modENCODE Blog » developmental stage

New resource: estimated expression levels for annotated genes and exons

sergio — Fri, 21 May 2010 09:57:37 +0000

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).

D. melanogaster Data Release Report for 8/24-8/30, 2009

nicole — Mon, 31 Aug 2009 18:43:04 +0000

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

Here’s the breakdown by project:

White Project

Data Type	Experiment type	Details	Links	Comments
chromatin binding sites (GFF) signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: pupal stage Antibodies: H3K9Ac, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…

C. elegans Data Release Report for 8/3-8/9, 2009

nicole — Mon, 10 Aug 2009 21:28:23 +0000

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

Here’s the breakdown by project:

Lieb Project

Data Type	Experiment type	Details	Links	Comments
chromatin binding site (GFF) signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: N2 Stages: embryo Antibodies: SDC-2, SDC-2 Embargoed until 9 months from 2009-06-17	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF) signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: N2 Stages: embryo Antibodies: RNA polII CTD domain unphosophorylated Embargoed until 9 months from 2009-06-26	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF) signal data W(G)	ChIP-chip	Tissues: whole organism Strains: N2 Stages: embryo Antibodies: Trimethylated Lys-9 on histone H3 Embargoed until 9 months from 2009-07-06	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF) signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: 11dh Stages: embryo Antibodies: DPY-27, No Antibody Control Embargoed until 9 months from 2009-07-08	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF) signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: YPT41 Stages: embryo Antibodies: DPY-27, No Antibody Control Embargoed until 9 months from 2009-07-08	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF) signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: YPT47 Stages: embryo Antibodies: DPY-27, No Antibody Control Embargoed until 9 months from 2009-07-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF) signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: YPT47 Stages: embryo Antibodies: SDC-3, No Antibody Control Embargoed until 9 months from 2009-07-10	ChadoXML \| Tracks \| Stanza \| Raw Data	details…

Waterston Project

Data Type	Experiment type	Details	Links	Comments
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: L2 larva Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: L4 larva Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: L3 larva Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: newly molted young adult hermaphrodite Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: blastula embryo, gastrulating embryo Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: L2 larva Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: CB4689 (him-8), N2 Stages: L4 larva male Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: elongating embryo, enclosing embryo, fully-elongated embryo, late cleavage stage embryo Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism, hermaphrodite gonad Strains: N2 Stages: newly molted young adult hermaphrodite Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: L1 larva Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: JK1107 (gonad-less) Stages: L4 larva Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… developmental time course
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: newly molted young adult hermaphrodite Pathogen: P. luminscens, 24h Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… pathogen set
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: newly molted young adult hermaphrodite Pathogen: E. faecalis, 48h Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… pathogen set
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: newly molted young adult hermaphrodite Pathogen: S. marcescans, 48h Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… pathogen set
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: newly molted young adult hermaphrodite Pathogen: S. marcescans, 24h Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… pathogen set
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: newly molted young adult hermaphrodite Pathogen: OP50, 48h (control) Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… pathogen set
transcriptional signal (WIG), transcriptional fragments (GFF)	RNA tiling array	Tissues: whole organism Strains: N2 Stages: newly molted young adult hermaphrodite Pathogen: OP50, 24h (control) Embargoed until 9 months from 2009-03-23	ChadoXML \| Tracks \| Stanza \| Raw Data	details… pathogen set

D. melanogaster Data Release Report for 7/27-8/2, 2009

nicole — Mon, 03 Aug 2009 20:58:52 +0000

This week we’ve released 21 D. melanogaster data sets:
Lai – 1 RNA-seq (small RNAs) data sets
White – 20 ChIP-chip data sets
on the following kinds of samples:
antibodies: h3k27me3, h3k4me1, h3k4me3, h3k9ac, h3k9me3, no antibody control
stages: adult stage, embryonic stage 10, embryonic stage 11, embryonic stage 12, embryonic stage 15, embryonic stage 16, embryonic stage 17, embryonic stage 9, first instar larval stage, second instar larval stage
strains: Canton-S, y; cn bw sp
tissues: adult head, whole organism

Here’s the breakdown by project:

Lai Project

Data Type	Experiment type	Details	Links	Comments
alignments (SAM)	RNA-seq (small RNAs)	Tissues: whole organism, adult head Strains: Canton-S Stages: adult stage Embargoed until 9 months from 2008-09-19	ChadoXML \| Tracks \| Stanza \| Raw Data	details… small RNAs captured, single read alignments, repeat regions not masked (some sequences align to more than 1 genomic location)

