~$144/96-well plate) Are the typical data delivery rates by the Genomics Facility satisfactory?

Other: . .  Option 5-a (Templates): ≤2-3 work days. Yes; No; Not applicable to me. 7) Option 5-b: When submitting cleaned  Option 5-b (electrophoresis): ~1 work day. BigDye sequencing reactions to the facility, Yes; No; Not applicable to me. a) your typical DNA sequencing reaction parameters are:  Comments?: . .  Total reaction volume: 7-μl; 10-μl; 20-μl 10) With regard to your actual sequencing reactions, who performs them? Other: . . My lab or LSU collaborator.  Volume of BigDye/rxn: other academic/non-profit facility 0.5-μl; 1.0-μl; 2.0-μl a commercial facility. Other: . . LSU Genomics Facility.  Cost per 0.5-μl of BigDye I do not know the cost: Other: . . ~$0.50; ~$0.70; ~$0.80 11) Who performs the Electrophoresis of Other: . . your sequencing reactions? b) you typically receive the data after other academic/non-profit facility how many work (business) days: a commercial facility. 1; 2; 3; 4; 5+ days. LSU Genomics Facility. c) the facility reimbursement rate is __?

I do not know the cost. Other: . . ~$1.50/well (~$144/96-well plate) 12) Why do you use a particular facility? ~$1.25/well (~$120/96-well plate) (Select all that apply.) ~$1.00/well (~$96/96-well plate) cost per sample. ~$0.75/well (~$72/96-well plate) convenience. ~$0.50/well (~$48/96-well plate) technical support. Other: . . speed of data delivery. Other: . . 8) Which DNA Sanger-Sequencing services provided by the Genomics Facility may 13) Do you use the LSU Genomics Facility for be of interest to you: Sanger-Sequencing services? Survey return methods: (a) Send electronic copies to [email protected]; (b) Drop off paper copies at either A628 Life Science Annex or put in Scott Herke’s mailbox in 202 LSB. L S U G e n o m i c s F a c i l i t y ( C o l l e g e o f S c i e n c e ) S u r v e y 3 of 5 Yes; No;  If “NO”, select a reason for ‘why’: Unaware of Genomics Facility (GF). Other options easier on my budget. GF doesn’t provide needed options. Inertia... just haven’t used GF. Other: . .  Answer “For Sanger-Sequencing, I would use the Genomics Facility (more) if ...”: (Please be specific, avoiding vague terms such as ‘more’, ‘less’, or ‘lower’... especially if ‘Cost per Sample’ is the primary issue.) .______. .______. .______. .______. .______.

Survey return methods: (a) Send electronic copies to [email protected]; (b) Drop off paper copies at either A628 Life Science Annex or put in Scott Herke’s mailbox in 202 LSB. L S U G e n o m i c s F a c i l i t y ( C o l l e g e o f S c i e n c e ) S u r v e y 4 of 5 Questions 14-24 are related to Next <500,000; ~2-3 million Generation Sequencing (NGS). ~5-7 million; ~10-15 million

14) Will you need NGS services in 2015? ~15-20 million; >20 million Yes (continuing with #15) Other: . . Maybe (continuing with #15) 19) Assuming an NGS platform could

No (skipping to #25) produce it, what is the MAXIMUM read LENGTH (of the library inserts) that 15) Who generates your NGS libraries? would be useful in your projects? My lab or LSU collaborator. ≥30 bp; ≥100 bp; ≥150 bp other academic/non-profit facility ≥200 bp; ≥300 bp; ≥400 bp a commercial facility. Other: . . Other: . . 20) Did you know that the Genomics 16) Who performs the actual NGS runs? Facility’s provides these PGM services: ☐ other academic/non-profit facility  Libraries: technical support for library ☐ a commercial facility. construction; library QC; and pooling for barcoded samples.... Yes No ☐ LSU Genomics Facility.  OneTouch2 (emPCR): generation, QC, ☐ Other: . . and enrichment of templated ISPs for sequencing sample...... Yes No 17) For 2014, identify NGS platforms that you used (# Runs = ‘flowcells’ or chips):  PGM: Sequencing prep; chip loading; Illumina MiSeq ... [~# Runs = ___] and PGM initialization... Yes No  Bioinformatics: BAM/FASTQ files (split by Illumina (HiSeq) .. [~# Runs = ___] barcode, if applicable); data alignment with Illumina (NextSeq) [~# Runs = ___] TMAP (software optimized for Ion data, which Illumina (GAIIx).... [~# Runs = ___] includes flow-space data for increased accuracy)...... Yes No Ion PGM...... [~# Runs = ___]  Discounted 318v2 runs: @ ~60% of

Ion Proton...... [~# Runs = ___] Ion’s Reagent List price.. Yes No. Pacific-Bio...... [~# Runs = ___] Roche (454)...... [~# Runs = ___] 21) With regard to systematic errors, Roche (454 Jr)..... [~# Runs = ___] identify whether Illumina or Ion Torrent has a greater problem with: Other: . __ .  insertion/deletions Illumina; Ion; Don’t know 18) For your least READ-intensive project, what is the minimum required number  substitution errors of final Library reads? (i.e., total reads Illumina; Ion; Don’t know remaining after filtering by platform’s software for quality or length issues) 22) For your lab, Paired-End (PE) reads are:

Survey return methods: (a) Send electronic copies to [email protected]; (b) Drop off paper copies at either A628 Life Science Annex or put in Scott Herke’s mailbox in 202 LSB. L S U G e n o m i c s F a c i l i t y ( C o l l e g e o f S c i e n c e ) S u r v e y 5 of 5 I don’t know what PE reads are! potentially useful in your research. For not useful or not cost-effective. application details, click on the links. Bacterial Genomics: bacterial used to make longer reads. identification (metagenomics) using used to make higher quality data. 16S rRNA sequencing. used for both length & data quality. Targeted RNA-Seq: Requires only 5 Other: . . ng of total RNA for AmpliSeq™ RNA sequencing of up to 1200 targets; ideal for fusion gene detection alone 23) The Genomics Facility (LSU) has an Ion or in combination with gene Torrent PGM (Personal Genome expression measurements and Machine). Mark which aspects of this mutation analysis. platform could aid your experiments. Ion Reporter™ Software: A secure, PGM runs can start the day after your hosted data analysis tool to simplify NGS library passes QC checks. informatics associated with routine Sequencing is completed in <8 hr. assays around DNA variation.

