modENCODE CAGE Read Density Track Settings
 
modENCODE CAGE Read Density for Different Developmental Stages   (All Expression and Regulation tracks)

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Embryos 0-2hr 
Embryos 2-4hr 
Embryos 4-6hr 
Embryos 6-8hr 
Embryos 8-10hr 
Embryos 12-14hr 
Embryos 16-18hr 
Embryos 20-22hr 
L1 
L2 
L3 12hr 
L3 Blue Gut 
L3 CNS 
L3 Carcass 
L3 Digestive 
L3 Imaginal Discs 
WPP 2d CNS 
WPP 2d Fat 
Pupae 12hr 
Pupae 2d 
Adult Mated Female 1d Heads 
Adult Mated Female 4d Ovaries 
Adult Mated Female 20d Heads 
Adult Mated Male 1d Heads 
Adult Mated Male 4d Testes 
Adult Mated Male 4d Glands 
Adult Mated Male 20d Heads 
Adult Virgin Female 4d Ovaries 
Adult 4d Carcass 
Adult 4d Digestive 
Adult 20d Digestive 
BG3 0hr 
BG3 5hr 
BG3 24hr 
Kc167 Cytoplasm 
Kc167 Nuclear 
S2 
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 Embryos, 0-2 hr (Plus)  modENCODE CAGE Read Density for 0-2 hr Embryos (Plus)   Schema 
 
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 Embryos, 0-2 hr (Minus)  modENCODE CAGE Read Density for 0-2 hr Embryos (Minus)   Schema 
 
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 Embryos, 2-4 hr (Plus)  modENCODE CAGE Read Density for 2-4 hr Embryos (Plus)   Schema 
 
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 Embryos, 2-4 hr (Minus)  modENCODE CAGE Read Density for 2-4 hr Embryos (Minus)   Schema 
 
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 Embryos, 4-6 hr (Plus)  modENCODE CAGE Read Density for 4-6 hr Embryos (Plus)   Schema 
 
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 Embryos, 4-6 hr (Minus)  modENCODE CAGE Read Density for 4-6 hr Embryos (Minus)   Schema 
 
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 Embryos, 6-8 hr (Plus)  modENCODE CAGE Read Density for 6-8 hr Embryos (Plus)   Schema 
 
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 Embryos, 6-8 hr (Minus)  modENCODE CAGE Read Density for 6-8 hr Embryos (Minus)   Schema 
 
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 Embryos, 8-10 hr (Plus)  modENCODE CAGE Read Density for 8-10 hr Embryos (Plus)   Schema 
 
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 Embryos, 8-10 hr (Minus)  modENCODE CAGE Read Density for 8-10 hr Embryos (Minus)   Schema 
 
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 Embryos, 12-14 hr (Plus)  modENCODE CAGE Read Density for 12-14 hr Embryos (Plus)   Schema 
 
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 Embryos, 12-14 hr (Minus)  modENCODE CAGE Read Density for 12-14 hr Embryos (Minus)   Schema 
 
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 Embryos, 16-18 hr (Plus)  modENCODE CAGE Read Density for 16-18 hr Embryos (Plus)   Schema 
 
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 Embryos, 16-18 hr (Minus)  modENCODE CAGE Read Density for 16-18 hr Embryos (Minus)   Schema 
 
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 Embryos, 20-22 hr (Plus)  modENCODE CAGE Read Density for 20-22 hr Embryos (Plus)   Schema 
 
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 Embryos, 20-22 hr (Minus)  modENCODE CAGE Read Density for 20-22 hr Embryos (Minus)   Schema 
 
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 L1 (Plus)  modENCODE CAGE Read Density for L1 Stage Larvae (Plus)   Schema 
 
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 L1 (Minus)  modENCODE CAGE Read Density for L1 Stage Larvae (Minus)   Schema 
 
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 L2 (Plus)  modENCODE CAGE Read Density for L2 Stage Larvae (Plus)   Schema 
 
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 L2 (Minus)  modENCODE CAGE Read Density for L2 Stage Larvae (Minus)   Schema 
 
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 L3, 12hr Post-Molt (Plus)  modENCODE CAGE Read Density for L3 Stage Larvae, 12 hr Post-Molt (Plus)   Schema 
 
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 L3, 12hr Post-Molt (Minus)  modENCODE CAGE Read Density for L3 Stage Larvae, 12 hr Post-Molt (Minus)   Schema 
 
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 L3, Blue Gut (Plus)  modENCODE CAGE Read Density for L3 Stage Larvae, Light Blue Gut (Plus)   Schema 
 
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 L3, Blue Gut (Minus)  modENCODE CAGE Read Density for L3 Stage Larvae, Light Blue Gut (Minus)   Schema 
 
