modENCODE Blog » Henikoff http://blog.modencode.org weblog of the modENCODE Data Coordination Center Wed, 01 Feb 2012 16:46:47 +0000 http://wordpress.org/?v=2.8.1 en hourly 1 Recent publications http://blog.modencode.org/recent-publications http://blog.modencode.org/recent-publications#comments Thu, 10 Dec 2009 11:04:05 +0000 sergio http://blog.modencode.org/?p=479 A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans.

Nucleic Acids Res. 2009 Dec 4. [Epub ahead of print]
Ooi SL, Henikoff JG, Henikoff S.
PMID: 19966274

The C. elegans dosage compensation complex propagates dynamically and independently of X chromosome sequence.

Curr Biol. 2009 Nov 17;19(21):1777-87. Epub 2009 Oct 22.
Ercan S, Dick LL, Lieb JD.
PMID: 19853451

]]> http://blog.modencode.org/recent-publications/feed 0 D. melanogaster Data Release Report for 6/15-6/21, 2009 http://blog.modencode.org/d-melanogaster-data-release-report-for-615-621-2009 http://blog.modencode.org/d-melanogaster-data-release-report-for-615-621-2009#comments Mon, 22 Jun 2009 19:07:23 +0000 nicole http://blog.modencode.org/?p=257 This week we’ve released 3 D. melanogaster data sets:
Henikoff – 1 RNA tiling array data sets
Lai – 2 RNA-seq data sets
on the following kinds of samples:

cell lines: S2, S2-DRSC
stages: adult stage, late embryonic stage
strain: Canton-S
tissues: abdomen, embryo-derived cell-line, imaginal disc, thorax, whole organism

Here’s the breakdown by project:

Henikoff Project

Data Type Experiment type Details Links Comments
transcriptional fragments (GFF), transcriptional signals (WIG) RNA tiling array Tissues: embryo-derived cell-line
Lines: S2, S2-DRSC

Stages: late embryonic stage

Embargoed until 9 months from 2009-06-08

 ChadoXML | Tracks | Stanza | Raw Data details…

Lai Project

Data Type Experiment type Details Links Comments
alignments (SAM) RNA-seq Tissues: whole organism, imaginal disc
Strains: Canton-S
Stages: adult stage

Embargoed until 9 months from 2008-09-19

 ChadoXML | Tracks | Stanza | Raw Data details…

small RNAs, single read alignments, no repeat masking,some sequences align to >>1 genomic location
alignments (SAM) RNA-seq Tissues: whole organism, abdomen, thorax
Strains: Canton-S
Stages: adult stage

Embargoed until 9 months from 2008-09-19

 ChadoXML | Tracks | Stanza | Raw Data details…

small RNAs, single read alignments, no repeat masking,some sequences align to >>1 genomic location
]]> http://blog.modencode.org/d-melanogaster-data-release-report-for-615-621-2009/feed 0 D. melanogaster Data Release Report for 4/27-5/3, 2009 http://blog.modencode.org/d-melanogaster-data-release-report-for-427-53-2009 http://blog.modencode.org/d-melanogaster-data-release-report-for-427-53-2009#comments Mon, 04 May 2009 18:04:02 +0000 nicole http://blog.modencode.org/?p=225 This week we’ve released 6 D. melanogaster data sets:
Celniker – 5 RNA tiling array data sets
Henikoff – 1 RNA tiling array data sets
on the following kinds of samples:

cell lines: S2, S2-DRSC
stages: embryonic stage, embryonic stage 5, embryonic stage 6, embryonic stage 7, embryonic stage 8, late embryonic stage, pharate adult stage, pharate adult stage p15, pharate adult stage p15(i), pharate adult stage p9, prepupal stage, prepupal stage p4, prepupal stage p4(i), prepupal stage p4(ii), pupal stage, pupal stage p6
strains: Oregon-R-modENCODE, y; cn bw sp
tissues: embryo-derived cell-line, whole organism


Here’s the breakdown by project:

