		D. melanogaster Genome Browser

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D. melanogaster Genomic Browser: 57 kbp from 2L:123,000..180,000

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Landmark or Region: Examples: ftz, sos, 2L:120000..140000, 2LHet:98860..298860, 2RHet:433159..633158, 3LHet:721028..1721027, 3RHet:1791377..1841377, YHet:103159..203158, U:3907234..4107234.
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FlyBase Genes

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Embryonic (PolyA) (Showing 11 of 11 subtracks)

Embryonic (PolyA)

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Chromatin states (9 state model, S2 cells)

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Tracks

Annotations for Curated and Predicted Genes from FlyBase

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AUGUSTUS [?]

CONGO exons [?]

FlyBase Genes [?]

Chromatin Structure

Chromatin Proteins

Agilent array

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Agilent Array [?] [showing 3/3 subtracks]

ChIP-chip (Grouped by Cell Line)

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Chrom. Silencers and Re-modellers in CME W1 cl.8+ cells [?]	Chromatin Proteins in ML-DmBG3-c2 cells [?] [showing 12/12 subtracks]	Dosage comp. Proteins in S2-DRSC cells [?] [showing 4/4 subtracks]
Chrom. Silencers and Re-modellers in Kc167 cells [?] [showing 4/4 subtracks]	Chromatin Proteins in Oregon strain [?] [showing 25/25 subtracks]	Polycomb Proteins in Kc167 cells [?] [showing 3/3 subtracks]
Chrom. Silencers and Re-modellers in ML-DmBG3-c2 cells [?]	Chromatin Proteins in S2-DRSC cells [?] [showing 29/29 subtracks]	Polycomb Proteins in ML-DmBG3-c2 cells [?] [showing 4/4 subtracks]
Chrom. Silencers and Re-modellers in Oregon strain [?]	Dosage comp. Proteins in CME W1 cl.8+ cells [?] [showing 2/2 subtracks]	Polycomb Proteins in Oregon strain [?]
Chrom. Silencers and Re-modellers in S2-DRSC cells [?] [showing 6/6 subtracks]	Dosage comp. Proteins in Kc167 cells [?] [showing 2/2 subtracks]	Polycomb Proteins in S2-DRSC cells [?] [showing 5/5 subtracks]
Chromatin Proteins in CME W1 cl.8+ cells [?] [showing 6/6 subtracks]	Dosage comp. Proteins in ML-DmBG3-c2 cells [?] [showing 2/2 subtracks]
Chromatin Proteins in Kc167 cells [?] [showing 10/10 subtracks]	Dosage comp. Proteins in Oregon strain [?]

ChIP-chip (RNAi depletion)

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RNAi depletion of Chromatin proteins (ML-DmBG3-C2 cells) [?] [showing 25/25 subtracks]

RNAi depletion of Chromatin proteins (S2-DRSC cells) [?] [showing 7/7 subtracks]

Insulators

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Binding Sites for Insulators [?]

Insulators ChIP-Chip [?] [showing 10/10 subtracks]

Insulators ChIP-Seq [?] [showing 2/2 subtracks]

ChIP-chip

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Chrom. Silencers and Re-modellers in L3 [?] [showing 2/2 subtracks]	Chromatin Proteins in L3 [?] [showing 11/11 subtracks]	Dosage comp. Proteins in L3 [?]
Chrom. Silencers and Re-modellers in L3 Mutants [?]	Chromatin Proteins in L3 Mutants [?] [showing 24/24 subtracks]
Chromatin Proteins in Adult Female Ovaries	Chromatin Proteins in L3 Oregon strain

Insulators (Grouped by Cell Line)

ChIP-chip

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Insulators in Kc167 cells [?] [showing 7/7 subtracks]	Insulators in Oregon strain
Insulators in ML-DmBG3-c2 cells [?] [showing 8/8 subtracks]	Insulators in S2-DRSC cells [?] [showing 11/11 subtracks]

ChIP-seq

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Insulators in Oregon strain [?] [showing 5/5 subtracks]

ChIP-seq (Grouped by Cell Line)

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Chrom. Silencers and Re-modellers in Oregon strain [?] [showing 3/3 subtracks]	Chromatin Proteins in Oregon strain [?] [showing 22/22 subtracks]
Chromatin Proteins in L3 Oregon strain [?] [showing 4/4 subtracks]	Polycomb Proteins in Oregon strain

Chromatin states

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Chromatin states (30 state model, BG3 cells) [?]	Chromatin states (9 state model, BG3 cells) [?]
Chromatin states (30 state model, S2 cells) [?]	Chromatin states (9 state model, S2 cells) [?]

Histone Modifications

ChIP-seq (Grouped by Cell Line)

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H3 Histone Modifications in L3 Oregon strain [showing 10/10 subtracks]	H3 Histone Modofications in Oregon strain [?] [showing 38/38 subtracks]	H4 Histone Modifications in Oregon strain [?] [showing 5/5 subtracks]
H3 Histone Modifications in S2-DRSC cells [?]	H4 Histone Modifications in L3 Oregon strain [?]

