Base Position
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Chromosome position in bases. (Clicks here zoom in 3x)
Chromosome Band
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Chromosome Bands
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Gap Locations
GC Percent
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GC Percent in 5-Base Windows
Assembly
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Assembly from Fragments
INSDC
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Accession at INSDC - International Nucleotide Sequence Database Collaboration
RefSeq Acc
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RefSeq Accession
Restr Enzymes
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Restriction Enzymes from REBASE
Short Match
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Perfect Matches to Short Sequence ()
Melting Temp.
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Melting Temperature Estimated by dan
RNASlider MFE
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Minimum Free Energy Estimated by RNASlider
1M-8M Screens (R5)
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1M-8M Screens (R5)
9M Screen (R5)
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9M Screen (R5)
GAA Screen
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GAA Mobilization Insertion Sites
Chr4 Constructs
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Chr4 Constructs
Landing Pad Lines (R5)
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phiC31 Landing Pad Insertion Lines (R5)
MiMIC Lines
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MiMIC Lines from the Gene Disruption Project
Het. Domains (R5)
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Broad H3K9me3+ Heterochromatin Domains (R5)
BG3 9-state (R5)
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modENCODE 9-state Model for BG3 cells (R5)
S2 9-state (R5)
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modENCODE 9-state Model for S2 cells (R5)
BG3 30-state (R5)
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modENCODE 30-state Model for BG3 cells (R5)
S2 30-state (R5)
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modENCODE 30-state Model for S2 cells (R5)
Kc 5-state (R5)
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5-state Model for Kc cells (R5)
hiHMM Models (R5)
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hiHMM Chromatin State Tracks (R5)
S2 Zhou 30-state (R5)
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30-state Model for S2 Cells Created by Zhou and Troyanskaya (R5)
LAD (R5)
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Lamina Associated Domains (LADs) in Kc Cells (R5)
Hi-C Domains (Embryos) (R5)
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Topological Domains Defined by Hi-C in Late Embryos (R5)
Topological Boundaries (R5)
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Topological Domain Boundaries Inferred from Chromatin States (R5)
TAD Boundaries (Nuc. Cycle 14)
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TAD Boundaries in Nuclear Cycle 14 Embryos
HiCseg Domains (Kc167) (R5)
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Domains Predicted by HiCseg Based Hi-C Data for Kc167 Cells (R5)
MARs (Embryos)
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Matrix Attachment Regions (MARs) in 0-16 Hour Embryos
Polytene TADs (R5)
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Polytene TADs Identified by Hi-C (R5)
GCSDI Models (R5)
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General Chromatin Sensitivity to DNase I Configuration Models (R5)
FlyBase Genes
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FlyBase Protein-Coding Genes
FlyBase Exons
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FlyBase Transcribed Exons
FlyBase CDS
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FlyBase Coding Exons
FlyBase Pseudogenes
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FlyBase Pseudogenes
FlyBase Non-coding
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FlyBase Non-protein Coding Genes
Drosophila RefSeq Transcripts
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BLAT Alignment of Drosophila RefSeq Transcripts
piRNA Clusters (R5)
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piRNA Clusters from Brennecke et al. 2007 (R5)
Pfam in RefSeq
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Pfam Domains in RefSeq Genes
UniProt
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UniProt SwissProt/TrEMBL Protein Annotations
InterProScan
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InterPro Signatures Identified by InterProScan
FlyBase 6.06 Genes
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FlyBase 6.06 Protein-Coding Genes
FlyBase 6.06 Proteins
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FlyBase 6.06 Protein-Coding Regions
FlyBase 6.06 Exons
