title: Control ChIP-seq from whole organism (ENCLB390LKF)

description:
https://www.encodeproject.org/experiments/ENCSR183CDG/
***************
biological replicate number: 2
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing TBX-9-eGFP fusion proteins.
experiment encode accession: ENCSR183CDG
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB390LKF
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP636 (unc-119(tm4063) III; wgIs636) mixed sex young adult 63 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans tbx-9

value: whole organism

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to TBX-9

value: young adult

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS574TOY at ENCODE; https://www.encodeproject.org/ENCBS574TOY/


title: Control ChIP-seq from whole organism (ENCLB179GJB)

status: Public on Feb 27 2024

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR594SSF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG15514-eGFP fusion proteins.
experiment encode accession: ENCSR594SSF
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB179GJB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strain CG15514-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG15514

value: whole organisms

tag: biosample encode accession

tag: collection date

tag: geographic location

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG15514

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

tag: age

value: 0-24 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS366GTW at ENCODE; https://www.encodeproject.org/ENCBS366GTW/


title: Control ChIP-seq from whole organism (ENCLB978LEA)

description:
https://www.encodeproject.org/experiments/ENCSR010UCR/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing tx-eGFP fusion proteins.
experiment encode accession: ENCSR010UCR
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB978LEA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain tx-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster tx

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to tx

value: ENCBS391ETJ at ENCODE; https://www.encodeproject.org/ENCBS391ETJ/


title: Control ChIP-seq from whole organism (ENCLB228CZF)

description:
https://www.encodeproject.org/experiments/ENCSR058URE/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing EGL-13-eGFP fusion proteins.
experiment encode accession: ENCSR058URE
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB228CZF
fragmentation methods: sonication (generic microtip)

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain GOU883 hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans egl-13

value: whole organism

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to EGL-13

value: hermaphrodite

value: L1 larva

value: unknown

tag: worm synchronization stage

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS159CKX at ENCODE; https://www.encodeproject.org/ENCBS159CKX/


title: Control ChIP-seq from whole organism (ENCLB567OBX)

description:
https://www.encodeproject.org/experiments/ENCSR112GYX/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in late-embryonic stage worms.
experiment encode accession: ENCSR112GYX
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB567OBX
size range: 150-350

source_name: Caenorhabditis elegans strain OP117 (unc-119(ed3) III; wgIs117) mixed sex late embryo insertion targeting C. elegans pax-1

extract_protocol: not provided

value: whole organisms

value: late embryonic

value: Michael Snyder, Stanford

value: CGC

value: ENCBS457FPZ at ENCODE; https://www.encodeproject.org/ENCBS457FPZ/


title: TF ChIP-seq from whole organism (ENCLB987KNU)

description:
https://www.encodeproject.org/experiments/ENCSR593ZMJ/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing mirr-eGFP fusion proteins.
experiment encode accession: ENCSR593ZMJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR286EOA
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB987KNU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain mirr-GFP mixed sex embryo (4-20 hours) insertion targeting D. melanogaster mirr

tag: antibody

value: mirr

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to mirr

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS410VQO at ENCODE; https://www.encodeproject.org/ENCBS410VQO/


title: TF ChIP-seq from whole organism (ENCLB905NZY)

description:
https://www.encodeproject.org/experiments/ENCSR057TFD/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing GMEB-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR057TFD
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR794SVC
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB905NZY
fragmentation methods: sonication (generic microtip)
instrument models: Illumina HiSeq 2000,Illumina HiSeq 4000

source_name: Caenorhabditis elegans strain OP622 (unc-119(tm4063) III; wgIs622) mixed sex late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans gmeb-2

value: whole organism

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to GMEB-2

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS131MCF at ENCODE; https://www.encodeproject.org/ENCBS131MCF/


title: Control ChIP-seq from whole organism (ENCLB878FLZ)

description:
https://www.encodeproject.org/experiments/ENCSR111HDC/
***************
biological replicate number: 3
technical replicate number: 1
description: Input ChIP-seq in starved L1 larva worms.
experiment encode accession: ENCSR111HDC
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB878FLZ
size range: 150-350

source_name: Caenorhabditis elegans strain YL474 (lin-35(n745) I; unc-119(ed3) III; vrIs64[pGES-1::HPL-2::GFP FLAG: HPL-2 3-UTR, unc-119 (+)]) mixed sex L1 larva at L1 larva starved after bleaching stage insertion targeting C. elegans hpl-2

value: whole organisms

value: L1 larva

value: unknown

value: Michael Snyder, Stanford

value: L1 larva starved after bleaching

value: ENCBS526FII at ENCODE; https://www.encodeproject.org/ENCBS526FII/


title: TF ChIP-seq from whole organism (ENCLB963CYL)

description:
https://www.encodeproject.org/experiments/ENCSR890AWM/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR890AWM
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR840JKR
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB963CYL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG17359 embryo (0-14 hours) insertion targeting D. melanogaster CG17359

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG17359

value: not collected

value: embryonic

value: 0-14 hour

value: ENCBS358XZN at ENCODE; https://www.encodeproject.org/ENCBS358XZN/


title: Control ChIP-seq from whole organism (ENCLB400MLB)

description:
https://www.encodeproject.org/experiments/ENCSR111HDC/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in starved L1 larva worms.
experiment encode accession: ENCSR111HDC
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB400MLB
size range: 150-350

value: whole organism

value: not applicable

value: pooled male and female

value: CGC

value: ENCBS667FNI at ENCODE; https://www.encodeproject.org/ENCBS667FNI/


title: TF ChIP-seq from whole organism (ENCLB734ACA)

description:
https://www.encodeproject.org/experiments/ENCSR593ZMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing mirr-eGFP fusion proteins.
experiment encode accession: ENCSR593ZMJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR286EOA
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB734ACA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: mirr

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to mirr

value: Kevin White, UChicago

value: Kevin White

value: ENCBS561XKG at ENCODE; https://www.encodeproject.org/ENCBS561XKG/


title: TF ChIP-seq from whole organism (ENCLB658KVE)

description:
https://www.encodeproject.org/experiments/ENCSR176TET/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NHR-48-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR176TET
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR866XOK
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB658KVE
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP518 (unc-119(tm4063) III; wgIs518) hermaphrodite L4 larva 48.5 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans nhr-48

