GSC Sample Submission Form
Date:
Your Name
Your email:
Lab Name:
Lab Address (Include Mail Stop):
Lab Phone Number:
Complete the following questionnaire for each sample you are submitting:
Sample Name (as labeled):
Organism, cell type and origin (indicate genus and species names, whether DNA is derived from tissue or cell
culture and whether DNA is plasmid, chromosomal or mitochondrial):
Identification of reference sequence (if it exists, e.g. Aspergillus niger NCBI AM270983). Please provide a 1-2
Mb file in a cd containing the sequence of the reference genome:
How was the DNA extracted?
Is the sample a product of whole genome amplification or other amplification techniques?
DNA Concentration:
Total Volume:
Solvent type:
If sample is barcoded, or has been adaptor-ligated at any time, please 1) indicate the barcode sequence and 2)
indicate how the sample was processed down-stream of the ligation:
Please indicate which lane on supporting gel image represents this sample.
On which platform do you wish to have this sample sequenced?
How many regions of the slide or plate do you wish to occupy with this sample?*
If providing library ready for ePCR:
1) Provide a brief overview of the library sample preparation
2) Inform origin of adaptors used for making libraries (e.g. IDT HPLC purified oligo-duplexes)
3) If barcoding libraries, inform sequence and barcode series used for preparing each library submitted for
sequencing (e.g. barcodes 1-4 serie B20 ATGTGCGGCCA). In order to obtain color balance during sequencing
we recommend design experiments to use as few as 4 barcodes, as long as at least one of the full sets of four
barcodes are used: barcodes 1-4, 5-8, 9-12, 13-16, and 17-20 for series B20 (fragment library), or all 10
barcodes for serie A10 (Srek kit).
4) If available, provide an Agilent Bioanalyzer file describing the libraries submitted.
Before submitting your sample, please confirm that:
1. Your sample has the minimum amount of DNA/RNA for sample preparation.
Pourmand Lab
831.459.4382
University of California, Santa Cruz
Baskin Engineering, 210
.
2. Your sample is in TE buffer (e.g., Qiagen EB) with a minimal concentration of 50 ng/ uL(DNA) or
5ng/ul (libraries).
3. Your sample does not contain single stranded DNA or RNA for preparing fragment and mate-paired
libraries.
4. Your sample does not contain particulate matter, organic solvents, salts or proteins.
5. DNA is intact and not degraded (fragments greater than 1.5 kb). It is mandatory that all customers
submit a well-labeled gel image showing the relative integrity and concentration of each sample.
6. If submitting a reference sequence, please do so in a fast.a format (s) (1 to 3 Mb).
7. If submitting more than one sample for sample preparation, please inform name, DNA concentration,
and total volume of individual samples. A minimum of 5 ug of DNA is recommended for preparing
fragment libraries, and 30 ug for mate-pair libraries (less complex genomes). Please consult with
Pourmand Lab about sample concentration if necessary.
8. If submitting more than one barcoded library for sequencing please inform: barcode set used (10
barcodes SREK kit, 16A Multiplexing Set or 20B Multiplexing Set); Assign library ID to each barcode
used for preparing the library; and specify the number of bases for sequencing Tag F3 (5, 10, 15, 20, 25,
30, 35, 40, 45 or 50 bases).
*454 Customers: The PTP can be divided up into 2, 4, 8 or 16 regions. For unamplified, whole genome
shotgun libraries, we hope to meet the following expectations:
 2-region: 180-280 M bases/ region, 450-650 K reads/ region
 4-region: 60-110 M bases/ region, 160-250 K reads/ region
 8-region: 30-55 M bases/ region, 80-120 K reads/ region
 16-region: 10-20 M bases/ region, 25-40 K reads/ region
Pourmand Lab
831.459.4382
University of California, Santa Cruz
Baskin Engineering, 210
.