A Next-Generation Sequencing Core Facility DNA and RNA sequencing capabilities of

Denny Porter, Director Steven Coon, Staff Scientist Alan Pang, Lab Supervisor James Iben, Bioinformatics

ABI SOLiD 5500xl

 Whole exome (PDEGEN)  Targeted exome (PRAE)  RNA-Seq (PDEGEN, PGD)  Microbiome (PDEGEN, PRAE)  Methylome (PGD)  microRNA-Seq (PDEGEN)  Ribosomal profiling (PGD)  ChIP-Seq (PGD)

 2 FlowChips, 6 lanes each  Up to 1.8 billion fragments per run  Up to 200 Gigabases per run

For example: Target 150 genes covering 500,000 bases Barcode and run 96 samples on one lane Expected average coverage is >150-fold For example: RNA-Seq Barcode and run 3 samples on one lane Average >40 million read pairs per sample

 Fee for service – pay per sample & per lane  Reagent costs only  Includes significant bioinformatics support

 All MGL sequencing projects  Maraia (PGD) – RNA-Seq, WGS, codon bias  Clark (PGD) – ChIP-Seq  Crouch (PGD) – WGS & assembly  Kino (PRAE) - WES  Levin (PCRM) - Integration analysis  Ozato (PGD) - ChIP-seq  Weinstein (PGD) – Methylome, WGS, WES  Hinnebusch (PCRM) - Ribosome profiling, ChIP- Seq  Porter (PDEGEN) – RNA-Seq, WES, microbiome  Stratakis (PDEGEN) – WES, WGS  Bailey-Wilson [NHGRI] - Recalling & mining of variant data

Application process (8-member committee)  * Number of Applications: 18 (18 PIs)  * Number of Programs: 7  (PDEGEN[5], PGD[5], OSD[3], PRAE[1], MMP[1], PDN[1], PPD[1])  * Sequencing types: 7  (RNA-Seq alone[8], microRNA-Seq[3], whole exome[3], RNA-Seq + ribosomal profiling[1], RNA-Seq + ChIP-Seq[1], bisulfite sequencing (RRBS)[1], microbiome[1]  * Total funding requested: $346,000  * Number of Applications Funded: 9 (9 PIs; 4 Programs)  * Sequencing types: 6  * Total subsidized: $150,000

Meetings: 3 rd Wednesday of the month from 12:00-1:00 in Bldg 10/Rm

Website: mgl.nichd.nih.gov List serv: MGL-USERS-L Phone: Walk-in: Bldg 10/Rm 9D41