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-48

value: hermaphrodite

value: L4 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS889YBY at ENCODE; https://www.encodeproject.org/ENCBS889YBY/


title: TF ChIP-seq from whole organism (ENCLB227EMJ)

description:
https://www.encodeproject.org/experiments/ENCSR120TCW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Atf3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR120TCW
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR437TND
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB227EMJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain A3-3-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Atf3

value: whole organism

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Atf3

value: pooled male and female

value: embryonic

value: 0-24 hour

value: ENCBS232BIS at ENCODE; https://www.encodeproject.org/ENCBS232BIS/


title: TF ChIP-seq from whole organism (ENCLB665JYB)

description:
https://www.encodeproject.org/experiments/ENCSR112URX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-mab-5 in mixed stage (embryonic) worms.
experiment encode accession: ENCSR112URX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR452WHZ
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB665JYB
size range: 150-350

source_name: Caenorhabditis elegans strain OP27 (unc-119(ed3) III; wgIs27) mixed sex mixed stage (embryo) insertion targeting C. elegans mab-5

value: whole organisms

value: mixed stage (embryonic)

value: Michael Snyder, Stanford

value: CGC

value: ENCBS364BUL at ENCODE; https://www.encodeproject.org/ENCBS364BUL/


title: TF ChIP-seq from whole organism (ENCLB528TLO)

description:
https://www.encodeproject.org/experiments/ENCSR194LIS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG18476-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR194LIS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR605LPC
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB528TLO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG18476-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG18476

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG18476

value: Kevin White, UChicago

value: Kevin White

value: ENCBS136TLN at ENCODE; https://www.encodeproject.org/ENCBS136TLN/


title: TF ChIP-seq from whole organism (ENCLB783LVL)

description:
https://www.encodeproject.org/experiments/ENCSR593ZMJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing mirr-eGFP fusion proteins.
experiment encode accession: ENCSR593ZMJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR286EOA
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB783LVL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: mirr

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to mirr

value: ENCBS401OFT at ENCODE; https://www.encodeproject.org/ENCBS401OFT/


title: TF ChIP-seq from whole organism (ENCLB883PNE)

description:
https://www.encodeproject.org/experiments/ENCSR194LIS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG18476-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR194LIS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR605LPC
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB883PNE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

value: ENCBS288KPT at ENCODE; https://www.encodeproject.org/ENCBS288KPT/


title: Control ChIP-seq from whole organism (ENCLB599JYA)

description:
https://www.encodeproject.org/experiments/ENCSR009OQO/
***************
biological replicate number: 3
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR009OQO
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB599JYA
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP193 (unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119)) mixed sex L3 larva insertion targeting C. elegans sea-2

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SEA-2

value: pooled male and female

value: L3 larva

value: unknown

value: Michael Snyder

value: ENCBS024CLD at ENCODE; https://www.encodeproject.org/ENCBS024CLD/


title: Control ChIP-seq from whole organism (ENCLB977AJY)

description:
https://www.encodeproject.org/experiments/ENCSR884AHC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR884AHC
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB977AJY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain E(spl)m8-HLH mixed sex embryo (4-14 hours) insertion targeting D. melanogaster E(spl)m8-HLH

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to E(spl)m8-HLH

value: embryonic

value: ENCBS696LPU at ENCODE; https://www.encodeproject.org/ENCBS696LPU/


title: TF ChIP-seq from whole organism (ENCLB762AAC)

description:
https://www.encodeproject.org/experiments/ENCSR120TCW/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Atf3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR120TCW
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR437TND
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB762AAC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Atf3

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS629NUM at ENCODE; https://www.encodeproject.org/ENCBS629NUM/


title: TF ChIP-seq from whole organism (ENCLB595ISN)

description:
https://www.encodeproject.org/experiments/ENCSR176TET/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NHR-48-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR176TET
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR866XOK
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB595ISN
fragmentation methods: sonication (generic microtip)

value: whole organism

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-48

value: hermaphrodite

value: L4 larva

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS052XBC at ENCODE; https://www.encodeproject.org/ENCBS052XBC/


title: Control ChIP-seq from whole organism (ENCLB710EMP)

description:
https://www.encodeproject.org/experiments/ENCSR335VJF/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing TBX-2-eGFP fusion proteins.
experiment encode accession: ENCSR335VJF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB710EMP
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP159 (unc-119(ed3) III; wgIs159) hermaphrodite L3 larva 48 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans tbx-2

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to TBX-2

value: L3 larva

value: unknown

value: ENCBS649AST at ENCODE; https://www.encodeproject.org/ENCBS649AST/


title: TF ChIP-seq from whole organism (ENCLB595AIN)

description:
https://www.encodeproject.org/experiments/ENCSR888UWA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR888UWA
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR530FXD
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB595AIN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain bab1-RA (bab1-s)-GFP female adult insertion targeting D. melanogaster bab1

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Bab1

value: female

value: adult

value: Kevin White, UChicago

value: Kevin White

value: ENCBS549NGS at ENCODE; https://www.encodeproject.org/ENCBS549NGS/


title: Control ChIP-seq from whole organism (ENCLB386MLR)

description:
https://www.encodeproject.org/experiments/ENCSR183CDG/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing TBX-9-eGFP fusion proteins.
experiment encode accession: ENCSR183CDG
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB386MLR
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP636 (unc-119(tm4063) III; wgIs636) mixed sex young adult 63 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans tbx-9

value: whole organism

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to TBX-9

value: pooled male and female

value: young adult

value: ENCBS790QIY at ENCODE; https://www.encodeproject.org/ENCBS790QIY/


title: Control ChIP-seq from whole organism (ENCLB785MTV)

description:
https://www.encodeproject.org/experiments/ENCSR117DPS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing fru-eGFP fusion proteins.
experiment encode accession: ENCSR117DPS
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB785MTV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain fru-MiMIC-GFP mixed sex wandering third instar larva insertion targeting D. melanogaster fru

value: whole organisms

value: D. mel line contraining an intronic eGFP exon to create a fru-GFP fusion gene

value: wandering third instar larva

value: Hugo Bellen

value: ENCBS727MYC at ENCODE; https://www.encodeproject.org/ENCBS727MYC/


title: Control ChIP-seq from whole organism (ENCLB495ZFV)

description:
https://www.encodeproject.org/experiments/ENCSR009OQO/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR009OQO
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB495ZFV
size range: 150-350

value: L3 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS135QPT at ENCODE; https://www.encodeproject.org/ENCBS135QPT/


title: TF ChIP-seq from whole organism (ENCLB393WNJ)

description:
https://www.encodeproject.org/experiments/ENCSR399FPR/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG7928-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR399FPR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR233YTV
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB393WNJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG7928-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster ZIPIC

