Lab Logo
people  |  projects  |  pictures  |  publications  |  protocols  |  places  |  play

Access to lab protocols:

 

Fulcrum Read Collapser "Leveraging the computer power you have into the results you need"

Our Lab has developed a pipeline to collapse near-duplicate reads resulting from Ultra Hight Throughput Sequencing (UHTS), specifically Illumina and 454. The pipeline uses the Parallel Python module to spread work across processors or networked computers, and uses MapReduce to allow processing of even larger datasets. Included in this archive are detailed manuals and several helper scripts.

fulcrum_v_042 (.zip)

http://www.ncbi.nlm.nih.gov/pubmed/22419786

Updated, Oct. 2012: We have updated fulcrum to be compatible with the new Illumina fastq output.

I have added a new option to linenumfast05.py. -n [int] Length of longest read. Default is 101-bp. If you are using shorter, just change it AND change the variable MAX_LENGTH at the top of parallel05.py. Finally, if you are using something besides FASTQ 1.8+, change the OFFSET value in parallel05.py from 33 to 64.

fulcrum_v_043 (.zip)

Identification and Optimization of qPCR Standards for Aiptasia pallida --June, 2012: (.pdf)

Table of antibodies tested by the Pringle Lab

Perez Anitbodies Table for download (.xls)

Expand: Table of Antibodies Tested by the Pringle Lab

Antibody Name
Immunogen
Applications (IHC, WB)
Successful?
Notes
Tested by
Supplier
Catalog Number
anti-histone H2A
Histone H2A (Human)
IHC of whole mounts and sections
Yes
Rabbit polyclonal; good for staining Aiptasia nuclei specifically; used at 1:500
Santiago Perez
Abcam
ab58550
anti-Histone H3 (phospho T3)
Histone H3 phosphorylated at T3 (S. cerevisiae)
IHC whole mounts and sections
Yes
Rabbit polyclonal, Stains mitotic chromatic of Aiptasia really well, very little background; used at 1:500 in IHC
Santiago Perez
Abcam
ab17352
anti-phospho-Histone H3 (Ser 10)
Histone H3 phosphorylated at Ser10 (Human)
IHC of whole mounts and sections
Yes
Rabbit polyclonal, Stains mitotic chromatic of Aiptasia very well with very little background; used at 1:500 in IHC
Santiago Perez
Millipore
06-570
anti-Ki67
Ki67 (Human)
IHC of sections
No
Rabbit monoclonal; tested to label proliferating cells; tested at 1:100; 1:500
Santiago Perez
Thermo Scientific
RM-9106
anti-YOL1/34
Tubulin (S. cerevisiae)
IHC of whole mounts, WB
Yes
Rat monoclonal; stains mitotic spindle; used at 1:500; band at 51 kD in WB
Santiago Perez, Liz Hambleton
Abcam
ab6161
anti-Actin, clone C4
Actin (Chicken)
IHC of whole mounts and sections, WB of Aiptasia protein extract
Yes
Mouse monoclonal, band at 42 kD in WB of Aiptasia protein; used at 1:500 in IHC
Santiago Perez, Liz Hambleton
Millipore
MAB1501
anti-coracle
Coracle (Drosophila)
IHC of whole mounts
No
Mouse monoclonal against a component of septate junctions, tested to delineate Aiptasia cell-perimeter (obtained from Dr. Richard G. Fehon of U. of Chicage, Dept. of Mol. Gen. and Cell Bio.);  tested at 1:50, 1:100, 1:500
Santiago Perez
Developmental Studies Hybridoma Bank

C566.9

and C615.16
anti-E-Cadherin
epithelial cadherin (Mouse)
IHC of whole mounts
No
Rat monoclonal; tested as a marker of cell perimeter (usuccessfully); tested at 1:50, 1:100, 1:500
Santiago Perez
Zymed (Invitrogen)
13-1800
anti-LC3
Residues 25-121of the human Microtuble-associated protein light chain 3 (LC3) protein sequence
WB
Yes
Rabbit polyclonal, band at 14 kD in WB of Aiptasia protein
Tamaki Bieri
Novus Biologicals
NB100-2331
gp62ap
recombinant portion of Aiptasia C3
IHC of whole mounts
Yes
Custom antibody, guinea pig polyclonal, affinity purified by Liz Hambleton; successful in whole mount IHC
Liz Hambleton
Cocalico Biologicals
-
gp64ap
recombinant portion of Aiptasia C3
IHC of whole mounts
Yes
Custom antibody, guinea pig polyclonal, affinity purified by Liz Hambleton; successful in whole mount IHC
Liz Hambleton
Cocalico Biologicals
-
gp65ap
recombinant portion of Aiptasia C3
IHC of whole mounts
Yes
Custom antibody, guinea pig polyclonal, affinity purified by Liz Hambleton; successful in whole mount IHC
Liz Hambleton
Cocalico Biologicals
-
anti-C3 
internal portion of human C3
WB
No
Goat polyclonal; successful in WB of mouse serum, but not with Aiptasia protein extract
Liz Hambleton
Santa Cruz Biotech
sc-14613