White Project

Data Type	Experiment type	Details	Links	Comments
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: adult stage Antibodies: H3K27me3, No Antibody Control Embargoed until 9 months from 2009-03-08	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: first instar larval stage Antibodies: H3K27me3, No Antibody Control Embargoed until 9 months from 2009-03-08	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: first instar larval stage Antibodies: H3K9me3, No Antibody Control Embargoed until 9 months from 2009-03-08	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: second instar larval stage Antibodies: H3K9me3, No Antibody Control Embargoed until 9 months from 2009-03-08	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: embryonic stage 17 Antibodies: H3K27me3, No Antibody Control Embargoed until 9 months from 2009-03-08	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: embryonic stage 17 Antibodies: H3K9me3, No Antibody Control Embargoed until 9 months from 2009-03-08	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: second instar larval stage Antibodies: H3K9Ac, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: second instar larval stage Antibodies: H3K4me3, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: first instar larval stage Antibodies: H3K9Ac, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: first instar larval stage Antibodies: H3K4me1, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: embryonic stage 10, embryonic stage 11, embryonic stage 12, embryonic stage 9 Antibodies: H3K4me1, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: embryonic stage 17 Antibodies: H3K4me1, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: embryonic stage 17 Antibodies: H3K4me1, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: embryonic stage 17 Antibodies: H3K4me1, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: embryonic stage 17 Antibodies: H3K4me1, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: embryonic stage 15, embryonic stage 16 Antibodies: H3K9Ac, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: embryonic stage 15, embryonic stage 16 Antibodies: H3K4me3, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: embryonic stage 15, embryonic stage 16 Antibodies: H3K4me1, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: adult stage Antibodies: H3K4me3, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding site (GFF), signal data (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: adult stage Antibodies: H3K4me1, No Antibody Control Embargoed until 9 months from 2009-03-09	ChadoXML \| Tracks \| Stanza \| Raw Data	details…

D. melanogaster Data Release Report for 7/20-7/26, 2009

nicole — Mon, 27 Jul 2009 20:50:23 +0000

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

Here’s the breakdown by project:

MacAlpine Project

Data Type	Experiment type	Details	Links	Comments
signal data (WIG)	CGH	Tissues: embryo-derived cell-line, whole organism Strains: w[1118] Lines: S2-DRSC Stages: cleavage stage, early extended germ band stage, embryonic stage, embryonic stage 1, embryonic stage 2, embryonic stage 3, and 9 more… Embargoed until 9 months from 2009-07-20	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
copy number variation (GFF), signal data (WIG)	CGH	Tissues: oocyte associated follicle cell, whole organism Strains: Oregon-R_Orr-Weaver Stages: cleavage stage, early extended germ band stage, embryonic stage, embryonic stage 1, embryonic stage 2, embryonic stage 3, and 8 more… Embargoed until 9 months from 2009-07-20	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
copy number variation (GFF), signal data (WIG)	CGH	Tissues: larval salivary gland, whole organism Strains: Oregon-R_Orr-Weaver Stages: cleavage stage, early extended germ band stage, embryonic stage, embryonic stage 1, embryonic stage 2, embryonic stage 3, and 8 more… Embargoed until 9 months from 2009-07-20	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
copy number variation (GFF), signal data (WIG)	CGH	Tissues: oocyte associated follicle cell Strains: Oregon-R-modENCODE Stages: cleavage stage, early extended germ band stage, embryonic stage, embryonic stage 1, embryonic stage 2, embryonic stage 3, and 8 more… Embargoed until 9 months from 2009-07-20	ChadoXML \| Tracks \| Stanza \| Raw Data	details…

White Project

Data Type	Experiment type	Details	Links	Comments
chromatin binding peaks (GFF), chromatin binding signal (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: third instar larval stage Antibodies: H3K27me3, No Antibody Control Embargoed until 9 months from 2009-03-06	ChadoXML \| Tracks \| Stanza \| Raw Data	details…

C. elegans Data Release Report for 7/20-7/26, 2009

nicole — Mon, 27 Jul 2009 20:47:44 +0000

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

Here’s the breakdown by project:

Lieb Project

Data Type	Experiment type	Details	Links	Comments
chromatin binding peaks (GFF), chromatin binding signal (WIG)	ChIP-chip	Tissues: whole organism Strains: N2 Stages: L4 larva Antibodies: RNA polII CTD domain unphosophorylated, No Antibody Control Embargoed until 9 months from 2009-06-08	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
chromatin binding peaks (GFF), chromatin binding signal (WIG)	ChIP-chip	Tissues: whole organism Strains: N2 Stages: L4 larva Antibodies: DPY-27, No Antibody Control Embargoed until 9 months from 2009-06-11	ChadoXML \| Tracks \| Stanza \| Raw Data	details…