ChIP-chip (Grouped by Cell Line)

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H3 Histone modifications in CME W1 cl.8+ cells [?] [showing 8/8 subtracks]	H3 Histone modifications in S2-DRSC cells [?] [showing 24/24 subtracks]	H4 Histone modifications in Oregon strain [?] [showing 5/5 subtracks]
H3 Histone modifications in Kc167 cells [?] [showing 20/20 subtracks]	H4 Histone modifications in CME W1 cl.8+ cells [?] [showing 2/2 subtracks]	H4 Histone modifications in S2-DRSC cells [?] [showing 7/7 subtracks]
H3 Histone modifications in ML-DmBG3-c2 cells [?] [showing 20/20 subtracks]	H4 Histone modifications in Kc167 cells [?] [showing 3/3 subtracks]
H3 Histone modifications in Oregon strain [?] [showing 34/34 subtracks]	H4 Histone modifications in ML-DmBG3-c2 cells [?] [showing 3/3 subtracks]

ChIP-Seq

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ChIP-Seq: Histone Modifications in Adult Female [?] [showing 4/4 subtracks]	ChIP-Seq: Histone Modifications in embryo 16-20hr [?] [showing 6/6 subtracks]	ChIP-Seq: Histone Modifications in L1 [?] [showing 6/6 subtracks]
ChIP-Seq: Histone Modifications in Adult Male [?] [showing 5/5 subtracks]	ChIP-Seq: Histone Modifications in embryo 20-24hr [?] [showing 6/6 subtracks]	ChIP-Seq: Histone Modifications in L2 [?] [showing 7/7 subtracks]
ChIP-Seq: Histone Modifications in embryo 0-4hr [?] [showing 6/6 subtracks]	ChIP-Seq: Histone Modifications in embryo 4-8hr [?] [showing 6/6 subtracks]	ChIP-Seq: Histone Modifications in L3 [?] [showing 5/5 subtracks]
ChIP-Seq: Histone Modifications in embryo 12-16hr [?] [showing 6/6 subtracks]	ChIP-Seq: Histone Modifications in embryo 8-12hr [?] [showing 6/6 subtracks]	ChIP-Seq: Histone Modifications in Pupae [?] [showing 6/6 subtracks]

ChIP-chip

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ChIP-chip: Histone Modifications in Adult Female [?] [showing 6/6 subtracks]	ChIP-chip: Histone Modifications in embryo 20-24hr [?] [showing 6/6 subtracks]	ChIP-chip: Histone Modifications in L3 (H3,Karpen) [?] [showing 13/13 subtracks]
ChIP-chip: Histone Modifications in Adult Female Ovaries [showing 2/2 subtracks]	ChIP-chip: Histone Modifications in embryo 4-8hr [?] [showing 6/6 subtracks]	ChIP-chip: Histone Modifications in L3 (H4, Karpen) [?] [showing 2/2 subtracks]
ChIP-chip: Histone Modifications in Adult Male [?] [showing 9/9 subtracks]	ChIP-chip: Histone Modifications in embryo 8-12hr [?] [showing 6/6 subtracks]	ChIP-chip: Histone Modifications in L3 Mutants (H3,Karpen) [?] [showing 32/32 subtracks]
ChIP-chip: Histone Modifications in embryo 0-12hr [?] [showing 4/4 subtracks]	ChIP-chip: Histone Modifications in Kc167 cells [?]	ChIP-chip: Histone Modifications in L3 Mutants (H4, Karpen) [?] [showing 3/3 subtracks]
ChIP-chip: Histone Modifications in embryo 0-4hr [?] [showing 9/9 subtracks]	ChIP-chip: Histone Modifications in L1 [?] [showing 6/6 subtracks]	ChIP-chip: Histone Modifications in Pupae [?] [showing 5/5 subtracks]
ChIP-chip: Histone Modifications in embryo 12-16hr [?] [showing 6/6 subtracks]	ChIP-chip: Histone Modifications in L2 [?] [showing 6/6 subtracks]	ChIP-chip: Histone Modifications in S2-DRSC cells [?]
ChIP-chip: Histone Modifications in embryo 16-20hr [?] [showing 6/6 subtracks]	ChIP-chip: Histone Modifications in L3 [?] [showing 6/6 subtracks]

Histone Modifying Enzymes

ChIP-seq (Grouped by Cell Line)

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Histone Modifying Enzymes in L3 Oregon strain [?] [showing 2/2 subtracks]

Histone Modifying Enzymes in Oregon strain [?] [showing 5/5 subtracks]

ChIP-chip (Grouped by Cell Line)

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Histone Modifying Enzymes in Kc167 cells [?] [showing 11/11 subtracks]	Histone Modifying Enzymes in Oregon strain [?] [showing 3/3 subtracks]
Histone Modifying Enzymes in ML-DmBG3-c2 cells [?] [showing 13/13 subtracks]	Histone Modifying Enzymes in S2-DRSC cells [?] [showing 15/15 subtracks]

ChIP-chip

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Histone Modifying Enzymes in L3 [?]

Histone Modifying Enzymes in L3 Mutants [?]

