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.
Nucleic Acids Res. 2009 Dec 4. [Epub ahead of print]
Ooi SL, Henikoff JG, Henikoff S.
PMID: 19966274
Curr Biol. 2009 Nov 17;19(21):1777-87. Epub 2009 Oct 22.
Ercan S, Dick LL, Lieb JD.
PMID: 19853451
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.
As per the (September) monthly conference call, Drosophila groups will be required to submit their data sets to the DCC by September 15th for the October 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 24 C. elegans data sets:
Lieb – 7 ChIP-chip data sets
Waterston – 17 RNA tiling array data sets
on the following kinds of samples:
antibodies: dpy-27, no antibody control, rna polii ctd domain unphosophorylated, sdc-2, sdc-3, trimethylated lys-9 on histone h3
stages: blastula embryo, elongating embryo, embryo, enclosing embryo, fully-elongated embryo, gastrulating embryo, l1 larva, l2 larva, l3 larva, l4 larva, l4 larva male, late cleavage stage embryo, newly molted young adult hermaphrodite
strains: 11dh, CB4689, JK1107, N2, YPT41, YPT47
tissues: hermaphrodite gonad, whole organism
Read more…
This week we’ve released 2 C. elegans data sets:
Lieb – 2 ChIP-chip data sets
on the following kinds of samples:
antibodies: dpy-27, no antibody control, rna polii ctd domain unphosophorylated
stage: l4 larva
strain: N2
tissue: whole organism
Read more…
This week we’ve released 7 C. elegans data sets:
Waterston – 7 RNA-seq data sets
on the following kinds of samples:
stages: adult male, embryo, l1 larva, l2 larva, l3 larva, l4 larva, newly molted young adult hermaphrodite
strains: CB4689, N2
tissue: whole organism
This week we’ve released 4 C. elegans data sets:
Lieb – 4 ChIP-chip data sets
on the following kinds of samples:
antibodys: dpy-27, htz-1, no antibody control, rna polii ctd domain unphosophorylated, sdc-3
stage: embryo
strain: N2
tissue: whole organism
This week we’ve released 7 C. elegans data sets:
Snyder – 7 ChIP-seq data sets
on the following kinds of samples:
antibodys: daf-16, pha-4, RNA pol II
stages: embryo, l1 larva, l4 larva, l4-adult molt, newly molted young adult hermaphrodite
strains: OP37, TJ356
tissue: whole organism
Read more…
This week we’ve released 8 C. elegans data sets:
Lieb – 3 ChIP-chip data sets
Snyder – 5 ChIP-seq data sets
on the following kinds of samples:
antibodies: ama-1, dpy-27, mab-5, pha-4, sdc-3, RNA Polymerase II
stages: embryo, l3 larva, l4 larva, l4-adult molt, newly molted young adult hermaphrodite
strains: N2, OP26, OP34, OP37
tissue: whole organism