D. melanogaster Data Release Report for 7/13-7/19, 2009

nicole — Mon, 20 Jul 2009 20:26:06 +0000

This week we’ve released 8 D. melanogaster data sets:
Celniker – 4 RNA-seq data sets
MacAlpine – 3 ChIP-chip and 1 RNA tiling array data sets
on the following kinds of samples:
cell lines: CME W1 Cl.8+, Kc167, ML-DmBG3-c2, S2-DRSC
stages: adult stage, cleavage stage, early extended germ band stage, embryonic stage, embryonic stage 1, embryonic stage 2, embryonic stage 3, late embryonic stage, third instar larval stage
strain: y; cn bw sp
tissues: cns-derived cell-line, dorsal mesothoracic disc, embryo-derived cell-line, larval salivary gland, whole organism

Here’s the breakdown by project:

Celniker Project

Data Type	Experiment type	Details	Links	Comments
alignments (SAM)	RNA-seq	Tissues: embryo-derived cell-line Lines: S2-DRSC Stages: late embryonic stage Embargoed until 9 months from 2009-06-22	ChadoXML \| Tracks \| Stanza \| Raw Data	details… paired-end sequencing with alignments to splice junctions
alignments (SAM)	RNA-seq	Tissues: CNS-derived cell-line Lines: ML-DmBG3-c2 Stages: third instar larval stage Embargoed until 9 months from 2009-06-22	ChadoXML \| Tracks \| Stanza \| Raw Data	details… paired-end sequencing with alignments to splice junctions
alignments (SAM)	RNA-seq	Tissues: dorsal mesothoracic disc Lines: CME W1 Cl.8+ Stages: third instar larval stage Embargoed until 9 months from 2009-06-22	ChadoXML \| Tracks \| Stanza \| Raw Data	details… paired-end sequencing with alignments to splice junctions
alignments (SAM)	RNA-seq	Tissues: whole organism Strains: y; cn bw sp Stages: adult stage Embargoed until 9 months from 2009-07-14	ChadoXML \| Tracks \| Stanza \| Raw Data	details… single reads with alignments to splice junctions

MacAlpine Project

Data Type	Experiment type	Details	Links	Comments
origins of replication (GFF), signal data (WIG)	tiling array	Tissues: embryo-derived cell-line Lines: Kc167 Stages: late embryonic stage Embargoed until 9 months from 2009-07-13	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
origins of replication (GFF), signal data (WIG)	tiling array	Tissues: embryo-derived cell-line Lines: S2-DRSC Stages: late embryonic stage Embargoed until 9 months from 2009-07-13	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
origins of replication (GFF), signal data (WIG)	tiling array	Tissues: CNS-derived cell-line Lines: ML-DmBG3-c2 Stages: third instar larval stage Embargoed until 9 months from 2009-07-13	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
copy number variation (GFF), signal data (WIG)	CGH	Tissues: larval salivary gland Strains: y; cn bw sp Stages: cleavage stage, early extended germ band stage, embryonic stage, embryonic stage 1, embryonic stage 2, embryonic stage 3, and 8 more… Embargoed until 9 months from 2009-07-17	ChadoXML \| Tracks \| Stanza \| Raw Data	details…

D. melanogaster Data Release Report for 7/6-7/12, 2009

nicole — Mon, 13 Jul 2009 19:38:37 +0000

This week we’ve released 2 D. melanogaster data sets:
Celniker – 1 RNA-seq data sets
White – 1 ChIP-chip data sets
on the following kinds of samples:
antibodies: h3k9me3, no antibody control
cell line: Kc167
stages: late embryonic stage, third instar larval stage
strain: 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
alignments (SAM)	RNA-seq	Tissues: embryo-derived cell-line Lines: Kc167 Stages: late embryonic stage Embargoed until 9 months from 2009-06-15	ChadoXML \| Tracks \| Stanza \| Raw Data	details… paired-end data, aligning to splice junctions

White Project

Data Type	Experiment type	Details	Links	Comments
chromatin binding peaks (GFF), chromatin binding signal (WIG)	ChIP-chip	Tissues: whole organism Strains: y; cn bw sp Stages: third instar larval stage Antibodies: H3K9me3, No Antibody Control Embargoed until 9 months from 2009-03-06	ChadoXML \| Tracks \| Stanza \| Raw Data	details…