Histone Variants

ChIP-seq (Grouped by Cell Line)

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Histone Variants in L3 Oregon strain [?] [showing 2/2 subtracks]

Histone Variants in Oregon strain [?] [showing 9/9 subtracks]

ChIP-seq (RNAi Depletion)

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RNAi Depletion of Histone Variants (S2-DRSC cells) [?] [showing 2/2 subtracks]

ChIP-chip (Grouped by Cell Line)

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Histone Variants in CME W1 cl.8+ cells [?] [showing 2/2 subtracks]	Histone Variants in ML-DmBG3-c2 cells [?] [showing 5/5 subtracks]	Histone Variants in S2-DRSC cells [?] [showing 6/6 subtracks]
Histone Variants in Kc167 cells [?] [showing 4/4 subtracks]	Histone Variants in Oregon strain [?] [showing 4/4 subtracks]

ChIP-chip

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Histone Variants in L3 [?] [showing 2/2 subtracks]

Nucleosome Structure

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CATCH-IT data, Aha labeling [?]	Chromatin NaCl fractions (Histone Variants) [?] [showing 8/8 subtracks]	H3 [?]
CATCH-IT data, Aha labeling timecourse [?]	Chromatin NaCl fractions (Kc167 cells) [?] [showing 4/4 subtracks]	H33 [?]
CATCH-IT data, pulse/chase Aha labeling [?]	Chromatin NaCl fractions (S2-DRSC cells) [?] [showing 5/5 subtracks]	Histone Variants [?]
Chromatin NaCl fractions (embryonic samples) [?] [showing 6/6 subtracks]	Chromatin NaCl fractions (wing disc) [?] [showing 4/4 subtracks]	Mononucleosomes [?] [showing 3/3 subtracks]

RNAi Salt Extraction

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L3 CME W1 Cl.8+ 150mM (control) [?]	L3 Kc167 150mM HP1 RNAi [?]	L3 ML-DmBG3-c2 80mM (control) [?]
L3 CME W1 Cl.8+ 80mM (control) [?]	L3 Kc167 150mM spt6 RNAi [?]
L3 Kc167 150mM (control) [?]	L3 ML-DmBG3-c2 150mM (control) [?]

DNA replication

Copy Number Variation

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CGH array scores (Cell lines) [?]	Copy Number Variation [?] [showing 4/4 subtracks]
CGH array scores (Tissues) [?] [showing 9/9 subtracks]	Pair-Ended Copy Number Variation [showing 3/3 subtracks]

Origins of Replication

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ChIP-Seq dORC2 [?] [showing 6/6 subtracks]	ChIP-Seq MCM [?] [showing 2/2 subtracks]
ChIP-Seq dORC2 (Tissues) [?] [showing 7/7 subtracks]	Early origins of replication [?] [showing 4/4 subtracks]

Replication Timing and pre-RC components

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BG3 WT Repliseq [showing 4/4 subtracks]	Kc167 Repli-Seq [?] [showing 3/3 subtracks]	Replication Timing [?] [showing 3/3 subtracks]
KC WT Repliseq [showing 4/4 subtracks]	pre-RC components [?] [showing 2/2 subtracks]	S2 WT Repliseq [showing 4/4 subtracks]

Gene Structure

5-ends and UTRS

5-prime-RACE products

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5' RLM-RACE sequencing, 0-24 hr embryo [?]	BDGP 5 prime RACE [?]
5' RLM-RACE sequencing, Adults [?]	Stranded RACE TSS density [?]

CAGE

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CAGE 0-24 hr Embryo [?]

CAGE 0-24 hr Embryo (read density) [?]

Developmental Timecourse

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CAGE Embryo 0-2 hr [?]	CAGE Embryo 4-6 hr [?]	CAGE L3 12 hr Post-molt [?]
CAGE Embryo 12-14 hr [?]	CAGE Embryo 6-8 hr [?]	CAGE L3 PS(3-6) [?]
CAGE Embryo 16-18 hr [?]	CAGE Embryo 8-10 hr [?]	CAGE White Pre-Pupae + 12 hr [?]
CAGE Embryo 2-4 hr [?]	CAGE L1 [?]	CAGE White Pre-Pupae + 2 days [?]
CAGE Embryo 20-22 hr [?]	CAGE L2 [?]

Cell Line

Compartment

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CAGE kc167 Cytoplasm RNA [?]

CAGE kc167 Nuclear RNA [?]

CAGE S2-DRSC Whole Cell [?]

Treatment

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CAGE BG3-c2 Whole Cell [?]	CAGE BG3-c2 Whole Cell 24 hr Ecdysone [?]
CAGE BG3-c2 Whole Cell 0 hr Ecdysone [?]	CAGE BG3-c2 Whole Cell 5 hr Ecdysone [?]

Tissues

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CAGE Accessory Glands Adult Mated Males Eclosion + 4 days [?]	CAGE L3 Central Nervous System [?]	CAGE Mixed-sex Digestive System Eclosion + 4 days [?]
CAGE Central Nervous System White Pre-Pupae + 2 days [?]	CAGE L3 Wandering Carcass [?]	CAGE Ovaries Adult Mated Females Eclosion + 4 days [?]
CAGE Fat Bodies White Pre-Pupae + 2 days [?]	CAGE L3 Wandering Digestive System [?]	CAGE Ovaries Adult Virgin Females Eclosion + 4 days [?]
CAGE Head Adult Mated Females Eclosion + 20 days [?]	CAGE L3 Wandring Imaginal Disc [?]	CAGE Testes Adult Mated Males Eclosion + 4 days [?]
CAGE Head Adult Mated Males Eclosion + 20 days [?]	CAGE Mixed-sex Carcass Eclosion + 4 days [?]	CAGE Trizol-isolated Adult Mated Females Eclosion + 1 day [?]
CAGE Head Trizol-isolated Adult Mated Males Eclosion + 1 day [?]	CAGE Mixed-sex Digestive System Eclosion + 20 days [?]

