modENCODE RNA-Seq (Development) Track Settings

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modENCODE RNA-Seq for Different Developmental Stages (All Updated Transcriptome Tracks)

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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 10-12hr
Embryos 12-14hr
Embryos 14-16hr
Embryos 16-18hr
Embryos 18-20hr
Embryos 20-22hr
Embryos 22-24hr
L1
L2
L3
L3 Dark Blue Gut
L3 Blue Gut
L3 Clear Gut
L3 Carcass
Prepupa
Prepupa 12hr
Prepupa 24hr
Pupa 2d
Pupa 3d
Pupa 4d
Adult Female 1d
Adult Female 5d
Adult Female 30d
Adult Male 1d
Adult Male 5d
Adult Male 30d
Adult Carcass 1d
Adult Carcass 4d
Adult Carcass 20d
Adult Female DGRP 321
Adult Female DGRP 399
Adult Female DGRP 509
Adult Female DGRP 589
Adult Male ENCSR282WLG
Adult Male ENCSR581YBD
Adult Male ENCSR956AYX
Adult Male ENCSR960BIV
*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)	RNA-seq for 0-2hr Embryos (Plus)	Schema
	hide Configure	Embryos, 0-2 hr (Minus)	RNA-seq for 0-2hr Embryos (Minus)	Schema
	hide Configure	Embryos, 2-4hr (Plus)	RNA-seq for 2-4hr Embryos (Plus)	Schema
	hide Configure	Embryos, 2-4hr (Minus)	RNA-seq for 2-4hr Embryos (Minus)	Schema
	hide Configure	Embryos, 4-6hr (Plus)	RNA-seq for 4-6hr Embryos (Plus)	Schema
	hide Configure	Embryos, 4-6hr (Minus)	RNA-seq for 4-6hr Embryos (Minus)	Schema
	hide Configure	Embryos, 6-8hr (Plus)	RNA-seq for 6-8hr Embryos (Plus)	Schema
	hide Configure	Embryos, 6-8hr (Minus)	RNA-seq for 6-8hr Embryos (Minus)	Schema
	hide Configure	Embryos, 8-10hr (Plus)	RNA-seq for 8-10hr Embryos (Plus)	Schema
	hide Configure	Embryos, 8-10hr (Minus)	RNA-seq for 8-10hr Embryos (Minus)	Schema
	hide Configure	Embryos, 10-12hr (Plus)	RNA-seq for 10-12hr Embryos (Plus)	Schema
	hide Configure	Embryos, 10-12hr (Minus)	RNA-seq for 10-12hr Embryos (Minus)	Schema
	hide Configure	Embryos, 12-14hr (Plus)	RNA-seq for 12-14hr Embryos (Plus)	Schema
	hide Configure	Embryos, 12-14hr (Minus)	RNA-seq for 12-14hr Embryos (Minus)	Schema
	hide Configure	Embryos, 14-16hr (Plus)	RNA-seq for 14-16hr Embryos (Plus)	Schema
	hide Configure	Embryos, 14-16hr (Minus)	RNA-seq for 14-16hr Embryos (Minus)	Schema
	hide Configure	Embryos, 16-18hr (Plus)	RNA-seq for 16-18hr Embryos (Plus)	Schema
	hide Configure	Embryos, 16-18hr (Minus)	RNA-seq for 16-18hr Embryos (Minus)	Schema
	hide Configure	Embryos, 18-20hr (Plus)	RNA-seq for 18-20hr Embryos (Plus)	Schema
	hide Configure	Embryos, 18-20hr (Minus)	RNA-seq for 18-20hr Embryos (Minus)	Schema
	hide Configure	Embryos, 20-22hr (Plus)	RNA-seq for 20-22hr Embryos (Plus)	Schema
	hide Configure	Embryos, 20-22hr (Minus)	RNA-seq for 20-22hr Embryos (Minus)	Schema
	hide Configure	Embryos, 22-24hr (Plus)	RNA-seq for 22-24hr Embryos (Plus)	Schema
	hide Configure	Embryos, 22-24hr (Minus)	RNA-seq for 22-24hr Embryos (Minus)	Schema
	hide Configure	L1 (Plus)	RNA-seq for L1 Stage Larvae (Plus)	Schema
	hide Configure	L1 (Minus)	RNA-seq for L1 Stage Larvae (Minus)	Schema
	hide Configure	L2 (Plus)	RNA-seq for L2 Stage Larvae (Plus)	Schema
	hide Configure	L2 (Minus)	RNA-seq for L2 Stage Larvae (Minus)	Schema