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7928

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS131WRT at ENCODE; https://www.encodeproject.org/ENCBS131WRT/


title: Control ChIP-seq from whole organism (ENCLB748QAP)

description:
https://www.encodeproject.org/experiments/ENCSR195OCT/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing NK7.1-eGFP fusion proteins.
experiment encode accession: ENCSR195OCT
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB748QAP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain NK7.1-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster NK7.1

value: whole organism

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to NK7.1

value: pooled male and female

value: ENCBS237IUC at ENCODE; https://www.encodeproject.org/ENCBS237IUC/


title: TF ChIP-seq from whole organism (ENCLB061LQM)

description:
https://www.encodeproject.org/experiments/ENCSR110QRS/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Dip3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR110QRS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR506OGY
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB061LQM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Dip3-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Dlip3

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Dip3

value: ENCBS057HVB at ENCODE; https://www.encodeproject.org/ENCBS057HVB/


title: TF ChIP-seq from whole organism (ENCLB412YUU)

description:
https://www.encodeproject.org/experiments/ENCSR334YYP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing Y116A8C.19-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR334YYP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR411ODP
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB412YUU
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP532 (unc-119(tm4063) III; wgIs532) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans Y116A8C.19

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to Y116A8C.19

value: hermaphrodite

value: L1 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS371ZNI at ENCODE; https://www.encodeproject.org/ENCBS371ZNI/


title: TF ChIP-seq from whole organism (ENCLB524IKK)

description:
https://www.encodeproject.org/experiments/ENCSR399FPR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG7928-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR399FPR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR233YTV
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB524IKK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7928

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS654XSF at ENCODE; https://www.encodeproject.org/ENCBS654XSF/


title: Control ChIP-seq from whole organism (ENCLB850BPO)

description:
https://www.encodeproject.org/experiments/ENCSR009OQO/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR009OQO
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB850BPO
size range: 150-350

value: whole organisms

value: not applicable

value: pooled male and female

value: L3 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS813ONM at ENCODE; https://www.encodeproject.org/ENCBS813ONM/


title: Control ChIP-seq from whole organism (ENCLB847WYK)

description:
https://www.encodeproject.org/experiments/ENCSR009OQO/
***************
biological replicate number: 4
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR009OQO
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB847WYK
fragmentation methods: sonication (generic microtip)

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SEA-2

value: unknown

value: Michael Snyder

value: ENCBS338MSD at ENCODE; https://www.encodeproject.org/ENCBS338MSD/


title: TF ChIP-seq from whole organism (ENCLB792UOE)

description:
https://www.encodeproject.org/experiments/ENCSR334YYP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing Y116A8C.19-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR334YYP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR411ODP
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB792UOE
fragmentation methods: sonication (generic microtip)

value: whole organism

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to Y116A8C.19

value: hermaphrodite

value: L1 larva

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS402JNA at ENCODE; https://www.encodeproject.org/ENCBS402JNA/


title: Control ChIP-seq from whole organism (ENCLB409WYM)

description:
https://www.encodeproject.org/experiments/ENCSR008GMV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in young adult worms.
experiment encode accession: ENCSR008GMV
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB409WYM
size range: 150-350

source_name: Caenorhabditis elegans strain YL390 (unc119(ed3)III; vrIs48 [pPIE-1::DPL-1::GFP FLAG: DPL-1 3'UTR, unc-119 (+)]) mixed sex young adult insertion targeting C. elegans dpl-1

value: whole organisms

value: not applicable

value: pooled male and female

value: young adult

value: ENCBS509MYT at ENCODE; https://www.encodeproject.org/ENCBS509MYT/


title: Control ChIP-seq from whole organism (ENCLB382DUC)

description:
https://www.encodeproject.org/experiments/ENCSR592WZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR592WZZ
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB382DUC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain gem mixed sex embryo (0-24 hours) insertion targeting D. melanogaster gem

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to gem

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS305MIE at ENCODE; https://www.encodeproject.org/ENCBS305MIE/


title: TF ChIP-seq from whole organism (ENCLB279ZOS)

description:
https://www.encodeproject.org/experiments/ENCSR110QRS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Dip3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR110QRS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR506OGY
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB279ZOS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Dip3

value: ENCBS497HZU at ENCODE; https://www.encodeproject.org/ENCBS497HZU/


title: TF ChIP-seq from whole organism (ENCLB181SBP)

description:
https://www.encodeproject.org/experiments/ENCSR050PRW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing AHR-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR050PRW
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR471NZA
encode release date: 2016-09-29
lab: Valerie Reinke, Yale
library encode accession: ENCLB181SBP
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP562 (unc-119(tm4063) III; wgIs562) hermaphrodite late embryo 3.5 hours post synchronization using egg bleaching insertion targeting C. elegans ahr-1

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to AHR-1

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS246KIR at ENCODE; https://www.encodeproject.org/ENCBS246KIR/


title: Control ChIP-seq from whole organism (ENCLB677GAO)

description:
https://www.encodeproject.org/experiments/ENCSR008GMV/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in young adult worms.
experiment encode accession: ENCSR008GMV
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB677GAO
size range: 150-350

value: whole organisms

value: not applicable

value: pooled male and female

value: young adult

value: Michael Snyder, Stanford

value: CGC

value: ENCBS780GUA at ENCODE; https://www.encodeproject.org/ENCBS780GUA/


title: TF ChIP-seq from whole organism (ENCLB910OBZ)

description:
https://www.encodeproject.org/experiments/ENCSR110QRS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Dip3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR110QRS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR506OGY
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB910OBZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Dip3

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS259HGP at ENCODE; https://www.encodeproject.org/ENCBS259HGP/


title: TF ChIP-seq from whole organism (ENCLB729OSF)

description:
https://www.encodeproject.org/experiments/ENCSR591PRH/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing sd-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR591PRH
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR559OGK
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB729OSF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster mixed sex embryo (4-20 hours) insertion targeting D. melanogaster sd

value: sd

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to sd

value: ENCBS335RKI at ENCODE; https://www.encodeproject.org/ENCBS335RKI/


title: TF ChIP-seq from whole organism (ENCLB554UUO)

description:
https://www.encodeproject.org/experiments/ENCSR050PRW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing AHR-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR050PRW
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR471NZA
encode release date: 2016-09-29
lab: Valerie Reinke, Yale
library encode accession: ENCLB554UUO
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to AHR-1