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FlyBase 6.06 Transcribed Exons
FlyBase 6.06 CDS
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FlyBase 6.06 Coding Exons
FlyBase 6.06 Pseudogenes
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FlyBase 6.06 Pseudogenes
FlyBase 6.06 Non-coding
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FlyBase 6.06 Non-protein Coding Genes
Phantom Peaks (R5)
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ChIP-Seq Phantom Peaks (R5)
modENCODE Histones ChIP-Seq
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modENCODE Chromatin State Mapping Using ChIP-Seq
PePr Histone Modifications Peaks
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ChIP-Seq Peaks Identified by PePr
MUSIC Histone Modifications Peaks
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ChIP-Seq Peaks Identified by MUSIC
Genome Mappability
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Genome Mappability
modENCODE PolII ChIP-Seq
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modENCODE RNA Polymerase II ChIP-Seq
MUSIC PolII ChIP-Seq Peaks
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modENCODE RNA Polymerase ChIP-Seq Peaks Identified by MUSIC
PolII ChIP-Seq (Cell Lines)
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RNA Polymerase II ChIP-Seq for Cell Lines
RNA PolII X-ChIP-Seq
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RNA PolII X-ChIP-Seq for Drosophila S2 Cells
Inhibit Topoisomerases PolII ChIP-Seq
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PolII ChIP-Seq After Inhibition of Topoisomerases
Basal Transcription Factors ChIP-Seq
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Basal Transcription Factors ChIP-Seq
GAF KD Differential Regions
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GAF vs. GAF_KD Differential Regions
Basal Transcription Factors ChIP-exo
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ChIP-exo of Basal Transcription Factors in S2R+ Cells
ORGANIC Enrichment (S2 Cells)
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ORGANIC Enrichment Profiles for S2 Cells (R5)
Architectural Proteins ChIP-Seq (Kc167)
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ChIP-Seq of Architectural Proteins in Kc167 Cells
Architectural Proteins ChIP-Seq (S2)
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ChIP-Seq of Architectural Proteins in S2 Cells
Heat Shock Proteins ChIP-Seq (S2)
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ChIP-Seq of Heat Shock Proteins in S2 Cells
TF ChIP-nexus
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ChIP-nexus of Basal Transcription Factors in Kc Cells
ChIP-Seq MBT Embryos
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ChIP-Seq of Embryos Under Midblastula Transition
CLAMP ChIP-Seq
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ChIP-Seq for Chromatin-linked Adapter for MSL Proteins (CLAMP)
Henriques 2018 ChIP-Seq
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ChIP-Seq Data from Henriques 2018 for S2 cells
Zelda ChIP-Seq
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ChIP-Seq of Zelda Transcription Factor
Su(H) ChIP-Seq
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ChIP-Seq of Suppressor of Hairless Proteins
Histone Variants ChIP-Seq (S2)
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ChIP-Seq of Histone Variants in S2 Cells
R-Loop DRIP-Seq (S2)
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R-Loop DRIP-Seq in S2 Cells
modENCODE Histone Modifications (R5)
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modENCODE ChIP-chip Data for Histone Modifications (R5)
modENCODE Chromosomal Proteins (R5)
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modENCODE ChIP-chip Data for Chromosomal Proteins (R5)
modERN TF Peaks
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modERN Optimal Peaks for Transcription Factors
Unique ChIP-chip Probes
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Uniquely-Placed ChIP-chip Probes
Pausing Factors ChIP-chip (S2 Cells)
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Pausing Factors ChIP-chip in S2 Cells
wAna Alignments
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Regions with Sequence Similarity to wAna Genome Assembly
wRi Alignments
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Regions with Sequence Similarity to wRi Genome Assembly
wMel Alignments
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Regions with Sequence Similarity to wMel Genome Assembly
Wolbachia Proteins
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TBLASTN Alignment of Proteins from Wolbachia
Detected DHS Positions (Cell Lines) (R5)
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Detected High-Magnitude DHS Positions (Cell Lines) (R5)
DHS Read Density (Cell Lines) (R5)
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Smoothed DNaseI Read Density (Cell Lines) (R5)
Detected DHS Positions (Embryos)
