Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M.
PLoS Computational Biology. 2011 Nov;7(11):
modMine: flexible access to modENCODE data.
Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, Kephart ET, Lloyd P, Stinson EO, Washington NL, Perry MD, Ruzanov P, Zha Z, Lewis SE, Stein LD, Micklem G.
Nucleic Acids Research. 2011 Nov 12
These two tables provide estimated expression levels for annotated genes and exons, using signals from Affymetrix Drosophila tiling arrays. The arrays were hybridized with total RNAs extracted from 25 cell lines and 30 developmental stages.
Drosophila_Cell_Lines_and_Developmental_Stages_Exon_Scores.txt
Drosophila_Cell_Lines_and_Developmental_Stages_Gene_Scores.txt
For more information, please see http://www.modencode.org/docs/flyscores.
The tables were compiled by the Bloomington group in the fly transcriptome project of modENCODE (Celniker, PI).
New documentation on the use of modMine is now available from the drop down menu of our blog.
Under the tag modMine you can find a general overview followed by an introductory video and a general help page with more detailed subsections devoted to the analysis of fly and worm data.
modMine release 15
New full release with 770 submissions. 568 concern fly, 202 worm.
This release contains a snapshot of all fly and worm data for analysis (data analysis freeze).
Please note that the submissions for fly of the Henikoff group have been updated respect release 14. The update has increased the number of submissions by 8.
A set of fly data has been frozen for analysis. It comprises 560 submissions and bulk downloads of the data are available from the Download Site.
The modMine data warehouse will be available shortly.
As per the (September) monthly conference call, C. elegans groups will be required to submit their data sets to the DCC by October 15th for the November 1st data freeze. These data sets should include proper metadata, and any next-gen sequences (in FASTQ or SFF format) should be submitted to GEO/SRA ASAP.
This week we’ve released 1 D. melanogaster data sets:
White – 1 ChIP-chip data sets
on the following kinds of samples:
antibodys: h3k9ac, no antibody control
stage: pupal stage
strain: y; cn bw sp
tissue: whole organism
Read more…
This week we’ve released 1 D. melanogaster data sets:
Celniker – 1 Computational annotation data sets
Read more…
This week we’ve released 5 D. melanogaster data sets:
Celniker – 5 RNA tiling array data sets
on the following kinds of samples:
cell lines: CME W1 Cl.8+, ML-DmBG3-c2, S2-DRSC
stages: late embryonic stage, third instar larval stage
tissues: cns-derived cell-line, dorsal mesothoracic disc, embryo-derived cell-line
Read more…
This week we’ve released 5 D. melanogaster data sets:
MacAlpine – 4 RNA tiling array data sets
White – 1 ChIP-chip data sets
on the following kinds of samples:
antibodys: h3k27me3, no antibody control
cell line: S2-DRSC
stages: cleavage stage, early extended germ band stage, embryonic stage, embryonic stage 1, embryonic stage 2, embryonic stage 3, third instar larval stage
strains: Oregon-R-modENCODE, Oregon-R_Orr-Weaver, w[1118], y; cn bw sp
tissues: embryo-derived cell-line, larval salivary gland, oocyte associated follicle cell, whole organism
Read more…