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: hour

value: ENCBS276CGG at ENCODE; https://www.encodeproject.org/ENCBS276CGG/


title: TF ChIP-seq from whole organism (ENCLB744STZ)

description:
https://www.encodeproject.org/experiments/ENCSR329YGE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CEH-32-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR329YGE
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR626CIE
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB744STZ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP516 (unc-119(tm4063) III; wgIs516) hermaphrodite L4 larva 52 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans ceh-32

value: whole organism

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-32

value: L4 larva

value: L1 larva starved after bleaching

value: ENCBS846NXY at ENCODE; https://www.encodeproject.org/ENCBS846NXY/


title: TF ChIP-seq from whole organism (ENCLB425AVB)

description:
https://www.encodeproject.org/experiments/ENCSR105OGL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing pum-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR105OGL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR441OGV
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB425AVB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Pum-MiMIC-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster pum

value: pum

value: D. mel line contraining an intronic eGFP exon to create a Pum-GFP fusion gene

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Hugo Bellen

value: ENCBS833CHI at ENCODE; https://www.encodeproject.org/ENCBS833CHI/


title: TF ChIP-seq from whole organism (ENCLB041MMF)

description:
https://www.encodeproject.org/experiments/ENCSR190CJZ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG9609-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR190CJZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR168MGM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB041MMF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG9609-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG9609

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG9609

value: Kevin White

value: ENCBS015UKX at ENCODE; https://www.encodeproject.org/ENCBS015UKX/


title: Control ChIP-seq from whole organism (ENCLB105EGK)

description:
https://www.encodeproject.org/experiments/ENCSR114JYK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing insv-eGFP fusion proteins.
experiment encode accession: ENCSR114JYK
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB105EGK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain insv-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster insv

value: whole organism

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to insv

value: ENCBS018GVO at ENCODE; https://www.encodeproject.org/ENCBS018GVO/


title: TF ChIP-seq from whole organism (ENCLB655CJC)

description:
https://www.encodeproject.org/experiments/ENCSR007MVL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-jun-1 in L3 larva worms.
experiment encode accession: ENCSR007MVL
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR540NNC
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB655CJC
size range: 150-350

source_name: Caenorhabditis elegans strain OP234 (unc-119(ed3) III; wgIs234) mixed sex L3 larva insertion targeting C. elegans jun-1

value: L3 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS326EEH at ENCODE; https://www.encodeproject.org/ENCBS326EEH/


title: TF ChIP-seq from whole organism (ENCLB757HJN)

description:
https://www.encodeproject.org/experiments/ENCSR591PRH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing sd-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR591PRH
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR559OGK
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB757HJN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: sd

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to sd

value: pooled male and female

value: embryonic

value: ENCBS989KVU at ENCODE; https://www.encodeproject.org/ENCBS989KVU/


title: TF ChIP-seq from whole organism (ENCLB778SML)

description:
https://www.encodeproject.org/experiments/ENCSR190CJZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG9609-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR190CJZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR168MGM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB778SML
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG9609

value: 0-24 hour

value: Kevin White, UChicago

value: ENCBS803ULG at ENCODE; https://www.encodeproject.org/ENCBS803ULG/


title: TF ChIP-seq from whole organism (ENCLB199PHL)

description:
https://www.encodeproject.org/experiments/ENCSR591PRH/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing sd-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR591PRH
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR559OGK
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB199PHL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

value: Kevin White

value: ENCBS193CNG at ENCODE; https://www.encodeproject.org/ENCBS193CNG/


title: TF ChIP-seq from whole organism (ENCLB543JGT)

description:
https://www.encodeproject.org/experiments/ENCSR329YGE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CEH-32-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR329YGE
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR626CIE
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB543JGT
fragmentation methods: sonication (generic microtip)

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-32

value: hermaphrodite

value: L4 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS924XGT at ENCODE; https://www.encodeproject.org/ENCBS924XGT/


title: TF ChIP-seq from whole organism (ENCLB087QSW)

description:
https://www.encodeproject.org/experiments/ENCSR007MVL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-jun-1 in L3 larva worms.
experiment encode accession: ENCSR007MVL
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR540NNC
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB087QSW
size range: 150-350

value: whole organisms

value: pooled male and female

value: L3 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS129JHM at ENCODE; https://www.encodeproject.org/ENCBS129JHM/


title: TF ChIP-seq from whole organism (ENCLB058EHS)

description:
https://www.encodeproject.org/experiments/ENCSR396LMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing YL-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR396LMJ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR317QFT
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB058EHS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain YL-1-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster YL-1

value: whole organism

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to YL-1

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS630ETI at ENCODE; https://www.encodeproject.org/ENCBS630ETI/


title: TF ChIP-seq from whole organism (ENCLB722IAM)

description:
https://www.encodeproject.org/experiments/ENCSR166DXK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F22D6.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR166DXK
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR206FGY
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB722IAM
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP399 (unc-119(tm4063) III; wgIs399) hermaphrodite young adult 67 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans F22D6.2

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F22D6.2

value: hermaphrodite

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS237BJO at ENCODE; https://www.encodeproject.org/ENCBS237BJO/


title: Control ChIP-seq from whole organism (ENCLB840XHT)

description:
https://www.encodeproject.org/experiments/ENCSR006GXP/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms grown at 26C.
experiment encode accession: ENCSR006GXP
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB840XHT
size range: 150-350

source_name: Caenorhabditis elegans strain N2 (C. elegans wild isolate) hermaphrodite L1 larva whole organism

value: whole organisms

value: L1 larva grown at 26C.

value: L1 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS765SAU at ENCODE; https://www.encodeproject.org/ENCBS765SAU/


title: TF ChIP-seq from whole organism (ENCLB898GDD)

description:
https://www.encodeproject.org/experiments/ENCSR190CJZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG9609-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR190CJZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR168MGM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB898GDD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG9609

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: ENCBS154HAG at ENCODE; https://www.encodeproject.org/ENCBS154HAG/


title: TF ChIP-seq from whole organism (ENCLB846TZH)

description:
https://www.encodeproject.org/experiments/ENCSR396LMJ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing YL-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR396LMJ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR317QFT
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB846TZH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to YL-1

value: Kevin White

value: ENCBS550UXW at ENCODE; https://www.encodeproject.org/ENCBS550UXW/


title: Control ChIP-seq from whole organism (ENCLB161KIK)

description:
https://www.encodeproject.org/experiments/ENCSR006GXP/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms grown at 26C.
experiment encode accession: ENCSR006GXP
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB161KIK
size range: 150-350

value: whole organisms

value: hermaphrodite

value: unknown

value: ENCBS050OZM at ENCODE; https://www.encodeproject.org/ENCBS050OZM/


title: TF ChIP-seq from whole organism (ENCLB278KGW)

description:
https://www.encodeproject.org/experiments/ENCSR394MHV/
***************
biological replicate number: 5
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR394MHV
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR981IYC
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB278KGW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain unpg-GFP embryo (4-16 hours) insertion targeting D. melanogaster unpg

