modENCODE Blog

Antibodies against 69 C. elegans chromosomal proteins
from the Lieb modENCODE Project are now commercially available:

Below is the list of antibodies that can be purchased through SDIX’s
pre-made antibody distributor, Novus Biologicals. These rabbit polyclonal antibodies have been affinity-purified.

Alphabetical list (multiple antibodies are available for
most of these targets):

AMA-1, BAF-1, BLMP-1, CAPG-1, CAPH-2, CHD-3, COH-1, COH-3, DPL-1,
DPY-21, DPY-28, DPY-30, EFL-1, EPC-1, GAK-1, GFL-1, HCP-3, HDA-1,
HIM-17, HIM-5, HIM-8, HIS-24, HMG-3, HPL-2, JMJD-2, KLE-2, KNL-2,
LEM-2, LET-418, LEX-1, LIN-13, LIN-15B, LIN-35, LIN-37, LIN-53,
LIN-54, LIN-61, LMN-1, MES-3, MES-4, MET-1, MIS-12, MRG-1, MSH-5,
MTF-1, MYS-3, MYS-4, NASP-1, NDC-80, NPP-13, NPP-16, NPP-9, ODD-3,
RAD-51, RBA-1, REC-8, RSD-6, SCC-1, SCC-3, SDC-2, SET-2, SUN-1,
T26A5.5, TAG-192, TBP-1, TSN-1, WAPL-1, Y55F3AM.14, ZFP-1

These antibodies are being used for chromatin immunoprecipitations
(ChIP) as part of the modENCODE (Model Organism Encyclopedia of DNA
Elements) project.

A URL link for further ordering information:

http://www.sdix.com/Special-Landing-Pages/celegans.aspx

Contact information for the company:

SDIX
Strategic Diagnostics Inc.
111 Pencader Drive
Newark DE
19702-3322 USA

www.sdix.com

Tel: (302) 456-6789
Fax: (302) 456-6782
Sales: (800) 544-8881

modMine release 21

Release 21 of modMine contains the same data of release 20, with the addition of the data concerning the hierarchical view of the Drosophila Regulatory Network (see “Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE”, 2010, Science 330: 1787-1797).

New in this release:

• Network displayer for the Drosophila Regulatory Network, where you explore the network and access reports on all the genes involved.
• An improved front page.

This February Data Coordination Center for modENCODE starts having regular User Group webinars using WebEx teleconference services. The goal of these webinars is to provide better understanding and facilitate analyses of the data generated by modENCODE project. The updated schedule is going to be available at DCC Wiki (people outside modENCODE project may use anonymous login to view the page). Webinars are run between 12 and 1pm every first Thursday of the month, with the first webinar ‘Understanding worm and fly chromatin modification data‘ scheduled for February 3rd. Gary Karpen and researchers from Jason Lieb’s group will be available for questions. This online webinar will introduce participants to the chromatin IP data, and describe how to visualize and download it from the modENCODE web site. Space is limited so advance registration is necessary. Please email help@modencode.org to reserve your spot. Instruction on how to log in to WebEx conference and dial-in information for audio part are provided along with the schedule.

The following modENCODE publications were published online on December 22, 2010 (the two integrative analysis papers are in the Dec. 24th issue of Science).

Gerstein MB et al., Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. (2010) Science 330: 1775-1787. Published online 22 December 2010 [DOI:10.1126/science.1196914]

The modENCODE Consortium et al., Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. (2010) Science 330: 1787-1797. Published online 22 December 2010 [DOI:10.1126/science.1198374]

Allen MA, Hillier LW, Waterston RH, Blumenthal T.  A global analysis of C. elegans trans-splicing. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.113811.110

Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, et al. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res. gr.116657.110; Published in Advance December 22, 2010, doi:10.1101/gr.116657.110

Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, et al. The transcriptional diversity of 25 drosophila cell lines. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.112961.110

Chung W, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS, Lai EC. Computational and experimental identification of mirtrons in Drosophila melanogaster and caenorhabditis elegans. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.113050.110

Eaton ML, Prinz JA, MacAlpine HK, Tretyakov G, Kharchenko PV, MacAlpine DM. Chromatin signatures of the drosophila replication program. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.116038.110

Ercan S, Lubling Y, Segal E, Lieb JD. High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.115931.110

Graveley BR, et al., The developmental transcriptome of Drosophila melanogaster. (2010) Nature DOI: doi:10.1038/nature09715 Published online 22 December 2010

Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.112466.110

Kharchenko PV, et al., Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. (2010) Nature DOI: doi:10.1038/nature09725 Published online 22 December 2010

Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I, Cheung M, Ercan S, Ikegami K, Jensen M, Kolasinska-Zwierz P, et al. Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.115519.110

Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, et al. Prediction and characterization of non-coding RNAs in C. elegans by integrating conservation, secondary structure and high throughput sequencing and array data. Genome Res. gr.110189.110; Published in Advance December 22, 2010, doi:10.1101/gr.110189.110

Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, et al. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.114587.110

Nordman J, Li S, Eng T, MacAlpine D, Orr-Weaver TL. Developmental control of the DNA replication and transcription programs. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.114611.110

Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, et al. Plasticity in patterns of histone modifications and chromosomal proteins in drosophila heterochromatin. Genome Res. gr.110098.110; Published in Advance December 22, 2010, doi:10.1101/gr.110098.110

Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen SC, Sreedharan VT, Widmer C, Jo J, et al. A spatial and temporal map of C. elegans gene expression. Genome Res. gr.114595.110; Published in Advance December 22, 2010, doi:10.1101/gr.114595.110