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 L3, CNS (Plus)  modENCODE CAGE Read Density for L3 Stage Larvae, CNS (Plus)   Schema 
 
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 L3, CNS (Minus)  modENCODE CAGE Read Density for L3 Stage Larvae, CNS (Minus)   Schema 
 
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 L3, Carcass (Plus)  modENCODE CAGE Read Density for L3 Stage Larvae, Carcass (Plus)   Schema 
 
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 L3, Carcass (Minus)  modENCODE CAGE Read Density for L3 Stage Larvae, Carcass (Minus)   Schema 
 
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 L3, Digestive System (Plus)  modENCODE CAGE Read Density for L3 Stage Larvae, Digestive System (Plus)   Schema 
 
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 L3, Digestive System (Minus)  modENCODE CAGE Read Density for L3 Stage Larvae, Digestive System (Minus)   Schema 
 
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 L3, Imaginal Discs (Plus)  modENCODE CAGE Read Density for L3 Stage Larvae, Imaginal Discs (Plus)   Schema 
 
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 L3, Imaginal Discs (Minus)  modENCODE CAGE Read Density for L3 Stage Larvae, Imaginal Discs (Minus)   Schema 
 
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 WPP, 2 days CNS (Plus)  modENCODE CAGE Read Density for WPP + 2 days, CNS (Plus)   Schema 
 
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 WPP, 2 days CNS (Minus)  modENCODE CAGE Read Density for WPP + 2 days, CNS (Minus)   Schema 
 
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 WPP, 2 days Fat (Plus)  modENCODE CAGE Read Density for WPP + 2 days, Fat (Plus)   Schema 
 
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 WPP, 2 days Fat (Minus)  modENCODE CAGE Read Density for WPP + 2 days, Fat (Minus)   Schema 
 
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 Pupae, 12 hrs after WPP (Plus)  modENCODE CAGE Read Density for Pupae, 12 hrs after WPP (Plus)   Schema 
 
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 Pupae, 12 hrs after WPP (Minus)  modENCODE CAGE Read Density for Pupae, 12 hrs after WPP (Minus)   Schema 
 
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 Pupae, 2 days after WPP (Plus)  modENCODE CAGE Read Density for Pupae, 2 days after WPP (Plus)   Schema 
 
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 Pupae, 2 days after WPP (Minus)  modENCODE CAGE Read Density for Pupae, 2 days after WPP (Minus)   Schema 
 
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 Adult Mated Female, 1 day Heads (Plus)  modENCODE CAGE Read Density for Adult Mated Female, 1 day Post-eclosion Heads (Plus)   Schema 
 
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 Adult Mated Female, 1 day Heads (Minus)  modENCODE CAGE Read Density for Adult Mated Female, 1 day Post-eclosion Heads (Minus)   Schema 
 
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 Adult Mated Female, 4 days Ovaries (Plus)  modENCODE CAGE Read Density for Adult Mated Female, 4 days Post-eclosion Ovaries (Plus)   Schema 
 
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 Adult Mated Female, 4 days Ovaries (Minus)  modENCODE CAGE Read Density for Adult Mated Female, 4 days Post-eclosion Ovaries (Minus)   Schema 
 
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 Adult Mated Female, 20 days Heads (Plus)  modENCODE CAGE Read Density for Adult Mated Female, 20 days Post-eclosion Heads (Plus)   Schema 
 
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 Adult Mated Female, 20 days Heads (Minus)  modENCODE CAGE Read Density for Adult Mated Female, 20 days Post-eclosion Heads (Minus)   Schema 
 
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 Adult Mated Male, 1 day Heads (Plus)  modENCODE CAGE Read Density for Adult Mated Male, 1 day Post-eclosion Heads (Plus)   Schema 
 
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 Adult Mated Male, 1 day Heads (Minus)  modENCODE CAGE Read Density for Adult Mated Male, 1 day Post-eclosion Heads (Minus)   Schema 
 
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 Adult Mated Male, 4 days Testes (Plus)  modENCODE CAGE Read Density for Adult Mated Male, 4 days Post-eclosion Testes (Plus)   Schema 
 
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 Adult Mated Male, 4 days Testes (Minus)  modENCODE CAGE Read Density for Adult Mated Male, 4 days Post-eclosion Testes (Minus)   Schema 
 
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 Adult Mated Male, 4 days Glands (Plus)  modENCODE CAGE Read Density for Adult Mated Male, 4 days Post-eclosion Male Accessory Glands (Plus)   Schema 
 
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 Adult Mated Male, 4 days Glands (Minus)  modENCODE CAGE Read Density for Adult Mated Male, 4 days Post-eclosion Male Accessory Glands (Minus)   Schema 
 
