Project Inquiry Form | UPMC Genome Center

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Principle Investigator Information

Principle Investigator (PI) Name(Required)

First Last Suffix

Institution, Company, or Department(Required)

Have you submitted a project to the UGC in the past 12 months?(Required)

Yes

PI Email Address(Required)

PI Mailing Address

Street Address Address Line 2 City State ZIP Code

PI Phone

Project Contact Information

Enter general project communication and invoicing contact(s) here.

Contact person's name and role

Who in addition to the Principal Investigator should receive routine communications about this project?

First Last Role

Contact person's preferred contact method

Please enter email or phone number below

Do you have an additional contact person?

Yes

Second contact person's name and role

Who in addition to the Principal Investigator and first contact should receive routine communications about this project?

First Last Role

Second contact person's preferred contact method

Please enter email or phone number below

Is there a separate INVOICE contact for this project?(Required)

Quotes will be sent to all contacts. If the INVOICE should be sent to an additional finance contact, select YES here.

Yes

Who should receive the invoice for this project?

Email address for invoicing contact:

Sample Information

Estimated sample drop off date:

8:00am-3:00pm Mon-Fri (Excluding UPMC holidays)

Estimated sample drop off time:

8:00am-3:00pm Mon-Fri (Excluding UPMC holidays)

What type of samples do you have?(Required)

Library(ies) Unpooled

Library(ies) Pooled

Peripheral Blood

Saliva

DNA

RNA

cDNA

Buccal Swab

Buffy Coat

Cell Pellets/PBMC

Fresh/Frozen Tissue

FFPE Tissue

Airway Brush

Cystic Fluid

OTHER

Is this breast or other lipid-rich tissue?

Yes

How many total pools will be dropped off?

How many samples per pool?

How many total samples are in your project?

Sample disposition(Required)

When your project is completed, how should any remaining sample be handled?

We will retrieve our samples from the UGC within 30 days of receiving data

Discard any remaining sample(s)

Store our samples long term for an additional annual charge

Project Information

If you don't know or have requirements which are not listed, our team will contact you to discuss your needs.

Please select the funding source(s) for your project so that we can invoice you properly.(Required)

ITTC

IPM

UPMC Departmental Funding

Grant Funding (Univ Pittsburgh)

Grant Funding (Other Institution)

Private Funds

Is this project affiliated with UPMC Hillman Cancer Center?(Required)

Yes

Please briefly describe your project:

Are you repeating the exact parameters from a previously submitted project?(Required)

Yes

Enter the name of the previous project whose parameters you would like to repeat:(Required)

The project name is typically in the format "PI Last Name_####." Enter "I don't know" if you need assistance locating the project name.

What type of test do you need?(Required)

Whole Exome Sequencing

Whole Genome Sequencing

Single Cell RNA-seq

RNA-seq

Single Cell ATAC-seq

PGX

QC Only

Amplicon Sequencing

Other

Please create one submission form for each type of test needed.

What type of library preparation do you need?

Whole Exome

Whole Genome

mRNA

total RNA

Other or Don't Know

Which wet lab service(s) do you need?(Required)

DNA/RNA extraction, library preparation, sequencing and QC for all steps

Library preparation, sequencing, and QC for all steps

QC and Sequencing Only

QC Only

DNA/RNA Extraction and QC only

DNA/RNA Extraction, Library Preparation and QC Only

Library Preparation and QC only

Other or Don't Know

What type(s) of QC do you need?

Please select at most two options.

Fragment Size (Agilent Fragment Analyzer)

Concentration (Qubit)

Concentration (Synergy)

Concentration (Tecan)

Concentration (qPCR)

NA/None

Other or Don't Know

Enter the name of the kit used to prepare your library(ies) here.(Required)

Enter the manufacturer and name of your INDEX kit here(Required)

(ex: 10x Genomics Dual Index Kit TT, Set A; Agilent SureSelect XT Single Index; IDT for Illumina TruSeq DNA_RNA Dual Index) Index sequences will be collected in the sample submission sheet.

Describe any special sample handling or library prep requirements:

How many total reads (ex, 8 B) or what depth of coverage (ex, 100x) do you require?(Required)

Specify sequencing parameters (i.e. Read1/Index1/Index2/Read2) or required read length (i.e. 2x100 paired end reads):(Required)

NovaSeq flow cell requested

If unsure leave blank and our Project Team will work with you

SP (800 M reads)

S1 (1.6 B reads)

S2 (4.1 B reads)

S4 (10B Reads)

MiSeq V3-600 (25 M reads)

Other

Number of Cycles

100

200

300

Other

Please specify if you need PhiX >1% (default), custom primers, or other special sequencing requirements:

Data Return and Bioinformatics Analysis

How do you want to receive your data?(Required)

Download Links or QC Report emailed to Project Investigator and Project Contact

Data transferred to AWS S3 Bucket

Other

S3 Bucket Path:

Which file type(s) do you require?(Required)

BCL (raw sequencing data)

fastq (from bcl2fastq)

fastq (from cellranger mkfastq)

Other or QC Only

What additional bioinformatics analysis do you need?(Required)

None

Germline Variant Calling (WGSg/WESg) - (Reference genome mapping, SNV/InDel variant calling; return fastq, bam, vcf files, Alignment and variant metrics)

Somatic Variant Calling (WGS/WES) - Reference genome mapping, SNV / InDel germline variant calling, somatic variant calling; return fastq, bam, vcf files (germline and somatic vcfs , Alignment and variant metrics)

CNV calling, tumor purity for WGSs - CNV calling and tumor purity estimation.

RNAseq Feature Count Analysis - (Raw sequence QC/Trimming adapters, mapping, count estimation/normalization; return fastq, trimmed fastq, bam, outputs numbers of reads assigned to features/gene)

RNAseq Feature Count and Variant Calling - RNAseq feature count analysis+variant calling; return fastq, trimmed fastq, bam, outputs numbers of reads assigned to features/gene, vcf file

RNAseq Differential Gene expression - RNAseq feature count + differential gene expression by Deseq2; returns fastq, trimmed fastq, bam, outputs numbers of reads assigned to features/gene, DGE result table and related plots.

scRNAseq 10X Genomics Cellranger Count Analysis (cellranger mkfastq + cellranger count ; return fastq, bam, gene-barcode matrix, metrics summary, cloupe file)

scRNAseq 10X Genomics Cellranger demultiplexing (Cellranger mkfastq ; return fastq )

Other

Which file type(s) do you require?

.CEL file

.VCF file

Other

What is the organism and version/build of your desired reference genome?(Required)

Project Submission

Please enter any additional comments or questions here:

NOTE: Please follow the link to complete our NEW sample submission sheet. Old versions are no longer compatible with our lab software. Thank you!

Sample Submission Sheet Upload(Required)

Accepted file types: xlsx, Max. file size: 40 MB.

You can download the sample submission form here https://upmcgenomecenter.com/wp-content/uploads/2023/06/SS-Version-7.xlsx and upload it here when you finish.

Additional Files

If you have other files related to the project such as a pooling sheet, plate map, index information, protocols etc., please upload it here.

Drop files here or

Max. file size: 40 MB.

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First Choice

Second Choice

Third Choice

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First Choice

Second Choice

Third Choice

Project Submission Form

Project Submission Form

Principle Investigator Information

Project Contact Information

Sample Information

Project Information

Data Return and Bioinformatics Analysis

Project Submission