value: unpg

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to unpg

value: not collected

value: ENCBS632HQI at ENCODE; https://www.encodeproject.org/ENCBS632HQI/


title: Control ChIP-seq from whole organism (ENCLB097NVL)

description:
https://www.encodeproject.org/experiments/ENCSR191TAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing F08F3.9-eGFP fusion proteins.
experiment encode accession: ENCSR191TAJ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB097NVL
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL485 hermaphrodite young adult insertion targeting C. elegans snpc-1.3

value: whole organism

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F08F3.9

value: young adult

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS236QQX at ENCODE; https://www.encodeproject.org/ENCBS236QQX/


title: TF ChIP-seq from whole organism (ENCLB851USV)

description:
https://www.encodeproject.org/experiments/ENCSR155UEF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing HLH-15-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR155UEF
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR852KZF
encode release date: 2016-09-29
lab: Valerie Reinke, Yale
library encode accession: ENCLB851USV
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP566 (unc-119(tm4063) III; wgIs566) hermaphrodite late embryo 3 hours post synchronization using egg bleaching insertion targeting C. elegans hlh-15

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to HLH-15

value: late embryonic

value: egg bleaching

value: hour

value: ENCBS237TVZ at ENCODE; https://www.encodeproject.org/ENCBS237TVZ/


title: TF ChIP-seq from whole organism (ENCLB828UMM)

description:
https://www.encodeproject.org/experiments/ENCSR283UXP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Slp2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR283UXP
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR426HJS
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB828UMM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain 9T-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster slp2

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Slp2

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS760GBX at ENCODE; https://www.encodeproject.org/ENCBS760GBX/


title: TF ChIP-seq from whole organism (ENCLB546WNZ)

description:
https://www.encodeproject.org/experiments/ENCSR283UXP/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Slp2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR283UXP
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR426HJS
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB546WNZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

value: ENCBS300FFX at ENCODE; https://www.encodeproject.org/ENCBS300FFX/


title: Control ChIP-seq from whole organism (ENCLB008LKE)

description:
https://www.encodeproject.org/experiments/ENCSR191QNY/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 worms.
experiment encode accession: ENCSR191QNY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB008LKE
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP602 mixed sex L4 larva insertion targeting C. elegans unc-62

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to UNC-62

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS591OWX at ENCODE; https://www.encodeproject.org/ENCBS591OWX/


title: TF ChIP-seq from whole organism (ENCLB923LKV)

description:
https://www.encodeproject.org/experiments/ENCSR155UEF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing HLH-15-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR155UEF
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR852KZF
encode release date: 2016-09-29
lab: Valerie Reinke, Yale
library encode accession: ENCLB923LKV
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to HLH-15

value: hermaphrodite

value: late embryonic

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: hour

value: ENCBS419MWP at ENCODE; https://www.encodeproject.org/ENCBS419MWP/


title: TF ChIP-seq from whole organism (ENCLB404JZJ)

description:
https://www.encodeproject.org/experiments/ENCSR396LMJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing YL-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR396LMJ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR317QFT
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB404JZJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to YL-1

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS964EYK at ENCODE; https://www.encodeproject.org/ENCBS964EYK/


title: 59_L2

city: Nouzilly

first: Julie

last: Collet

address: Centre INRAE

country: France

institute: INRAE

description:
extraction 117 sample 04_L2 pool 19_21
DGRP59 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

library_source: transcriptomic

data_processing:
The quality of the obtained sequences was checked using FastQC [19], with particular attention given to per-base-sequence quality. We used Trimmomatic [20] to: (i) remove the first 10 bases from the start of the read; (ii) trim slide windows, using the window size of 4 and an average base quality across each window of Q=30; and (iii) to keep reads of a minimum of 35 bp at a minimum average quality of 30. To quantify gene expression, we aligned single-end RNAseq reads to the reference genome of D. melanogaster released in Aug.2014 (BDGP Release 6 + ISO 1 IT/dm6) (dm6) using STAR [21]. We applied all default parameters, except for a minimum intron size of 5 and max intron size of 200,000. We used dm6_FlyBase_Genes_assembled_chromosomes-r6.22.gtf for gene annotation. All bioinformatic analyses were done using the Galaxy portal (https://usegalaxy.org.au/).
Assembly: dm6
Supplementary files format and content: .csv raw counts

molecule: polyA RNA

source_name: whole body

extract_protocol:
For each sample, we extracted RNA using phenol chloroform phase separation. We first added 500 µl of TRIzol (Thermo Fisher Scientific) to the frozen specimens and crushed them with a pestle. We then added 100 µl of chloroform to the crushed specimens, agitated the samples for 15 seconds, and incubated them at room temperature for 3 minutes. The samples were centrifuged at 12,000 RCF for 15 minutes at 4°C. We transferred the aqueous phase into fresh tubes, added an additional 250 µl of isopropanol, and inverted the tube four times to ensure mixing. After allowing the tubes to incubate at room temperature for 10 minutes, the samples were centrifuged at 12,000 RCF for 10 minutes at 4°C. We removed the supernatant, washed the pellet with 500 µl of 75% ethanol, and again centrifuged the samples at 7,500 RCF for 5 minutes at 4°C. A second wash was then carried out using 500 µl of 75% ethanol. After a final centrifugation at 7,500 RCF for 5 minutes at 4°C, the supernatant was carefully removed. The pellet was left to dry at room temperature for 30 min. RNA was resuspended in 100 µl of nuclease-free water and then the samples were heated to 55°C in a drybath for 15 minutes. We verified RNA concentration and integrity on the Bioanalyzer (Agilent) with the RNA 6000 Pico Kit according the manufacturer instructions, as well as on the NanoDrop™ 8000 Spectrophotometer (Thermo Fisher Scientific). All RNA samples were stored at -80°C.
We prepared the cDNA libraries using the Illumina® TruSeq® Stranded mRNA Sample Preparation Kit, following the manufacturer’s protocol and using a Biomek NXᴾ Automated Workstation (Biomek NXP Span-8 by Beckman). In brief, poly-A-containing mRNA molecules were purified from 1 µg total RNA using poly-T oligo-attached magnetic beads. The purified mRNA was fragmented by adding the fragmentation buffer and then heated to 94°C in a thermocycler for 8 minutes. We primed the cleaved RNA fragments with random hexamers and used reverse transcriptase to synthesize first-strand cDNA. Second-strand cDNA synthesis, end repair, A-tailing, adapter ligation, and enrich DNA fragments were carried out in accordance with the manufacturer supplied protocols. Each indexed cDNA library was verified and quantified using a dsDNA 915 Reagent Kit on a Fragment Analyzer (Agilent). We equally mixed 12 to 13 indexed cDNA libraries in each final library. The final libraries were quantified by real-time PCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms (Kapa Biosystems Ltd, SA), adjusted to 10 nM in water, and provided to the Montpellier Genomix platform (http://www.mgx.cnrs.fr/) for sequencing.
Each final mixed cDNA library was denatured with NaOH and diluted to a concentration of 18 pM using the standard library PhiX (1%) from Illumina. Flow cell was clustered using TruSeq SR Cluster Kit v3-cBot-HS, and then loaded into the Illumina HiSeq 2500 instrument following the manufacturer’s instructions. The v3 sequencing chemistry (TruSeq SBS Kit v3-HS) was used, applying a 50 cycle, single-read, indexed protocol. Image analyses and basecalling were carried out using the Hiseq Control Software (Illumina HCS) and Real-Time Analysis Software (Illumina RTA).