D. melanogaster Data Release Report for 6/29-7/5, 2009

nicole — Mon, 06 Jul 2009 19:21:32 +0000

This week we’ve released 6 D. melanogaster data sets:
Lai – 1 RNA-seq data sets
MacAlpine – 5 ChIP-chip data sets
on the following kinds of samples:

antibodies: drosophila orc2p, mcm2-7 complex
cell lines: Kc167, ML-DmBG3-c2, S2-DRSC
stages: first instar larval stage, late embryonic stage, third instar larval stage
strain: Canton-S
tissues: cns-derived cell-line, embryo-derived cell-line, whole organism

Here’s the breakdown by project:

Lai Project

Data Type	Experiment type	Details	Links	Comments
alignments (SAM)	RNA-seq	Tissues: whole organism Strains: Canton-S Stages: first instar larval stage Embargoed until 9 months from 2009-07-02	ChadoXML \| Tracks \| Stanza \| Raw Data	details… small RNAs, single read alignments, no repeat masking,some sequences align to >>1 genomic location

Data Type

Experiment type

Details

Links

Comments

alignments (SAM)

RNA-seq

Tissues: whole organism
Strains: Canton-S
Stages: first instar larval stage

Embargoed until 9 months from 2009-07-02

ChadoXML | Tracks | Stanza | Raw Data

details…
small RNAs, single read alignments, no repeat masking,some sequences align to >>1 genomic location

MacAlpine Project

Data Type	Experiment type	Details	Links	Comments
replication timing signal (WIG)	tiling array	Tissues: embryo-derived cell-line Lines: Kc167 Stages: late embryonic stage Embargoed until 9 months from 2009-06-30	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
replication timing signal (WIG)	tiling array	Tissues: embryo-derived cell-line Lines: S2-DRSC Stages: late embryonic stage Embargoed until 9 months from 2009-06-30	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
replication timing signal (WIG)	tiling array	Tissues: CNS-derived cell-line Lines: ML-DmBG3-c2 Stages: third instar larval stage Embargoed until 9 months from 2009-06-30	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
replication complex binding site (GFF), replication binding signal (WIG)	ChIP-chip	Tissues: embryo-derived cell-line Lines: Kc167 Stages: late embryonic stage Antibodies: Drosophila ORC2p Embargoed until 9 months from 2009-06-30	ChadoXML \| Tracks \| Stanza \| Raw Data	details…
replication complex binding site (GFF), replication binding signal (WIG)	ChIP-chip	Tissues: embryo-derived cell-line Lines: Kc167 Stages: late embryonic stage Antibodies: MCM2-7 complex Embargoed until 9 months from 2009-06-30	ChadoXML \| Tracks \| Stanza \| Raw Data	details…

C. elegans Data Release Report for 6/22-6/28, 2009

nicole — Mon, 29 Jun 2009 19:14:44 +0000

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

Here’s the breakdown by project:

Waterston Project

Data Type	Experiment type	Details	Links	Comments
alignments (SAM)	RNA-seq	Tissues: whole organism Strains: N2 Stages: embryo Embargoed until 9 months from 2009-06-15	ChadoXML \| Tracks \| Stanza \| Raw Data	details… small RNAs
alignments (SAM)	RNA-seq	Tissues: whole organism Strains: N2 Stages: L1 larva Embargoed until 9 months from 2009-06-15	ChadoXML \| Tracks \| Stanza \| Raw Data	details… small RNAs
alignments (SAM)	RNA-seq	Tissues: whole organism Strains: N2 Stages: L2 larva Embargoed until 9 months from 2009-06-15	ChadoXML \| Tracks \| Stanza \| Raw Data	details… small RNAs
alignments (SAM)	RNA-seq	Tissues: whole organism Strains: N2 Stages: L3 larva Embargoed until 9 months from 2009-06-15	ChadoXML \| Tracks \| Stanza \| Raw Data	details… small RNAs
alignments	RNA-seq	Tissues: whole organism Strains: N2 Stages: L4 larva Embargoed until 9 months from 2009-06-15	ChadoXML \| Tracks \| Stanza \| Raw Data	details… small RNAs
alignments (SAM)	RNA-seq	Tissues: whole organism Strains: N2 Stages: newly molted young adult hermaphrodite Embargoed until 9 months from 2009-06-15	ChadoXML \| Tracks \| Stanza \| Raw Data	details… small RNAs
alignments (SAM)	RNA-seq	Tissues: whole organism Strains: CB4689 Stages: adult male Embargoed until 9 months from 2009-06-15	ChadoXML \| Tracks \| Stanza \| Raw Data	details… small RNAs