modENCODE CAGE Read Density Track Settings

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

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Type of graph:
Track height:	pixels (range: 11 to 110)
Data view scaling:	Always include zero:
Vertical viewing range:	min:	max: (range: 0 to 100000)
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Windowing function:		Smoothing window:	pixels
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Draw y indicator lines:	at y = 0.0: at y =

Graph configuration help

Select subtracks by strand and stage: (help)

All	*Strand*	Plus	Minus
*Stage*
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
*Stage*
All	*Strand*	Plus	Minus

Select subtracks further by: (select multiple categories and items - help)

StageGroup:

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