Celniker Project

Data Type Experiment type Details Links Comments
transcriptional fragments (GFF), transcriptional signals (WIG) RNA tiling array Tissues: whole organism
Strains: Oregon-R-modENCODE
Stages: embryonic stage, embryonic stage 5, embryonic stage 6, embryonic stage 7, embryonic stage 8

Embargoed until 9 months from 2009-04-14

 ChadoXML | Tracks | Stanza | Raw Data details…
transcriptional fragments (GFF), transcriptional signals (WIG) RNA tiling array Tissues: whole organism
Strains: y; cn bw sp
Stages: pharate adult stage, pharate adult stage P9

Embargoed until 9 months from 2009-04-29

 ChadoXML | Tracks | Stanza | Raw Data details…
transcriptional fragments (GFF), transcriptional signals (WIG) RNA tiling array Tissues: whole organism
Strains: y; cn bw sp
Stages: pharate adult stage, pharate adult stage P15, pharate adult stage P15(i)

Embargoed until 9 months from 2009-04-29

 ChadoXML | Tracks | Stanza | Raw Data details…
transcriptional fragments (GFF), transcriptional signals (WIG) RNA tiling array Tissues: whole organism
Strains: y; cn bw sp
Stages: prepupal stage, prepupal stage P4, prepupal stage P4(i), prepupal stage P4(ii)

Embargoed until 9 months from 2009-04-29

 ChadoXML | Tracks | Stanza | Raw Data details…
transcriptional fragments (GFF), transcriptional signals (WIG) RNA tiling array Tissues: whole organism
Strains: y; cn bw sp
Stages: pupal stage, pupal stage P6

Embargoed until 9 months from 2009-04-29

 ChadoXML | Tracks | Stanza | Raw Data details…

Henikoff Project

Data Type Experiment type Details Links Comments
transcriptional fragments (GFF), transcriptional signals (WIG) RNA tiling array Tissues: embryo-derived cell-line
Lines: S2, S2-DRSC
Stages: late embryonic stage

Embargoed until 9 months from 2009-04-27

 ChadoXML | Tracks | Stanza | Raw Data details…
]]> http://blog.modencode.org/d-melanogaster-data-release-report-for-427-53-2009/feed 0 D. melanogaster Data Release Report for 3/16-3/22, 2009 http://blog.modencode.org/d-melanogaster-data-release-report-for-316-322-2009 http://blog.modencode.org/d-melanogaster-data-release-report-for-316-322-2009#comments Mon, 23 Mar 2009 17:35:32 +0000 nicole http://blog.modencode.org/?p=202 This week we’ve released 4 D. melanogaster data sets:
Celniker – 2 Computational annotation and 1 RTPCR data sets
Henikoff – 1 RNA tiling array data sets

on the following kinds of samples:
cell lines: CME L1, S2
stages: late embryonic stage, third instar larval stage
tissues: embryo-derived cell-line, ventral prothoracic disc


Here’s the breakdown by project:

Celniker Project

Data Type Experiment type Details Links Comments
gene models (GFF) Computational annotation Embargoed until 9 months from 2008-09-01 ChadoXML | Tracks | Stanza | Raw Data details…
gene models (GFF) Computational annotation Embargoed until 9 months from 2009-02-09 ChadoXML | Tracks | Stanza | Raw Data details…
trace reads, EST alignments (GFF) RTPCR Tissues: ventral prothoracic disc

Lines: CME L1

Stages: third instar larval stage

Embargoed until 9 months from 2009-02-27

 ChadoXML | Tracks | Stanza | Raw Data details…

Henikoff Project

Data Type Experiment type Details Links Comments
signal data (WIG) RNA tiling array Tissues: embryo-derived cell-line
Lines: S2

Stages: late embryonic stage

Embargoed until 9 months from 2009-03-16

 ChadoXML | Tracks | Stanza | Raw Data details…
]]> http://blog.modencode.org/d-melanogaster-data-release-report-for-316-322-2009/feed 0