User Information

User Guide

1. Register your samples and payment information on iLAB.

2. Login with your Cedars-Sinai webmail username and password.  Register samples for each new service (please note there is a surcharge for external users).

3. Bring your samples to the Genomics Core.

  • Generally, 2 micrograms of RNA or DNA (depending on the assay of interest), at concentration of ~100 nanograms/microliter. We will assess the quality of your samples.
  • For samples that meet our quality control standards, the appropriate reagents will be ordered.

3. Login to iLAB to retrieve data.

Acknowledging Our Contribution

Please do remember us when you are preparing scholarly reports, presentations, posters, papers and all other publications. All work performed in any Cedars-Sinai institutional shared facilities should be acknowledged. Authorship and acknowledgment are important metrics that our success is measured by. Proper acknowledgment of core facilities enables us to obtain financial and other support, so that we may continue to provide essential services in the best ways possible.

Core facility personnel are scientists. When we make an intellectual and/or experimental contribution to a publication, or the work carried out has been significantly more than would normally be expected, you might consider naming that core staff in the acknowledgment or adding that individual as a co-author on the paper. Of course, it's up to you to decide authorship and/or acknowledgment.

As a courtesy, we offer read alignment for RNA-Seq services for free in human/mouse samples. Please use the following example description in your manuscript:

Library preparation and sequencing

Library construction was performed using the Illumina TruSeq Stranded mRNA library preparation kit. Briefly, Total RNA samples were assessed for concentration using the Nanodrop 8000 (Thermo Scientific) and quality using the 2100 Bioanalyzer (Agilent). One microgram of total RNA per sample was used for poly-A mRNA selection using streptavidin-coated magnetic beads. cDNA was synthesized from enriched and fragmented RNA using reverse transcriptase (Super-Script II, Invitrogen) and random primers. The cDNA was further converted into double-stranded DNA, and the resulting dsDNA was enriched with PCR for library preparation. The PCR-amplified library was purified using Agencourt AMPure XP beads (Beckman Coulter Genomics). The concentration of the amplified library was measured with a NanoDrop spectrophotometer and an aliquot of the library is resolved on an Agilent 2100 TapeStation. Sample libraries are multiplexed and sequenced on a NextSeq 500 platform (Illumina) using 75bp single-end sequencing. On average, about 20 million reads were generated from each sample.

Data analysis

Raw reads obtained from RNA-Seq are aligned to the transcriptome using Bowtie (version 1.1.1) (Langmead B et al., 2009) / RSEM (version 1.2.20) (Li B and Dewey CN, 2011) with default parameters, using a custom human GRCh38 (or mouse CRCm38) transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 23 (or Mouse GENCODE M3) annotation. Expression counts for each gene (TPM: transcripts per million or FPKM: Fragments Per Kilobase of transcript per Million) in all samples were normalized by the sequencing depth.

References

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009 10:R25.

Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011 4;12:323.