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

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