	hide Configure	L3 (Plus)	RNA-seq for L3 Stage Larvae (Plus)	Schema
	hide Configure	L3 (Minus)	RNA-seq for L3 Stage Larvae (Minus)	Schema
	hide Configure	L3, Dark Blue Gut (Plus)	RNA-seq for L3 Puff Stage, Dark Blue Gut (Plus)	Schema
	hide Configure	L3, Dark Blue Gut (Minus)	RNA-seq for L3 Puff Stage, Dark Blue Gut (Minus)	Schema
	hide Configure	L3, Blue Gut (Plus)	RNA-seq for L3 Puff Stage, Light Blue Gut (Plus)	Schema
	hide Configure	L3, Blue Gut (Minus)	RNA-seq for L3 Puff Stage, Light Blue Gut (Minus)	Schema
	hide Configure	L3, Clear Gut (Plus)	RNA-seq for L3 Puff Stage, Clear Gut (Plus)	Schema
	hide Configure	L3, Clear Gut (Minus)	RNA-seq for L3 Puff Stage, Clear Gut (Minus)	Schema
	hide Configure	L3_Carcass (Plus)	RNA-seq for L3 Carcass (Plus)	Schema
	hide Configure	L3_Carcass (Minus)	RNA-seq for L3 Carcass (Minus)	Schema
	hide Configure	WPP (Plus)	RNA-seq for White Prepupa (Plus)	Schema
	hide Configure	WPP (Minus)	RNA-seq for White Prepupa (Minus)	Schema
	hide Configure	WPP, 12 hrs (Plus)	RNA-seq for 12 hrs after White Prepupa (Plus)	Schema
	hide Configure	WPP, 12 hrs (Minus)	RNA-seq for 12 hrs after White Prepupa (Minus)	Schema
	hide Configure	WPP, 24 hrs (Plus)	RNA-seq for 24 hrs after White Prepupa (Plus)	Schema
	hide Configure	WPP, 24 hrs (Minus)	RNA-seq for 24 hrs after White Prepupa (Minus)	Schema
	hide Configure	WPP, 2 days (Plus)	RNA-seq for 2 days after White Prepupa (Plus)	Schema
	hide Configure	WPP, 2 days (Minus)	RNA-seq for 2 days after White Prepupa (Minus)	Schema
	hide Configure	WPP, 3 days (Plus)	RNA-seq for 3 days after White Prepupa (Plus)	Schema
	hide Configure	WPP, 3 days (Minus)	RNA-seq for 3 days after White Prepupa (Minus)	Schema
	hide Configure	WPP, 4 days (Plus)	RNA-seq for 4 days after White Prepupa (Plus)	Schema
	hide Configure	WPP, 4 days (Minus)	RNA-seq for 4 days after White Prepupa (Minus)	Schema
	hide Configure	Adult Female, 1 day (Plus)	RNA-seq for Adult Female 1 day Post-eclosion (Plus)	Schema
	hide Configure	Adult Female, 1 day (Minus)	RNA-seq for Adult Female 1 day Post-eclosion (Minus)	Schema
	hide Configure	Adult Female, 5 day (Plus)	RNA-seq for Adult Female 5 days Post-eclosion (Plus)	Schema
	hide Configure	Adult Female, 5 day (Minus)	RNA-seq for Adult Female 5 days Post-eclosion (Minus)	Schema
	hide Configure	Adult Female, 30 day (Plus)	RNA-seq for Adult Female 30 days Post-eclosion (Plus)	Schema
	hide Configure	Adult Female, 30 day (Minus)	RNA-seq for Adult Female 30 days Post-eclosion (Minus)	Schema
	hide Configure	Adult Male, 1 day (Plus)	RNA-seq for Adult Male 1 day Post-eclosion (Plus)	Schema
	hide Configure	Adult Male, 1 day (Minus)	RNA-seq for Adult Male 1 day Post-eclosion (Minus)	Schema
	hide Configure	Adult Male, 5 day (Plus)	RNA-seq for Adult Male 5 days Post-eclosion (Plus)	Schema
	hide Configure	Adult Male, 5 day (Minus)	RNA-seq for Adult Male 5 days Post-eclosion (Minus)	Schema
	hide Configure	Adult Male, 30 day (Plus)	RNA-seq for Adult Male 30 days Post-eclosion (Plus)	Schema
	hide Configure	Adult Male, 30 day (Minus)	RNA-seq for Adult Male 30 days Post-eclosion (Minus)	Schema
	hide Configure	Mixed Adult Carcass, 1 day (Plus)	RNA-seq for Mixed Adult Carcass 1 day Post-eclosion (Plus)	Schema