96 standard barcodes available; Ion AmpliSeq Designer™: Order Ion’s extended list has 384 barcodes. pre-made gene panels or create 314-v2 chip: typical yield = 300,000 custom gene panels to interrogate genomes with ultrahigh-multiplex PCR to 500,000 Final Library reads. primer pools (up to 6,144 primers per

316-v2 chip: typical yield = ~2-3 pool) designed for fast and simple million Final Library reads. production of thousands of targeted 318-v2 chip: typical yield = ~5-7 amplicons (from one to hundreds of million Final Library reads. genes). Requires only 10 ng DNA per up to 400-bp insert read lengths pool; application is FFPE-compatible; and barcoding allows combining up to from 314v2, 316v2, and 318v2 chips. 96 pools on a single PGM chip. New HiQ chemistry with improved Customizing AmpliSeq Designer™: accuracy and data output. Genome selection: (a) human and More accurate homopolymer calls mouse [standard]; (b) cow, chicken, with HiQ chemistry. pig, sheep, maize, rice, soybean, and Greater run configuration flexibility tomato [extended]; and, (c) user- with HiQ kit (sufficient reagents for a uploaded genomes [custom]. total of twelve 100 bp, eight 200 bp, or Torrent Variant Caller: Variant four 400 bp sequencing reactions on each detection optimized for Ion Torrent™ of the four PGM initializations provided sequencing data. in the kit). Questions 25-27 are related to 24) Here is a subset of special applications DNA/RNA/Protein assays. available for use with the Ion Torrent PGM. Mark those applications that are

Survey return methods: (a) Send electronic copies to [email protected]; (b) Drop off paper copies at either A628 Life Science Annex or put in Scott Herke’s mailbox in 202 LSB. L S U G e n o m i c s F a c i l i t y ( C o l l e g e o f S c i e n c e ) S u r v e y 6 of 5 25) The Genomics Facility has an Agilent E-Gel 48/96 sample agarose gels. Bioanalyzer. Currently, we stock the DNA None of the above (Comments?). HS chip; other Agilent assays exist. Select all assays of interest to you: 28) Please suggest additional supplies, DNA High Sensitivity kit. reagents/kits, instruments, or services DNA 1000 kit. that you would like to see the Genomics DNA 7500 kit. Facility (LSU) offer. DNA 12000 kit. I have no suggestions. RNA 6000 Nano kit. RNA 6000 Pico kit. .______. .______. small RNA kit. .______. Protein kits (80, 230, or 250). Cell kit (fluorescently labeled cells). Questions 29-32: Tell us about yourself.

None of the above (Comments?). 29) Where is your primary laboratory 26) The Genomics Facility has an Invitrogen located within the College of Science? Qubit 2.0. Currently, we stock the dsDNA Choppin Hall HS kit; other Qubit assays exist.

Select all assays of interest to you: Life Sciences (original or Annex). dsDNA High Sensitivity kit. Museum of Natural Science. dsDNA BR Assay kit. Other: . . 30) Total RNA. What is the classification of the head of your lab (i.e., the PI or major professor)

microRNA or small RNA. with respect to the College of Science: ssDNA/Oligo. Faculty. Protein. Adjunct Faculty. None of the above (Comments?). Other: . .

27) The Genomics Facility has an 31) What is your classification? Invitrogen E-gel™ unit: 10-15’ run Faculty. times; blue-light visualization with

SYBR-Safe dye. Currently, we stock Adjunct Faculty. SizeSelect™ Agarose Gels (2%) for NGS Staff. library size-selection. Student. Select all E-Gel Products of interest: Other: . . E-Gel SizeSelect™ agarose gels (pipette desired fragments directly from collection wells). 32) Members of the Dept. of Biological E-Gel EX agarose gels. Sciences who submit completed surveys E-Gel NGS agarose gels. (by noon, 02 Feb. 2015) are eligible for a E-Gel Clonewell agarose gels.

Survey return methods: (a) Send electronic copies to [email protected]; (b) Drop off paper copies at either A628 Life Science Annex or put in Scott Herke’s mailbox in 202 LSB. L S U G e n o m i c s F a c i l i t y ( C o l l e g e o f S c i e n c e ) S u r v e y 7 of 5 drawing for two prizes ($25 gift card; $15 a) Name: cash). Do you want to participate? b) Email: c) Phone: NO. I want to be anonymous. NO; however, to aid in assessing Departmental For more information, click on the Contact Us needs, I am providing some or all of my contact link on the facility’s website or visit A628 in information below. the Life Science Annex. YES (Name & Email Address are required). SPACE FOR ADDITIONAL COMMENTS:

Survey return methods: (a) Send electronic copies to [email protected]; (b) Drop off paper copies at either A628 Life Science Annex or put in Scott Herke’s mailbox in 202 LSB.