treatment_protocol: The flies that were collected from two vials of each biological replicate were placed together before RNA extraction. As a result of our strict age conditions, we were unable to always gather 20 flies per sample, and the total number of flies per sample ranged from 2 to 31 flies, with a median number of 20 and 17 individuals in larval and adult samples respectively.

tag: tissue

value: whole body

tag: genotype

tag: developmental stage

value: Larvae


title: Control ChIP-seq from whole organism (ENCLB463AKT)

description:
https://www.encodeproject.org/experiments/ENCSR191QNY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L4 worms.
experiment encode accession: ENCSR191QNY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB463AKT
fragmentation methods: sonication (generic microtip)

value: whole organisms

tag: biosample encode accession

tag: collection date

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to UNC-62

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS865PQI at ENCODE; https://www.encodeproject.org/ENCBS865PQI/


title: TF ChIP-seq from whole organism (ENCLB863QIO)

description:
https://www.encodeproject.org/experiments/ENCSR394MHV/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR394MHV
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR981IYC
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB863QIO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: unpg

value: whole organism

value: not applicable

tag: geographic location

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to unpg

value: not collected

value: ENCBS785LHT at ENCODE; https://www.encodeproject.org/ENCBS785LHT/


title: 332_L2

description:
extraction 102 sample 18_L2 pool 19_27
DGRP332 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB894IHO)

description:
https://www.encodeproject.org/experiments/ENCSR154XWT/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F10B5.3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR154XWT
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR420ZTI
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB894IHO
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP529 (unc-119(tm4063) III; wgIs529) hermaphrodite L4 larva 48 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans F10B5.3

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F10B5.3

tag: Sex

value: hermaphrodite

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS557ZVG at ENCODE; https://www.encodeproject.org/ENCBS557ZVG/


title: TF ChIP-seq from whole organism (ENCLB654CST)

description:
https://www.encodeproject.org/experiments/ENCSR394MHV/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR394MHV
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR981IYC
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB654CST
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: dev stage

value: embryonic

tag: age

value: Kevin White, UChicago

value: Kevin White

value: ENCBS732UPX at ENCODE; https://www.encodeproject.org/ENCBS732UPX/


title: Control ChIP-seq from whole organism (ENCLB446NYN)

description:
https://www.encodeproject.org/experiments/ENCSR284TTZ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ODD-2-eGFP fusion proteins.
experiment encode accession: ENCSR284TTZ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2019-01-26
lab: Valerie Reinke, Yale
library encode accession: ENCLB446NYN
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP405 (unc-119(tm4063) III; wgIs405) hermaphrodite late embryo insertion targeting C. elegans odd-2

value: whole organism

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to ODD-2

value: late embryonic

value: unknown

tag: lab

tag: source

value: ENCBS943JXV at ENCODE; https://www.encodeproject.org/ENCBS943JXV/


title: TF ChIP-seq from ovary (ENCLB205TRD)

description:
https://www.encodeproject.org/experiments/ENCSR588OSO/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG17801-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR588OSO
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR354RHJ
encode release date: 2019-07-09
lab: Kevin White, UChicago
library encode accession: ENCLB205TRD
size range: 200-800

source_name: Drosophila melanogaster strain CG17801-GFP female adult ovary tissue genetically modified (insertion) using site-specific recombination targeting D. melanogaster CG17801

value: ovary

value: tissue

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG17801

value: female

value: adult

tag: link

value: ENCBS085MOJ at ENCODE; https://www.encodeproject.org/ENCBS085MOJ/


title: Control ChIP-seq from whole organism (ENCLB396SQE)

description:
https://www.encodeproject.org/experiments/ENCSR320VBK/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing LET-607-eGFP fusion proteins.
experiment encode accession: ENCSR320VBK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB396SQE
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL529 hermaphrodite young adult 67 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans let-607

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to LET-607

value: hermaphrodite

value: young adult

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

value: hour

value: ENCBS269PRN at ENCODE; https://www.encodeproject.org/ENCBS269PRN/


title: TF ChIP-seq from whole organism (ENCLB376NOR)

description:
https://www.encodeproject.org/experiments/ENCSR154XWT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F10B5.3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR154XWT
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR420ZTI
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB376NOR
fragmentation methods: sonication (generic microtip)

tag: antibody

value: whole organism

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F10B5.3

value: L4 larva

value: unknown

tag: post synchronization time units

value: ENCBS324WFL at ENCODE; https://www.encodeproject.org/ENCBS324WFL/


title: 217_L1

description:
extraction 095 sample 12_L1 pool 19_16
DGRP217 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB968IOV)

description:
https://www.encodeproject.org/experiments/ENCSR187ZBO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-6 in L4 larva worms.
experiment encode accession: ENCSR187ZBO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR149RDA
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB968IOV
size range: 150-350

source_name: Caenorhabditis elegans strain OP90 (unc-119(ed3) III; wgIs90) mixed sex L4 larva insertion targeting C. elegans nhr-6

tag: biosample encode accession

value: not applicable

value: pooled male and female

value: Michael Snyder, Stanford

value: CGC

value: ENCBS613XOJ at ENCODE; https://www.encodeproject.org/ENCBS613XOJ/


title: TF ChIP-seq from whole organism (ENCLB386BSH)

description:
https://www.encodeproject.org/experiments/ENCSR187ZBO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-6 in L4 larva worms.
experiment encode accession: ENCSR187ZBO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR149RDA
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB386BSH
size range: 150-350

value: whole organisms

tag: collection date

value: ENCBS136CYM at ENCODE; https://www.encodeproject.org/ENCBS136CYM/


title: TF ChIP-seq from whole organism (ENCLB828OBX)

description:
https://www.encodeproject.org/experiments/ENCSR587CWK/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Deaf1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR587CWK
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR251JRS
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB828OBX
size range: 200-800

source_name: Drosophila melanogaster strain Deaf1 mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Deaf1

