The following is important information for those who are interested in using our Illumina sequencer system:
Samples (cDNA or DNA) and libraries can be dropped off on the top shelf of in the freezer closest to the door in Krk 108. Please fill out the online sample submission form before dropping off your sample.
Samples for RNAseq should be dropped off on the middle shelf of the freezer by the chemical hood in Ker108 before 2pm. Please email Vijaya Kumar ( firstname.lastname@example.org ) before you drop your samples off.
Please fill out a seperate sample form for every sample tube you drop off. Igor Antoshechkin ( email@example.com ) will be happy to help you if you have any questions about any of the fields.
Contact Name/Email: Feel free to include multiple names and email addresses; relevent autogenerated emails will be sent to all people listed. It's often helpful to include the person who will be handling the data, as well as the person who built the samples (if they're different people). Indicating which is which is even more helpful.
Sample Name: Names should be detailed. Good names include "Ap1-3d-2 mRNA from Ap1 domain of floral meristems, 3day", "HNDHT 4H8 hnd-1 strain HT115 fed 4H8 2% fix plate", and "TCR alpha -/- ThyDP 7/21/9 Input". Poor names include "Input 6/10/6" and "bag1 sup". Please remember we have over a thousand libraries, so any short name you can think of has probably already been used.
Sample Concentration: The nanodrop is noticably unreliable at measuring dsDNA concentration (and entirely useless at <5ng/ul). We've found fluorometer measurements to be far more consistant. Sequencer users are welcome to use the GEC's qubit fluorometer: it needs only 1ul of sample, and uses premixed standards. Please email or stop by to learn to use it. If the nanodrop is your only source of measurement, we strongly recommended you bring us at least twice as much starting material as you think we need.
Please note the measuring method on the sample form next to the concentration.
Sample Volume: Please provide your samples in no more than 50ul of buffer/water.
Species: Make sure to note the species you want us to align data to, if different than the actual sample species.
Desired Gel Cut Size: ChIPseq libraries are usually cut at 250-350bp, and RNAseq libraries are usually cut around 300-350bp. Note that these sizes are including the adaptors, so the size of your insert will be 100-150bp smaller than the cut size. Genomic libraries are usually cut higher, but it varies. If you're not sure, you can request additional slices to be frozen and saved, in case your preferred size doesn't turn out well. Please note which size is your preferred size! If you are dropping off a completed library, you MUST still fill out this field! We can't load your library on a flowcell without knowing what physical size your library is.
Note: If you're dropping off a control or experimental sample that is going to be matched against an experimental or control built at a different time, please note that so we can try to limit protocol differences between them.
- There is no strict lower bound on the amount of sample that can be successfully built into a library; we have had success with two rounds of PCR on less than 1ng of starting ChIPseq DNA, and one round of PCR on only 30ng of unfragmented genomic DNA (although it was obviously very low complexity). However, the library building process is much more reliable with more starting material. The ideal amount of sample varies depending on its type and the desired protocol:
2ug of unfragmented DNA, to account for the significant sample loss during fragmentation
1ug of fragmented DNA, the "ideal" starting amount according to Illumina
100ng RNAseq cDNA
at least 1ug of DNase-treated total RNA for RNAseq libraries
100ng ChIPseq/Input DNA, for best results
As much ChIPseq DNA as possible, for low-yield ChIPseqs
An automated email will be sent when your library is run on a flowcell. This email will list the library names and IDs that were run, and will include a URL that will contain the flowcell data after the run finishes. Note that as space fills up, older runs are archived, so after a few weeks, your data may no longer be at that location. Usually data for the most recent handful of flowcells can be found at runfolders.
You can access this searchable list of all created libraries; in addition to library names and IDs, you can see summary results of every time that a given library has been sequenced.
If you have unanswered questions about your samples or the sequencer, please email Igor Antoshechkin ( firstname.lastname@example.org ).