Gene Models

Gene Structures from modENCODE

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Genomic DNA alignment Oregon-R Bloomington [?]	Interspecific Comparison: Cufflink Models [?]
Ginormous gene Annotations [?]	Interspecific Comparison: Novel Models [?]

RTPCR from modENCODE

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DMG1 RTPCR [?]	DMG2 RTPCR target gene models [?]	DMG4 RTPCR [?]
DMG1 RTPCR target gene models [?]	DMG3 RTPCR [?]	DMG4 RTPCR target gene models [?]
DMG2 RTPCR [?]	DMG3 RTPCR target gene models [?]	MB6 RTPCR [?]

Genomic Sequencing

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1182-4H [?]	D8 [?]	S2R+ [?]
CME W1 Cl.8+ [?]	D9 [?]	S3 [?]
D16C3 [?]	L1 [?]	Sg4 [?]
D17-C3 [?]	mbn2 [?]	W2 [?]
D20-C2 [?]	ML-DMD20-C5 [?]
D4-C1 [?]	S1 [?]

Splice Junction Annotation

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0-2h embryo	embryo 16-18h	L3 12hr post-molt
Adult Female eclosion+1d	embryo 18-20h	L3 clear gut PS7-9
Adult Female eclosion+30d	embryo 2-4h	L3 dark blue gut PS1-2
Adult Female eclosion+5d	embryo 20-22h	L3 light blue gut PS3-6
Adult Male eclosion+1d	embryo 22-24h	WPP
Adult Male eclosion+30d	embryo 4-6h	WPP+12h
Adult Male eclosion+5d	embryo 6-8h	WPP+24h
embryo 10-12h	embryo 8-10h	WPP+2d
embryo 12-14h	L1	WPP+3d
embryo 14-16h	L2	WPP+4d

cDNA

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Full-length cDNA Sequencing v6 [?]	Long RT-PCR for transcript validation v1 [?]
Full-length cDNA Sequencing vFinal [?]	Long RT-PCR for transcript validation v2 [?]

polyA Sites Annotation

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L3, CNS Unique mapper [?]	Males+Females, Eclosion+4 days, carcass Unique mapper [?]	mated Male, Eclosion+4 days, testes Unique mapper [?]
L3, wandering stage, carcass Unique mapper [?]	Males+Females, Eclosion+4 days, digestive system Unique mapper [?]	virgin Female, Eclosion+1 day, heads Unique mapper [?]
L3, wandering stage, digestive system Unique mapper [?]	mated Female, Eclosion+1 day, heads Unique mapper [?]	virgin Female, Eclosion+20 days, heads Unique mapper [?]
L3, wandering stage, fat body Unique mapper [?]	mated Female, Eclosion+20 days, heads Unique mapper [?]	virgin Female, Eclosion+4 days, heads Unique mapper [?]
L3, wandering stage, imaginal discs Unique mapper [?]	mated Female, Eclosion+4 days, heads Unique mapper [?]	virgin Female, Eclosion+4 days, ovaries Unique mapper [?]
L3, wandering stage, salivary glands Unique mapper [?]	mated Female, Eclosion+4 days, ovaries Unique mapper [?]	WPP+2d, CNS Unique mapper [?]
Males+Females, Eclosion+1 day, carcass Unique mapper [?]	mated Male, Eclosion+1 day, heads Unique mapper [?]	WPP+2d, fat Unique mapper [?]
Males+Females, Eclosion+1 day, digestive system Unique mapper [?]	mated Male, Eclosion+20 days, heads Unique mapper [?]	WPP, fat body Unique mapper [?]
Males+Females, Eclosion+20 days, carcass Unique mapper [?]	mated Male, Eclosion+4 days, accessory glands Unique mapper [?]	WPP, salivary glands Unique mapper [?]
Males+Females, Eclosion+20 days, digestive system Unique mapper [?]	mated Male, Eclosion+4 days, heads Unique mapper [?]

RNA Expression Profiling

mRNA

RNA tiling arrays (38bp)

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Cell Lines [?] [showing 32/32 subtracks]	Embryonic (Total) [?] [showing 12/12 subtracks]	Post-embryonic (Total) [?] [showing 18/18 subtracks]
Embryonic (PolyA) [?] [showing 11/11 subtracks]	Oregon-R Embryonic (polyA) [?] [showing 2/2 subtracks]	Tissues [?] [showing 3/3 subtracks]

RNA tiling arrays (53bp)

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NimbleGen Tiling Arrays [?] [showing 3/3 subtracks]

RNA tiling arrays (7bp)

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Embryonic (7b array, poly A) [?]

Embryonic (7b array, Total) [?]

RNA-Seq 454

Developmental Stage

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454 Embryo 12-14 hr [?]	454 Mated Male Testes Eclosion + 4 days (polyA+ RNA) [?]	454 Oregon-R Adult Female (polyA+ RNA) [?]
454 L3 Wandering Imaginal Discs (polyA+ RNA) [?]	454 Mixed-stage Embryo (polyA+ RNA) [?]	454 Oregon-R Adult Male (polyA+ RNA) [?]