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DHS Peaks Identified by MACS (Embryos)
DHS Read Density (Embryos)
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DNaseI Read Density (Embryos)
MACS2 DHS
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DNaseI Hypersensitive Sites Identified by MACS2
TSS (Embryonic) (R5)
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Transcription Start Sites (Embryonic) (R5)
TSS (Celniker) (R5)
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Transcription Start Sites (Celniker Group) (R5)
Combined modENCODE CAGE TSS
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Combined Transcription Start Sites Identified by modENCODE CAGE
modENCODE CAGE Tag Clusters
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modENCODE CAGE Tag Clusters for Different Developmental Stages
modENCODE CAGE Read Density
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modENCODE CAGE Read Density for Different Developmental Stages
Combined RAMPAGE TSS (R5)
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Combined RAMPAGE Transcription Start Sites (R5)
RAMPAGE TSS Read Density (R5)
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Combined RAMPAGE TSS (Replicate 2) (R5)
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Combined RAMPAGE Transcription Start Sites (Replicate 2) (R5)
RAMPAGE TSS Read Density (Replicate 2) (R5)
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RAMPAGE Read Density for Different Developmental Stages (Replicate 2) (R5)
Combined MachiBase TSS
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Combined MachiBase Transcription Start Sites
MachiBase TSS Read Density
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MachiBase Read Density for Different Developmental Stages
Combined Exo-seq TSS
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Combined Transcription Start Sites Identified by Exo-seq
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Exo-seq Read Density at Different Zeitgeber Times and Temperatures
Exo-seq Tag Clusters
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Exo-seq Tag Clusters at Different Zeitgeber Times and Temperatures
MACE TSS
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TSS Identified by 5' Massive Amplification of cDNA Ends (5' MACE)
Exosome RNAi CAGE
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Exosome RNAi Knockdown CAGE TSS
Exosome RNAi CAGE Tag Clusters
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Exosome RNAi Knockdown CAGE Tag Clusters
PEAT (S2 Cells)
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Paired-End Analysis of Transcription Start Sites for S2 Cells
TES (Celniker) (R5)
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Transcription End Sites (Celniker Group) (R5)
TFBS HOT Spots (R5)
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Transcription Factor Binding Sites HOT Spots (R5)
MACS STARR-seq Peaks
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STARR-Seq Peaks Identified by MACS
MACS STARR-seq Enrichment
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Log Likelihood Ratio of STARR-seq Enrichment Versus Input
MUSIC STARR-seq Peaks
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STARR-seq Peaks Identified by MUSIC
MUSIC STARR-seq Enrichment
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MUSIC STARR-seq Smoothed Signal Profiles
PePr STARR-seq Peaks
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Sharp STARR-seq Peaks Identified by PePr
hkCP dCP STARR-Seq
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Housekeeping and Developmental Enhancers Identified by STARR-Seq
Enhancers (R5)
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Enhancers Identified by CBP ChIP-chip and ChIP-Seq (R5)
Silencers (R5)
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Putative Polycomb Response Elements (Silencers) (R5)
Insulators (R5)
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Class I and Class II Insulator Elements (R5)
Origins of Replication (R5)
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Early Activating Origins of Replication (R5)
SNS Origins of Replication (R5)
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Origins of Replication Detected by SNS (R5)
EPDnew Promoters
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D. melanogaster Curated Promoter Database (EPDnew)
Schor 2017 CAGE Peaks (R5)
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CAGE Peaks and TSS Clusters Identified by Schor et al. 2017 (R5)
REDfly Regulatory Elements
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Regulatory Elements Annotated by REDfly
CORE Promoters
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Promoters Annotated by the CORE Database
GRO-Seq (R5)
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GRO-Seq for Untreated S2 Cells (R5)
Core LJ 2012 GRO-Seq (R5)
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GRO-Seq for Drosophila S2 Cells (Core LJ, 2012) (R5)