	hide Configure	Mixed Adult Carcass, 1 day (Minus)	RNA-seq for Mixed Adult Carcass 1 day Post-eclosion (Minus)	Schema
	hide Configure	Mixed Adult Carcass, 4 day (Plus)	RNA-seq for Mixed Adult Carcass 4 day Post-eclosion (Plus)	Schema
	hide Configure	Mixed Adult Carcass, 4 day (Minus)	RNA-seq for Mixed Adult Carcass 4 day Post-eclosion (Minus)	Schema
	hide Configure	Mixed Adult Carcass, 20 day (Plus)	RNA-seq for Mixed Adult Carcass 20 day Post-eclosion (Plus)	Schema
	hide Configure	Mixed Adult Carcass, 20 day (Minus)	RNA-seq for Mixed Adult Carcass 20 day Post-eclosion (Minus)	Schema
	hide Configure	Adult Female, DGRP 321 (Plus)	RNA-seq for Adult Female DGRP line 321 (Plus)	Schema
	hide Configure	Adult Female, DGRP 321 (Minus)	RNA-seq for Adult Female DGRP line 321 (Minus)	Schema
	hide Configure	Adult Female, DGRP 399 (Plus)	RNA-seq for Adult Female DGRP line 399 (Plus)	Schema
	hide Configure	Adult Female, DGRP 399 (Minus)	RNA-seq for Adult Female DGRP line 399 (Minus)	Schema
	hide Configure	Adult Female, DGRP 509 (Plus)	RNA-seq for Adult Female DGRP line 509 (Plus)	Schema
	hide Configure	Adult Female, DGRP 509 (Minus)	RNA-seq for Adult Female DGRP line 509 (Minus)	Schema
	hide Configure	Adult Female, DGRP 589 (Plus)	RNA-seq for Adult Female DGRP line 589 (Plus)	Schema
	hide Configure	Adult Female, DGRP 589 (Minus)	RNA-seq for Adult Female DGRP line 589 (Minus)	Schema
	hide Configure	Adult Male, ENCSR282WLG (Plus)	RNA-seq for Adult Male Experiment ENCSR282WLG (Plus)	Schema
	hide Configure	Adult Male, ENCSR282WLG (Minus)	RNA-seq for Adult Male Experiment ENCSR282WLG (Minus)	Schema
	hide Configure	Adult Male, ENCSR581YBD (Plus)	RNA-seq for Adult Male Experiment ENCSR581YBD (Plus)	Schema
	hide Configure	Adult Male, ENCSR581YBD (Minus)	RNA-seq for Adult Male Experiment ENCSR581YBD (Minus)	Schema
	hide Configure	Adult Male, ENCSR956AYX (Plus)	RNA-seq for Adult Male Experiment ENCSR956AYX (Plus)	Schema
	hide Configure	Adult Male, ENCSR956AYX (Minus)	RNA-seq for Adult Male Experiment ENCSR956AYX (Minus)	Schema
	hide Configure	Adult Male, ENCSR960BIV (Plus)	RNA-seq for Adult Male Experiment ENCSR960BIV (Plus)	Schema
	hide Configure	Adult Male, ENCSR960BIV (Minus)	RNA-seq for Adult Male Experiment ENCSR960BIV (Minus)	Schema

Description

These tracks show the strand-specific RNA-Seq coverage for different developmental stages of D. melanogaster. The RNA-Seq read coverage was normalized by a wigsum of 100,000,000 (1 million 100bp reads) using the bam2wig.py program in RSeQC.

The RNA-Seq reads were obtained from the ENCODE data portal at UCSC on August 2019, and then mapped against the D. melanogaster dm6 genome assembly using HISAT2. For each stage of development, results from multiple replicates were combined into a single RNA-Seq read coverage track.

References

Brown JB, et al. Diversity and dynamics of the Drosophila transcriptome. Nature. 2014 Aug 28;512(7515):393-9.

Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015 Apr;12(4):357-60.

Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012 Aug 15;28(16):2184-5.