RNA-Seq

Capped small RNA

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Cl.8+ [?]	ML-DmBG3.c2 [?]
Kc-167 [?]	S2-DRSC [?]

Cell Line

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CME W1 cl.8+ (C-tailed RNA), Unique mapper [?]	Kc167 (C-tailed RNA), Unique mapper [?]	ML-DmBG3-c2 (polyA RNA), Unique mapper [?]
CME W1 cl.8+ (polyA RNA), Multi mapper [?]	Kc167 (polyA RNA), Multi mapper [?]	S2-DRSC (C-tailed RNA), Unique mapper [?]
CME W1 cl.8+ (polyA RNA), Unique mapper [?]	Kc167 (polyA RNA), Unique mapper [?]	S2-DRSC (polyA RNA), Multi mapper [?]
embryo 16-18h (C-tailed), NexAlign [?]	ML-DmBG3-c2 (C-tailed RNA), Unique mapper [?]	S2-DRSC (polyA RNA), Unique mapper [?]
Kc167 (C-tailed polyA RNA), Multi mapper [?]	ML-DmBG3-c2 (polyA RNA), Multi mapper [?]	Whole Adult Fly, Unique mapper [?]

Cell Line (stranded)

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	MultiMapper	UniqueMapper
1182-4H	1182-4H, Multi mapper [?]	1182-4H, Unique mapper [?]
ML-DmBG1-c1	ML-DmBG1-c1, Multi mapper [?]	ML-DmBG1-c1, Unique mapper [?]
BG2c2	ML-DmBG2-c2, Multi mapper [?]	ML-DmBG2-c2, Unique mapper [?]
CME_L1	CME L1, Multi mapper [?]	CME_L1, Unique mapper [?]
CME_W2	CME W2, Multi mapper [?]	CME W2, Unique mapper [?]
GM2	GM2, Multi mapper [?]	GM2, Unique mapper [?]
Kc167	Kc167, Multi mapper [?]	Kc167, Unique mapper [?]
MBN2	MBN2, Multi mapper [?]	MBN2, Unique mapper [?]
ML-DmD11	ML-DmD11, Multi mapper [?]	ML-DmD11, Unique mapper [?]
ML-DmD16-c3	ML-DmD16-3, Multi mapper [?]	ML-DmD16-c3, Unique mapper [?]
ML-DmD17-c3	ML-DmD17-c3, Multi mapper [?]	ML-DmD17-c3, Unique mapper [?]
ML-DMD20-c5	ML-DmD20-c5, Multi mapper [?]	ML-DmD20-c5, Unique mapper [?]
ML-DmD21	ML-DmD2, Multi mapper [?]	ML-DmD21, Unique mapper [?]
ML-DmD32	ML-DmD32, Multi mapper [?]	ML-DmD32, Unique mapper [?]
ML-DmD4-c1	ML-DmD4-c1, Multi mapper [?]	ML-DmD4-c1, Unique mapper [?]
ML-DmD8	ML-DmD8, Multi mapper [?]	ML-DmD8, Unique mapper [?]
ML-DmD9	ML-DmD9, Multi mapper [?]	ML-DmD9, Unique mapper [?]
S1	S1, Multi mapper [?]	S1, Unique mapper [?]
S2Rplus	S2R+, Multi mapper [?]	S2R+, Unique mapper [?]
S3	S3, Multi mapper [?]	S3, Unique mapper [?]
Sg4	Sg4, Multi mapper [?]	Sg4, Unique mapper [?]
OSS	OSS, Multi mapper [?]	OSS, Unique mapper [?]
OSC	OSC, Multi mapper [?]	OSC, Unique mapper [?]
fGS	fGS, Multi mapper [?]	fGS, Unique mapper [?]

Cell Line cap-enriched 5 monoP small RNA

Cytoplasmic

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	CIP-TAP	Untreated
BG3	BG3_Cyto_CIP-TAP [?]	BG3_Cyto_Untreated [?]
Cl.8	Cl.8_Cyto_CIP-TAP [?]	Cl.8_Cyto_Untreated [?]
Kc167	Kc167_Cyto_CIP-TAP [?]	Kc167_Cyto_Untreated [?]
S2-DRSC	S2-DRSC_Cyto_CIP-TAP [?]	S2-DRSC_Cyto_Untreated [?]
S2R+	S2R+_Cyto_CIP-TAP [?]	S2R+_Cyto_Untreated [?]

Nuclear

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	CIP-TAP	Untreated
BG3	BG3_Nuclear_CIP-TAP [?]	BG3_Nuclear_Untreated [?]
Cl.8	Cl.8_Nuclear_CIP-TAP [?]	Cl.8_Nuclear_Untreated [?]
Kc167	Kc167_Nuclear_CIP-TAP [?]	Kc167_Nuclear_Untreated [?]
S2-DRSC	S2-DRSC_Nuclear_CIP-TAP [?]	S2-DRSC_Nuclear_Untreated [?]
S2R+	S2R+_Nuclear_CIP-TAP [?]	S2R+_Nuclear_Untreated [?]