PRO-seq (R5)
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PRO-seq for Drosophila S2 Cells (R5)
Schaaf CA 2013 BG3 PRO-seq
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PRO-seq for Drosophila BG3 Cells (Schaaf CA, 2013)
Duarte FM 2016 PRO-seq
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PRO-seq for Drosophila S2 Cells (Duarte FM, 2016)
FStitch Nascent Transcripts
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Nascent RNA Transcripts Predicted by FStitch
3'NT (S2 Cells)
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Three Prime Position of Nascent Transcript (3'NT)
CapSeq Tag Clusters
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CapSeq Tag Clusters for w1118 (wildtype) Ovaries
CapSeq Read Density
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CapSeq Read Density for w1118 (wildtype) Ovaries
Start-Seq TSS (Larvae) (R5)
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Transcription Start Sites Identified by Start-Seq (Larvae) (R5)
scRNAs (S2 Cells)
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Short Capped RNAs (scRNAs) in S2 Cells
Permanganate ChIP-Seq (R5)
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Permanganate ChIP-Seq on Drosophila Cell Lines (R5)
Embryos FAIRE-Seq
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FAIRE-Seq of Drosophila Embryos
Schulz FAIRE-Seq
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FAIRE-Seq of Drosophila Embryos (Schulz et al. 2015)
Embryos ATAC-Seq
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ATAC-Seq of Drosophila Embryos
3rd Instar Larvae ATAC-Seq
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ATAC-Seq of Whole 3rd Instar Larvae
Eye Discs ATAC-Seq
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ATAC-Seq of D. melanogaster Eye Discs
Pupal Wings ATAC-Seq
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ATAC-Seq of Pupal Wings
Ovaries ATAC-Seq
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ATAC-Seq of Female Ovaries
MNase Accessibility (R5)
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MNase Accessibility of S2 Cells (R5)
GAF RNAi MNase
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GAF RNAi MNase-Seq for Drosophila S2 Cells
GAF vs. LacZ RNAi MNase
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GAF vs. LacZ RNAi MNase-Seq for Drosophila S2 Cells
NELF RNAi MNase
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NELF RNAi MNase-Seq for Drosophila S2 Cells
NELF RNAi vs. Mock MNase
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NELF RNAi vs. Mock MNase-Seq for Drosophila S2 Cells
MBT Embryos MNase
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MNase-Seq of Drosophila Embryos Under Midblastula Transition
FlyBase Exon Junctions
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FlyBase RNA-Seq Exon Junctions
Combined modENCODE RNA-Seq (Development) (R5)
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Combined modENCODE RNA-Seq for Multiple Developmental Stages (R5)
modENCODE RNA-Seq (Development) (R5)
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modENCODE RNA-Seq for Different Developmental Stages (R5)
modENCODE RNA-Seq (Cell Lines)
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modENCODE RNA-Seq for Different Cell Lines
Aggregated RNA-Seq Coverage
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NCBI SRA Aggregated RNA-Seq Coverage (Oliver Lab)
CIA Transcriptome (GffCompare)
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GffCompare Analysis of Combined Isoform Assembly (CIA) Transcriptome
CIA Transcriptome (ORFanage)
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ORFanage Analysis of Combined Isoform Assembly (CIA) Transcriptome
Drosophila Conservation (36 Species)
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ROAST Alignment and Conservation (36 RefSeq Drosophila Genomes)
RefSeq Drosophila Chain/Net
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RefSeq Drosophila Genomes, Chain and Net Alignments
Drosophila Conservation (28 Species)
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ROAST Alignments & Conservation (28 Drosophila Species)
Drosophila Conservation (26 Species)
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ROAST Alignments & Conservation (26 Drosophila Species)
PhyloP (14 Species)
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PhyloP Basewise Conservation Scores (14 Drosophila Species)
PhastCons (14 Species)
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PhastCons Conserved Elements (14 Drosophila Species)
Conservation (14 Species)
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Drosophila Multiz Alignments & phastCons Scores for 14 Drosophila Species
Drosophila Chain/Net
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Drosophila Genomes, Chain and Net Alignments
(dm3) D. mel. Chain