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 Adult Mated Male, 20 days Heads (Plus)  modENCODE CAGE Read Density for Adult Mated Male, 20 days Post-eclosion Heads (Plus)   Schema 
 
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 Adult Mated Male, 20 days Heads (Minus)  modENCODE CAGE Read Density for Adult Mated Male, 20 days Post-eclosion Heads (Minus)   Schema 
 
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 Adult Virgin Female, 4 days Ovaries (Plus)  modENCODE CAGE Read Density for Adult Virgin Female, 4 days Post-eclosion Ovaries (Plus)   Schema 
 
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 Adult Virgin Female, 4 days Ovaries (Minus)  modENCODE CAGE Read Density for Adult Virgin Female, 4 days Post-eclosion Ovaries (Minus)   Schema 
 
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 Mixed Adults, 4 days Carcass (Plus)  modENCODE CAGE Read Density for Adult Mixed Male and Female, 4 days Post-eclosion Carcass (Plus)   Schema 
 
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 Mixed Adults, 4 days Carcass (Minus)  modENCODE CAGE Read Density for Adult Mixed Male and Female, 4 days Post-eclosion Carcass (Minus)   Schema 
 
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 Mixed Adults, 4 days Digestive System (Plus)  modENCODE CAGE Read Density for Adult Mixed Male and Female, 4 days Post-eclosion Digestive System (Plus)   Schema 
 
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 Mixed Adults, 4 days Digestive System (Minus)  modENCODE CAGE Read Density for Adult Mixed Male and Female, 4 days Post-eclosion Digestive System (Minus)   Schema 
 
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 Mixed Adults, 20 days Digestive System (Plus)  modENCODE CAGE Read Density for Adult Mixed Male and Female, 20 days Post-eclosion Digestive System (Plus)   Schema 
 
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 Mixed Adults, 20 days Digestive System (Minus)  modENCODE CAGE Read Density for Adult Mixed Male and Female, 20 days Post-eclosion Digestive System (Minus)   Schema 
 
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 BG3, 0 hr Ecdysone (Plus)  modENCODE CAGE Read Density for BG3 Cells, 0 hr Ecdysone (Plus)   Schema 
 
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 BG3, 0 hr Ecdysone (Minus)  modENCODE CAGE Read Density for BG3 Cells, 0 hr Ecdysone (Minus)   Schema 
 
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 BG3, 5 hrs Ecdysone (Plus)  modENCODE CAGE Read Density for BG3 Cells, 5 hrs Ecdysone (Plus)   Schema 
 
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 BG3, 5 hrs Ecdysone (Minus)  modENCODE CAGE Read Density for BG3 Cells, 5 hrs Ecdysone (Minus)   Schema 
 
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 BG3, 24hrs Ecdysone (Plus)  modENCODE CAGE Read Density for BG3 Cells, 24 hrs Ecdysone (Plus)   Schema 
 
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 BG3, 24hrs Ecdysone (Minus)  modENCODE CAGE Read Density for BG3 Cells, 24 hrs Ecdysone (Minus)   Schema 
 
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 Kc167, Cytoplasm (Plus)  modENCODE CAGE Read Density for Kc167 Cells, Cytoplasm RNA (Plus)   Schema 
 
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 Kc167, Cytoplasm (Minus)  modENCODE CAGE Read Density for Kc167 Cells, Cytoplasm RNA (Minus)   Schema 
 
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 Kc167, Nuclear (Plus)  modENCODE CAGE Read Density for Kc167 Cells, Nuclear RNA (Plus)   Schema 
 
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 Kc167, Nuclear (Minus)  modENCODE CAGE Read Density for Kc167 Cells, Nuclear RNA (Minus)   Schema 
 
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 S2 (Plus)  modENCODE CAGE Read Density for S2 Cells, DRSC (Plus)   Schema 
 
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 S2 (Minus)  modENCODE CAGE Read Density for S2 Cells, DRSC (Minus)   Schema 
    

Description

These tracks show the normalized density of CAGE reads from different developmental stages of D. melanogaster. The CAGE datasets were produced by the modENCODE project and were obtained from the NCBI Sequence Read Archive database under the accession number SRP001602.

Methods

Each dataset was mapped to the D. melanogaster release 6 assembly using bwa with default parameters. The alignment results were analyzed by CAGEr. The tag counts were normalized by the normalizeTagCount function in CAGEr with the following parameters:

method = "powerLaw", fitInRange = c(10, 1000), alpha = 1.05, T = 1*10^6

Credits

Hoskins RA, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011 Feb;21(2):182-92.

Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res. 2015 Apr 30;43(8):e51.