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Deaf1

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS777GZB at ENCODE; https://www.encodeproject.org/ENCBS777GZB/


title: 142_L1

description:
extraction 093 sample 06_L1 pool 19_25
DGRP142 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: developmental stage


title: TF ChIP-seq from whole organism (ENCLB031MPL)

description:
https://www.encodeproject.org/experiments/ENCSR320MVY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing SNU-23-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR320MVY
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR779STX
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB031MPL
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP528 (wgIs528(snu-23::TY1 EGFP 3xFLAG(p_wTRG5_insertion_c_0094_4B11);unc-119(+));unc-119 (tm4063)) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. ele...

value: whole organism

tag: encode accession

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SNU-23

value: hermaphrodite

value: L1 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS346GXU at ENCODE; https://www.encodeproject.org/ENCBS346GXU/


title: TF ChIP-seq from ovary (ENCLB770VIT)

description:
https://www.encodeproject.org/experiments/ENCSR588OSO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG17801-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR588OSO
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR354RHJ
encode release date: 2019-07-09
lab: Kevin White, UChicago
library encode accession: ENCLB770VIT
size range: 200-800

value: ovary

value: tissue

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG17801

tag: Sex

value: female

tag: dev stage

value: adult

value: ENCBS996FYF at ENCODE; https://www.encodeproject.org/ENCBS996FYF/


title: TF ChIP-seq from whole organism (ENCLB993UNP)

description:
https://www.encodeproject.org/experiments/ENCSR320MVY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing SNU-23-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR320MVY
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR779STX
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB993UNP
fragmentation methods: sonication (generic microtip)

value: whole organism

value: whole organisms

tag: age

tag: lab

value: ENCBS643HGH at ENCODE; https://www.encodeproject.org/ENCBS643HGH/


title: TF ChIP-seq from whole organism (ENCLB081HID)

description:
https://www.encodeproject.org/experiments/ENCSR166DXK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F22D6.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR166DXK
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR206FGY
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB081HID
fragmentation methods: sonication (generic microtip)

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F22D6.2

value: hermaphrodite

value: young adult

tag: source

tag: link

value: ENCBS216FQL at ENCODE; https://www.encodeproject.org/ENCBS216FQL/


title: Control ChIP-seq from whole organism (ENCLB972MCL)

description:
https://www.encodeproject.org/experiments/ENCSR100ITO/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing HLH54F-eGFP fusion proteins.
experiment encode accession: ENCSR100ITO
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB972MCL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain HLH54F-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster HLH54F

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to HLH54F

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS049KNV at ENCODE; https://www.encodeproject.org/ENCBS049KNV/


title: Control ChIP-seq from whole organism (ENCLB481FZG)

description:
https://www.encodeproject.org/experiments/ENCSR283RSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR283RSJ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB481FZG
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP367 (unc-119(tm4063) III; wgIs367) mixed sex L2 larva insertion targeting C. elegans lsy-2

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to LSY-2

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS787XAQ at ENCODE; https://www.encodeproject.org/ENCBS787XAQ/


title: 315_L1

description:
extraction 023 sample 17_L1 pool 19_08
DGRP315 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB515MHK)

description:
https://www.encodeproject.org/experiments/ENCSR320EEP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing REF-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR320EEP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR973ZVP
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB515MHK
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP520 (unc-119(tm4063) III; wgIs520) hermaphrodite late embryo 3 hours post synchronization using egg bleaching insertion targeting C. elegans ref-2

value: whole organism

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to REF-2

value: hermaphrodite

value: late embryonic

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

tag: post synchronization time

value: hour

value: ENCBS382IPY at ENCODE; https://www.encodeproject.org/ENCBS382IPY/


title: 897_L2

description:
extraction 086 sample 49_L2 pool 19_07
DGRP897 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB760DCQ)

description:
https://www.encodeproject.org/experiments/ENCSR587CWK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Deaf1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR587CWK
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR251JRS
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB760DCQ
size range: 200-800

tag: antibody

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Deaf1

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS974YJS at ENCODE; https://www.encodeproject.org/ENCBS974YJS/


title: TF ChIP-seq from whole organism (ENCLB998UOU)

description:
https://www.encodeproject.org/experiments/ENCSR587CWK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Deaf1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR587CWK
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR251JRS
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB998UOU
size range: 200-800

value: whole organism

value: whole organisms

value: ENCBS704UQA at ENCODE; https://www.encodeproject.org/ENCBS704UQA/


title: Control ChIP-seq from whole organism (ENCLB311TID)

description:
https://www.encodeproject.org/experiments/ENCSR222HUE/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing PAG-3-eGFP fusion proteins.
experiment encode accession: ENCSR222HUE
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB311TID
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP154 (unc-119(ed3) III; wgIs154) hermaphrodite late embryo 4 hours post synchronization using egg bleaching insertion targeting C. elegans pag-3

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to PAG-3

value: hermaphrodite

value: late embryonic

value: unknown

tag: post synchronization time units

value: ENCBS322QYU at ENCODE; https://www.encodeproject.org/ENCBS322QYU/


title: Control ChIP-seq from whole organism (ENCLB263DMF)

description:
https://www.encodeproject.org/experiments/ENCSR394EAL/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG15710-eGFP fusion proteins.
experiment encode accession: ENCSR394EAL
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB263DMF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster mixed sex pupa (24 hours) insertion targeting D. melanogaster CG15710

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG15710

value: pupa

value: 24 hour

value: ENCBS746ZVN at ENCODE; https://www.encodeproject.org/ENCBS746ZVN/


title: TF ChIP-seq from whole organism (ENCLB267WDT)

description:
https://www.encodeproject.org/experiments/ENCSR005SGO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-ces-1 in L4 larva worms.
experiment encode accession: ENCSR005SGO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR841ZAM
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB267WDT
size range: 150-350

source_name: Caenorhabditis elegans strain OP174 (unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119)) mixed sex L4 larva insertion targeting C. elegans ces-1

value: not applicable

value: pooled male and female

value: L4 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS586OKO at ENCODE; https://www.encodeproject.org/ENCBS586OKO/


title: Control ChIP-seq from whole organism (ENCLB021IXG)

description:
https://www.encodeproject.org/experiments/ENCSR702TBJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing jing-eGFP fusion proteins.
experiment encode accession: ENCSR702TBJ
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB021IXG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain jing-GFP mixed sex embryo (0-16 hours) insertion targeting D. melanogaster jing