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D. melanogaster (Apr. 2006 (BDGP R5/dm3)) Chained Alignments
(dm3) D. mel. Net
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D. melanogaster (Apr. 2006 (BDGP R5/dm3)) Alignment Net
Variants in lacO Mutants (All)
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Genetic Variations in lacO Mutants (All)
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Genetic Variations in lacO Mutants (Filtered)
UniProt Variants
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UniProt/SwissProt Amino Acid Substitutions
dbSNP
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Short Genetic Variations in dbSNP (v149)
dbVar
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Structural Variations in dbVar
DGRP v2 (R5)
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Drosophila Genetics Reference Panel 2 (R5)
DGRP TE Insertions (ngs_te_mapper) (R5)
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Transposon Insertions in DGRP Lines Identified by ngs_te_mapper (R5)
DGRP TE Insertions (TEMP)
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Transposon Insertions in DGRP Lines Identified by TEMP
FlyVar EMS Screen
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Variants Identified in FlyVar EMS Mutagenesis Screen
Natural TE
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Transposable Elements Annotated by FlyBase
Interrupted Rpts
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Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite
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Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
Simple Repeats
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Simple Tandem Repeats by TRF
WM + SDust
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Genomic Intervals Masked by WindowMasker + SDust
RepeatMasker
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Repeating Elements by RepeatMasker
TE Density
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RepeatMasker Transposon Density (1kb window, 100bp step size)
Combined Library
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Repeats Identified by the Combined Repeat Library
TransposonPSI
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Transposons Fragments Identified by TransposonPSI
TANTAN
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Simple Repeats Identified by TANTAN
Tallymer
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Repetitive Regions Identified by Tallymer
RepeatDetector
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Repeats Identified by RepeatDetector
Inverted Repeats
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Inverted Repeats Identified by Inverted Repeats Finder
Combined modENCODE RNA-Seq (Development)
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Combined modENCODE RNA-Seq for Multiple Developmental Stages
Combined Splice Junctions (Development)
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Combined Splice Junctions for Multiple Developmental Stages
modENCODE RNA-Seq (Development)
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modENCODE RNA-Seq for Different Developmental Stages
Combined modENCODE RNA-Seq (Tissues)
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Combined modENCODE RNA-Seq for Multiple Tissues
Combined Splice Junctions (Tissues)
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Combined Splice Junctions for Multiple Tissues
modENCODE RNA-Seq (Tissues)
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modENCODE RNA-Seq for Different Tissues
Combined modENCODE RNA-Seq (Cell Lines)
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Combined modENCODE RNA-Seq for Multiple Cell Lines
Combined Splice Junctions (Cell Lines)
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Combined Splice Junctions for Multiple Cell Lines
modENCODE RNA-Seq (Cell Lines)
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modENCODE RNA-Seq for Different Cell Lines
Combined RAMPAGE Embryos TSS
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Combined RAMPAGE Embryos Transcription Start Sites
TSRchitect RAMPAGE Embryos TSS
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TSRchitect RAMPAGE Embryos Transcription Start Sites
TSRchitect Combined RAMPAGE TSS (Replicate 1)
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TSRchitect Combined RAMPAGE Transcription Start Sites (Replicate 1)
TSRchitect RAMPAGE TSS Read Density (Replicate 1)
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TSRchitect RAMPAGE Read Density for Different Developmental Stages (Replicate 1)
TSRchitect Combined RAMPAGE TSS (Replicate 2)
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TSRchitect Combined RAMPAGE Transcription Start Sites (Replicate 2)
TSRchitect RAMPAGE TSS Read Density (Replicate 2)
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TSRchitect RAMPAGE Read Density for Different Developmental Stages (Replicate 2)