Inter-Lab Project Submission Form Please complete the sample submission sheet and the form below. Upon submission, you can drop off the samples to us at scheduled time. If you have any questions or concerns regarding this form please email Genome_Center_PM@upmc.edu or call 412-623-7155. Inter-lab Submission Form For laboratory staff use only Step 1 of 6 16% Submitting Lab InformationCore Lab Name(Required) Form Completed By:(Required) Principle Investigator InformationPrinciple Investigator (PI) Name(Required) First Last Suffix PI Email Address(Required) Project Contact InformationEnter general project communication and invoicing contact(s) here.Contact person's name and roleWho in addition to the Principal Investigator should receive routine communications about this project? First Last Role Contact person's preferred contact methodPlease enter email or phone number below Who should receive the invoice for this project? Email address for invoicing contact: Sample InformationEstimated sample drop off date: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 DNA RNA cDNA OTHER 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? PI will retrieve samples from the UGC within 30 days of receiving data Discard any remaining sample(s) Store samples long term for an additional annual charge Project InformationWhat type of test do you need?(Required)Please select at most two options. Whole Exome Sequencing Whole Genome Sequencing Single Cell RNA-Seq RNA-seq Single Cell ATAC-Seq PGX QC Only Amplicon Sequencing Other or Don't Know 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) QC and Sequencing Only DNA/RNA extraction, library preparation, sequencing and QC for all steps Library preparation, sequencing, and QC for all steps 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. UGC to determine 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), reads per sample, or 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 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 AnalysisHow should data be returned?(Required) Download Links emailed to Project Investigator and Project Contact Data transferred to AWS S3 Bucket Other S3 Bucket Path: Which file type(s) are required? BCL (raw sequencing data) fastq (from bcl2fastq) fastq (from cellranger mkfastq) Other What additional bioinformatics analysis is 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 What is the organism and version/build of the desired reference genome? Project SubmissionPlease 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: 32 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 FilesIf 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 Select files Max. file size: 32 MB.