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to jing

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS761UPL at ENCODE; https://www.encodeproject.org/ENCBS761UPL/


title: 370_L1

description:
extraction 007 sample 24_L1 pool 19_05
DGRP370 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Larvae


title: 149_L1

description:
extraction 003 sample 07_L1 pool 19_04
DGRP149 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB304ECS)

description:
https://www.encodeproject.org/experiments/ENCSR005SGO/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq against eGFP-ces-1 in L4 larva worms.
experiment encode accession: ENCSR005SGO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR841ZAM
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB304ECS
fragmentation methods: sonication (generic microtip)

tag: biosample encode accession

tag: collection date

value: unknown

value: Michael Snyder

value: ENCBS767NMW at ENCODE; https://www.encodeproject.org/ENCBS767NMW/


title: TF ChIP-seq from whole organism (ENCLB595BJJ)

description:
https://www.encodeproject.org/experiments/ENCSR583EFI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ss-RA-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR583EFI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR474FXV
encode release date: 2018-02-01
lab: Kevin White, UChicago
library encode accession: ENCLB595BJJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain ss-GFP mixed sex prepupa (24 hours) insertion targeting D. melanogaster ss

value: ss

value: not applicable

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to ss-RB

value: pooled male and female

value: prepupa

value: 24 hour

value: ENCBS386TZQ at ENCODE; https://www.encodeproject.org/ENCBS386TZQ/


title: TF ChIP-seq from whole organism (ENCLB317NQT)

description:
https://www.encodeproject.org/experiments/ENCSR005SGO/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq against eGFP-ces-1 in L4 larva worms.
experiment encode accession: ENCSR005SGO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR841ZAM
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB317NQT
fragmentation methods: sonication (generic microtip)

value: whole organism

value: whole organisms

tag: encode accession

value: L4 larva

value: Michael Snyder, Stanford

value: ENCBS218MFV at ENCODE; https://www.encodeproject.org/ENCBS218MFV/


title: Control ChIP-seq from whole organism (ENCLB614BST)

description:
https://www.encodeproject.org/experiments/ENCSR310FMI/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing SYD-9-eGFP fusion proteins.
experiment encode accession: ENCSR310FMI
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB614BST
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP488 (unc-119(tm4063) III; wgIs488) hermaphrodite late embryo 4 hours post synchronization using egg bleaching insertion targeting C. elegans syd-9

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SYD-9

value: hermaphrodite

value: late embryonic

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: hour

value: ENCBS824PRL at ENCODE; https://www.encodeproject.org/ENCBS824PRL/


title: TF ChIP-seq from whole organism (ENCLB216KDQ)

description:
https://www.encodeproject.org/experiments/ENCSR133RTP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing MADF-10-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR133RTP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR555GJK
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB216KDQ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP508 (unc-119(tm4063) III; wgIs508) hermaphrodite young adult 68 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans madf-10

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to MADF-10

tag: Sex

value: young adult

value: unknown

value: L1 larva starved after bleaching

value: ENCBS064BDE at ENCODE; https://www.encodeproject.org/ENCBS064BDE/


title: 158_L1

description:
extraction 018 sample 09_L1 pool 19_03
DGRP158 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

source_name: whole body

value: whole body

tag: developmental stage

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB163SLY)

description:
https://www.encodeproject.org/experiments/ENCSR583EFI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ss-RA-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR583EFI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR474FXV
encode release date: 2018-02-01
lab: Kevin White, UChicago
library encode accession: ENCLB163SLY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: ss

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to ss-RB

value: pooled male and female

tag: dev stage

value: prepupa

tag: age

value: 24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS362LUT at ENCODE; https://www.encodeproject.org/ENCBS362LUT/


title: TF ChIP-seq from whole organism (ENCLB908VIM)

description:
https://www.encodeproject.org/experiments/ENCSR320EEP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing REF-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR320EEP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR973ZVP
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB908VIM
fragmentation methods: sonication (generic microtip)

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to REF-2

value: hermaphrodite

value: late embryonic

tag: lab

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

value: egg bleaching

value: hour

value: ENCBS459GVA at ENCODE; https://www.encodeproject.org/ENCBS459GVA/


title: Control ChIP-seq from whole organism (ENCLB442PNZ)

description:
https://www.encodeproject.org/experiments/ENCSR206FGY/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing F22D6.2-eGFP fusion proteins.
experiment encode accession: ENCSR206FGY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB442PNZ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP399 (unc-119(tm4063) III; wgIs399) hermaphrodite young adult 67 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans F22D6.2

value: whole organism

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F22D6.2

value: young adult

value: unknown

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: link

value: ENCBS022BCG at ENCODE; https://www.encodeproject.org/ENCBS022BCG/


title: 801_L2

description:
extraction 080 sample 41_L2 pool 18_27
DGRP801 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB670APQ)

description:
https://www.encodeproject.org/experiments/ENCSR005SGO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-ces-1 in L4 larva worms.
experiment encode accession: ENCSR005SGO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR841ZAM
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB670APQ
size range: 150-350

tag: antibody

value: not applicable

value: pooled male and female

value: L4 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS800DFU at ENCODE; https://www.encodeproject.org/ENCBS800DFU/


title: Control ChIP-seq from whole organism (ENCLB367YZQ)

description:
https://www.encodeproject.org/experiments/ENCSR101SVT/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR101SVT
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB367YZQ
size range: 150-350

source_name: Caenorhabditis elegans strain OP353 (unc-119(tm4063) III; wgIs353) mixed sex L2 larva insertion targeting C. elegans nhr-77

value: L2 larva

value: ENCBS679CON at ENCODE; https://www.encodeproject.org/ENCBS679CON/


title: TF ChIP-seq from whole organism (ENCLB615AUU)

description:
https://www.encodeproject.org/experiments/ENCSR204WOO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing SOX-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR204WOO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR745QHO
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB615AUU
fragmentation methods: sonication (generic microtip)
instrument models: Illumina HiSeq 2000,Illumina HiSeq 4000

source_name: Caenorhabditis elegans strain OP517 (unc-119(tm4063) III; wgIs517) mixed sex late embryo 4 hours post synchronization using egg bleaching insertion targeting C. elegans sox-4

value: whole organism

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SOX-4

value: late embryonic

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS508TJU at ENCODE; https://www.encodeproject.org/ENCBS508TJU/


title: 832_L2

description:
extraction 084 sample 45_L2 pool 18_25
DGRP832 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Larvae