PolyA-tail

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Kc-167 polyA [?]	S2-DRSC polyA [?]
ML-DmBG3.c2 polyA [?]	W1-Cl.8+ polyA [?]

Whole cell

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	CIP-TAP	Untreated
BG3	BG3_Whole_cell_CIP-TAP [?]	BG3_Whole_cell_Untreated [?]
Cl.8	Cl.8_Whole_cell_CIP-TAP [?]	Cl.9_Whole_cell_Untreated [?]
Kc167	Kc167_Whole_cell_CIP-TAP [?]	Kc167_Whole_cell_Untreated [?]
S2-DRSC	S2-DRSC_Whole_cell_CIP-TAP [?]	S2-DRSC_Whole_cell_Untreated [?]
S2R+	S2R+_Whole_cell_CIP-TAP [?]	S2R+_Whole_cell_Untreated [?]

ChIP Samples

All on All off

AdultFemale [?]	Embryo 16-20h [?]	L1 [?]
AdultMale [?]	Embryo 20-24h [?]	L2 [?]
Embryo 0-4h [?]	Embryo 4-8h [?]	L3 RNA-seq [?]
Embryo 12-16h [?]	Embryo 8-12h [?]	Pupae RNA-seq [?]

Developmental Stage

All on All off

	MultiMapper	UniqueMapper
embryo_0-2hr	Embryo 0-2h RNA-Seq Multi mapper [?]	Embryo 0-2h RNA-Seq Unique mapper [?]
embryo_2-4hr	Embryo 2-4h RNA-Seq Multi mapper [?]	Embryo 2-4h RNA-Seq Unique mapper [?]
embryo_4-6hr	Embryo 4-6h RNA-Seq Multi mapper [?]	Embryo 4-6h RNA-Seq Unique mapper [?]
embryo_6-8hr	Embryo 6-8h RNA-Seq Multi mapper [?]	Embryo 6-8h RNA-Seq Unique mapper [?]
embryo_8-10hr	Embryo 8-10h RNA-Seq Multi mapper [?]	Embryo 8-10h RNA-Seq Unique mapper [?]
embryo_10-12hr	Embryo 10-12h RNA-Seq Multi mapper [?]	Embryo 10-12h RNA-Seq Unique mapper [?]
embryo_12-14hr	Embryo 12-14h RNA-Seq Multi mapper [?]	Embryo 12-14h RNA-Seq Unique mapper [?]
embryo_14-16hr	Embryo 14-16h RNA-Seq Multi mapper [?]	Embryo 14-16h RNA-Seq Unique mapper [?]
embryo_16-18hr	Embryo 16-18h RNA-Seq Multi mapper [?]	Embryo 16-18h RNA-Seq Unique mapper [?]
embryo_18-20hr	Embryo 18-20h RNA-Seq Multi mapper [?]	Embryo 18-20h RNA-Seq Unique mapper [?]
embryo_20-22hr	Embryo 20-22h RNA-Seq Multi mapper [?]	Embryo 20-22h RNA-Seq Unique mapper [?]
embryo_22-24hr	Embryo 22-24h RNA-Seq Multi mapper [?]	Embryo 22-24h RNA-Seq Unique mapper [?]
L1	L1 RNA-Seq Multi mapper [?]	L1 RNA-Seq Unique mapper [?]
L2	L2 RNA-Seq Multi mapper [?]	L2 RNA-Seq Unique mapper [?]
L3+12hr	L3 + 12hr RNA-Seq Multi mapper [?]	L3+12hr RNA-Seq Unique mapper [?]
L3_PS1-2	L3 PS1-2 RNA-Seq Multi mapper [?]	L3 PS1-2 RNA-Seq Unique mapper [?]
L3_PS3-6	L3 PS3-6 RNA-Seq Multi mapper [?]	L3 PS3-6 RNA-Seq Unique mapper [?]
L3_PS7-9	L3 PS7-9 RNA-Seq Multi mapper [?]	L3 PS7-9 RNA-Seq Unique mapper [?]
WPP	WPP RNA-Seq Multi mapper [?]	White Pre-pupae RNA-Seq Unique mapper [?]
WPP+12hr	WPP + 12hr RNA-Seq Multi mapper [?]	White Pre-pupae 12hr RNA-Seq Unique mapper [?]
WPP+24hr	WPP + 24hr RNA-Seq Multi mapper [?]	White Pre-pupae 24hr RNA-Seq Unique mapper [?]
WPP+2d	WPP + 2days RNA-Seq Multi mapper [?]	White Pre-pupae 2days RNA-Seq Unique mapper [?]
WPP+3d	WPP + 3days RNA-Seq Multi mapper [?]	White Pre-pupae 3days RNA-Seq Unique mapper [?]
WPP+4d	WPP + 4days RNA-Seq Multi mapper [?]	White Pre-pupae 4days RNA-Seq Unique mapper [?]
Adult_Female+1d	Female Eclosion + 1 day RNA-Seq Multi mapper [?]	Adult Female Eclosion 1 day RNA-Seq Unique mapper [?]
Adult_Female+5d	Female Eclosion + 5 days RNA-Seq Multi mapper [?]	Adult Female Eclosion 5 day RNA-Seq Unique mapper [?]
Adult_Female+30d	Female Eclosion + 30 days RNA-Seq Multi mapper [?]	Adult Female Eclosion 30 day RNA-Seq Unique mapper [?]
Adult_Male+1d	Male Eclosion + 1 days RNA-Seq Multi mapper [?]	Adult Male Eclosion 1 day RNA-Seq Unique mapper [?]
Adult_Male+5d	Male Eclosion + 5 days RNA-Seq Multi mapper [?]	Adult Male Eclosion 5 day RNA-Seq Unique mapper [?]
Adult_Male+30d	Male Eclosion + 30 days RNA-Seq Multi mapper [?]	Adult Male Eclosion 30 day RNA-Seq Unique mapper [?]

