modENCODE Blog

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).

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 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 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
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…

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 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
Read more…

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
Read more…

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

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

Read more…