RNAi depletion of splicing factors (S2 cells)

All on All off

	UniqueMapper	MultiMapper
Control	Untreated control, Unique mapper [?]	=Untreated.Control
CG10128	CG10128 (tra2), Unique mapper [?]	CG10128 (tra2), Multi mapper [?]
CG9373	CG9373 (rump), Unique mapper [?]	=CG9373
CG8781	CG8781 (tsu), Unique mapper [?]	=CG8781
CG8636	CG8636 (eIF3-S4), Unique mapper [?]	CG8636 (elF3-S4), Multi mapper [?]
CG7437	CG7437 (mub), Unique mapper [?]	CG7437 (mub), Multi mapper [?]
CG6779	CG6779 (RpS3), Unique mapper [?]	CG6779 (RpS3), Multi mapper [?]
CG6227	CG6227, Unique mapper [?]	CG6227, Multi mapper [?]
CG5655	CG5655 (Rsf1), Unique mapper [?]	=CG5655
CG33106	CG33106 (mask), Unique mapper [?]	=CG33106
CG32423	CG32423 (shep), Unique mapper [?]	=CG32423
CG17838	CG17838, Unique mapper [?]	CG17838, Multi mapper [?]
CG1101	CG1101 (Aly), Unique mapper [?]	=CG1101
CG10203	CG10203 (xl6), Unique mapper [?]	CG10203(xl6), Multi mapper [?]
CG8749	CG8749 (snRNP-U1-70K), Unique mapper [?]	CG8749 (snRNP-U1-70K), Multi mapper [?]
CG5821	CG5821 (qkr58E-2), Unique mapper [?]	=CG5821
CG5170	CG5170 (Dp1), Unique mapper [?]	=CG5170
CG4602	CG4602 (Srp54), Unique mapper [?]	CG4602 (Srp54), Multi mapper [?]
CG6841	CG6841, Unique mapper [?]	CG6841, Multi mapper [?]
CG6203	CG6203 (Fmr1), Unique mapper [?]	CG6203 (Fmr1), Multi mapper [?]
CG5422	CG5422 (Rox8), Unique mapper [?]	=CG5422
CG8912	CG8912 (Psi), Unique mapper [?]	=CG8912
CG8241	CG8241 (pea), Unique mapper [?]	=CG8241
CG16901	CG16901 (sqd), Unique mapper [?]	CG16901 (sqd), Multi mapper [?]
CG13425	CG13425 (bl), Unique mapper [?]	=CG13425
CG10279	CG10279 (Rm62), Unique mapper [?]	CG10279 (Rm62), Multi mapper [?]
CG6049	CG6049, Unique mapper [?]	=CG6049
CG3312	CG3312 (Rnp4F), Unique mapper [?]	=CG3312
CG31716	CG31716 (NOT4), Unique mapper [?]	CG31716 (NOT4), Multi mapper [?]
CG30122	CG30122, Unique mapper [?]	=CG30122
CG1126	CG11266 (CAPER), Unique mapper [?]	=CG1126
CG8019	CG8019 (hay), Unique mapper [?]	=CG8019
CG7971	CG7971, Unique mapper [?]	=CG7971
CG4816	CG4816 (qkr54B), Unique mapper [?]	CG4816 (qkr54B), Multi mapper [?]
CG3584	CG3584 (qkr58E-3), Unique mapper [?]	=CG3584
CG1646	CG1646 (Prp39), Unique mapper [?]	=CG1646
CG10851	CG10851 (B52), Unique mapper [?]	CG10851 (B52), Multi mapper [?]
CG5099	CG5099 (msi), Unique mapper [?]	CG5099 (msi), Multi mapper [?]
CG4760	CG4760 (bol), Unique mapper [?]	=CG4760
CG18350	CG18350 (Sxl), Unique mapper [?]	=CG18350
CG16788	CG16788 (RnpS1), Unique mapper [?]	CG16788 (RnpS1), Multi mapper [?]
CG1559	CG1559 (Upf1), Unique mapper [?]	CG1559 (Upf1), Multi mapper [?]
CG10377	CG10377 (Hrb27C), Unique mapper [?]	=CG10377
CG9412	CG9412 (rin), Unique mapper [?]	=CG9412
CG6946	CG6946 (glo), Unique mapper [?]	=CG6946
CG1987	CG1987 (Rbp1-like), Unique mapper [?]	=CG1987
CG9983	CG9983 (Hrb98DE), Unique mapper [?]	=CG9983
CG5442	CG5442 (SC35), Unique mapper [?]	CG5442 (SC35), Multi mapper [?]
CG31000	CG31000 (heph), Unique mapper [?]	=CG31000
CG17136	CG17136 (Rbp1), Unique mapper [?]	CG17136 (Rbp1), Multi mapper [?]
B.Control	Untreated-B control, Unique mapper [?]	=Untreated.B.Control
CG4878	CG4878 (eIF3-S9), Unique mapper [?]	=CG4878
CG4262	CG4262 (elav), Unique mapper [?]	CG4262 (elav), Multi mapper [?]
CG18426	CG18426 (ytr), Unique mapper [?]	=CG18426
CG12749	CG12749 (Hrb87F), Unique mapper [?]	CG12749 (Hrb87F), Multi mapper [?]
CG7878	CG7878, Unique mapper [?]	=CG7878
CG5836	CG5836 (SF1), Unique mapper [?]	=CG5836
CG3249	CG3249 (yu), Unique mapper [?]	=CG249
CG10328	CG10328 (nonA-like), Unique mapper [?]	=CG10328
CG8144	CG8144 (ps), Unique mapper [?]	=CG8144
CG12357	=CG12357	CG12357, Multi mapper [?]
CG16725	=CG16725	CG16725, Multi mapper [?]
CG3613	=CG3613	CG3613, Multi mapper [?]
CG42670	=CG42670	CG42670, Multi mapper [?]
CG6987	=CG6987	CG6987, Multi mapper [?]
CG9998	=CG9998	CG9998, Multi mapper [?]
EmptyVector	=EmptyVector	Empty Vector, Multi mapper [?]

Stranded Total RNA-Seq (SOLiD)

Multiply mapped reads

All on All off

Embryo 0-2hr [?]	Embryo 16-18hr [?]	Embryo 22-24hr [?]
Embryo 10-12hr [?]	Embryo 18-20hr [?]	Embryo 4-6hr [?]
Embryo 12-14hr [?]	Embryo 2-4hr [?]	Embryo 6-8hr [?]
Embryo 14-16hr [?]	Embryo 20-22hr [?]	Embryo 8-10hr [?]

Uniquely mapped reads

All on All off

Embryo time course RNA-seq read density [?] [showing 12/12 subtracks]

Tissues (stranded)

All on All off

Adult Male/Female Ecl+1day Carcass, Multi mapper [?]	Adult Mated Male Ecl+1day Heads, Multi mapper [?]	L3 CNS, Multi mapper [?]
Adult Male/Female Ecl+1day Digestive System, Multi mapper [?]	Adult Mated Male Ecl+20days Heads, Multi mapper [?]	L3 Digestive System, Multi mapper [?]
Adult Male/Female Ecl+20days Carcass, Multi mapper [?]	Adult Mated Male Ecl+4days Accessory Glands, Multi mapper [?]	L3 Fat Body, Multi mapper [?]
Adult Male/Female Ecl+20days Digestive System, Multi mapper [?]	Adult Mated Male Ecl+4days Heads, Multi mapper [?]	L3 Imaginal Discs, Multi mapper [?]
Adult Male/Female Ecl+4day DigestiveSystem, Multi mapper [?]	Adult Mated Male Ecl+4days Testes, Multi mapper [?]	L3 Salivary Glands, Multi mapper [?]
Adult Male/Female Ecl+4days Carcass, Multi mapper [?]	Adult Virgin Female Ecl+1day Heads, Multi mapper [?]	WPP 2days CNS, Multi mapper [?]
Adult Mated Female Ecl+20days Heads, Multi mapper [?]	Adult Virgin Female Ecl+20days Heads, Multi mapper [?]	WPP 2days Fat, Multi mapper [?]
Adult Mated Female Ecl+4days Heads, Multi mapper [?]	Adult Virgin Female Ecl+4days Heads, Multi mapper [?]	WPP Fat Body, Multi mapper [?]
Adult Mated Female Ecl+4days Ovaries, Multi mapper [?]	Adult Virgin Female Ecl+4days Ovaries, Multi mapper [?]	WPP Salivary Glands, Multi mapper [?]
Adult Mated Female_Ecl+1day Heads, Multi mapper [?]	L3 Carcass, Multi mapper [?]

Treated samples (stranded)

Multiply mapped reads

All on All off

10% EtOH L3 [?]	CdCl2 0.05mM Late L3 12hr [?]	Heat shock 1hr@36C wet heat 30min@25C Adults 4day [?]
2.5% EtOH L3 [?]	CdCl2 0.05mM Late Third Instar Larvae 6hr [?]	Paraquat 10mM Adults 4day [?]
5% EtOH L3 [?]	CdCl2 0.1M Adults 4day [?]	Paraquat 5mM Adults 4day [?]
Caffeine 1.5 mg/ml L3 [?]	Cold Method 2 Adults 4day [?]	Rotenone 2ug/ml L3 [?]
Caffeine 2.5 mg/ml Adults 4day [?]	Cold treatment Method 1 Adults 4day [?]	Rotenone 8ug/ml L3 [?]
Caffeine Pre Lethal Adults 4day [?]	Copper 0.5mM L3 [?]	Zn 4.5mM Adults 4day [?]
CdCl2 0.05M Adults 4day [?]	Copper 15mM Adults 4day [?]	Zn 5mM Late L3 [?]

Uniquely mapped reads

All on All off