title: TF ChIP-seq from whole organism (ENCLB459QUN)

description:
https://www.encodeproject.org/experiments/ENCSR697DSK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-lin-13 in L4 larva worms.
experiment encode accession: ENCSR697DSK
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR809ILU
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB459QUN
size range: 150-350

source_name: Caenorhabditis elegans strain OP49 (unc119(ed3);wgIs49(lin-13::TY1 EGFP FLAG;unc119)) mixed sex L4 larva insertion targeting C. elegans lin-13

value: L4 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS895BLX at ENCODE; https://www.encodeproject.org/ENCBS895BLX/


title: NIH3T3_EZdirect_10cell_WorkflowL_13cycle_10

status: Public on Feb 27 2024

type: genomic

city: Phialdelphia

first: Wanding

last: Zhou

state: Pennsylvania

address: 3501 Civic Center Blvd, Philadelphia, PA 19104, Colket Translational Research Building, 9300, Colket Translational Research Building

department: Pathology & Lab Medicine

country: USA

institute: Children's Hospital of Philadelphia

description:
Testing MM285 Array on low input DNA
205333480069_R04C01

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.18
Normalized average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Mus musculus

source_name: NIH3T3 ATCC, P4

label_protocol: Standard Illumina Protocol

growth_protocol: After obtaining cells from ATCC, they were cultured according to the instructions provided in the product sheet

extract_protocol: Genomic DNA was isolated using The DNeasy Blood and Tissue Kit (Qiagen, 69504) with the manufactural protocols

tag: cell type

value: 10 cells


title: NIH3T3_EZdirect_10cell_WorkflowL_16cycle_10

description:
Testing MM285 Array on low input DNA
205333480069_R05C01


title: Control ChIP-seq from whole organism (ENCLB159KJY)

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR577MAM/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR577MAM
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB159KJY
size range: 150-350

library_source: genomic

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

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP18 (unc-119(ed3) III; wgIs18) mixed sex L4 larva insertion targeting C. elegans lin-39

extract_protocol: not provided

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: Sex

value: pooled male and female

tag: dev stage

tag: age

value: unknown

tag: lab

tag: source

tag: link

value: ENCBS262DYR at ENCODE; https://www.encodeproject.org/ENCBS262DYR/


title: TF ChIP-seq from whole organism (ENCLB160DLR)

description:
https://www.encodeproject.org/experiments/ENCSR697DSK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-lin-13 in L4 larva worms.
experiment encode accession: ENCSR697DSK
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR809ILU
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB160DLR
size range: 150-350

tag: antibody

value: ENCBS467CIH at ENCODE; https://www.encodeproject.org/ENCBS467CIH/


title: NIH3T3_EZdirect_10cell_WorkflowI_10

description:
Testing MM285 Array on low input DNA
205333480069_R03C01


title: TF ChIP-seq from whole organism (ENCLB680PCP)

description:
https://www.encodeproject.org/experiments/ENCSR042XCV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing salr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR042XCV
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR315IPI
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB680PCP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strain salr-GFP mixed sex prepupa insertion targeting D. melanogaster salr

value: salr

tag: note

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

value: prepupa

value: Kevin White, UChicago

value: Kevin White

value: ENCBS761IOB at ENCODE; https://www.encodeproject.org/ENCBS761IOB/


title: TF ChIP-seq from whole organism (ENCLB407GKN)

description:
https://www.encodeproject.org/experiments/ENCSR042XCV/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing salr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR042XCV
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR315IPI
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB407GKN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: ENCBS353AKN at ENCODE; https://www.encodeproject.org/ENCBS353AKN/


title: TF ChIP-seq from whole organism (ENCLB471BGW)

description:
https://www.encodeproject.org/experiments/ENCSR325UBZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Su(H)-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR325UBZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR624TOZ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB471BGW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: Su(H)

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Su(H)

value: embryonic

value: 0-24 hour

value: ENCBS033FMR at ENCODE; https://www.encodeproject.org/ENCBS033FMR/


title: NIH3T3_EZdirect_100cell_WorkflowI_10

description:
Testing MM285 Array on low input DNA
205333480069_R02C01

value: 100 cells


title: Control ChIP-seq from whole organism (ENCLB180NQP)

description:
https://www.encodeproject.org/experiments/ENCSR577MAM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR577MAM
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB180NQP
size range: 150-350

value: whole organism

value: whole organisms

value: not applicable

value: pooled male and female

value: L4 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS535NRV at ENCODE; https://www.encodeproject.org/ENCBS535NRV/


title: TF ChIP-seq from whole organism (ENCLB718JTM)

description:
https://www.encodeproject.org/experiments/ENCSR042XCV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing salr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR042XCV
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR315IPI
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB718JTM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: salr

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

value: prepupa

value: unknown

value: Kevin White, UChicago

value: Kevin White

value: ENCBS923KCJ at ENCODE; https://www.encodeproject.org/ENCBS923KCJ/


title: NIH3T3_EZdirect_100ng_WorkflowC_10

description:
Testing MM285 Array on low input DNA
205333480069_R01C01


title: TF ChIP-seq from whole organism (ENCLB445GVK)

description:
https://www.encodeproject.org/experiments/ENCSR697KIC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against ELT-3 in L1 larva worms.
experiment encode accession: ENCSR697KIC
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR544TSB
encode release date: 2018-02-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB445GVK
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP75 (unc-119(ed3) III; wgIs75) mixed sex L1 larva insertion targeting C. elegans elt-3

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

value: L1 larva

value: Michael Snyder

value: ENCBS082KCC at ENCODE; https://www.encodeproject.org/ENCBS082KCC/


title: NIH3T3_EZkit_0.5ng_WorkflowG_07

description:
Testing MM285 Array on low input DNA
205333480137_R04C02

source_name: NIH3T3 ATCC, P2


title: Control ChIP-seq from whole organism (ENCLB965DIM)

description:
https://www.encodeproject.org/experiments/ENCSR389KDY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR389KDY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB965DIM
size range: 150-350

source_name: Caenorhabditis elegans strain OP43 (unc-119(ed3) III; wgIs43) mixed sex L3 larva insertion targeting C. elegans nhr-23

value: whole organism

value: whole organisms

value: not applicable

value: L3 larva

value: ENCBS011PJQ at ENCODE; https://www.encodeproject.org/ENCBS011PJQ/


title: NIH3T3_EZgold_0.5ng_WorkflowJ_07

description:
Testing MM285 Array on low input DNA
205333480137_R01C02


title: NIH3T3_EZgold_0.5ng_WorkflowI_07

description:
Testing MM285 Array on low input DNA
205333480137_R06C01


title: NIH3T3_EZdirect_0.5ng_WorkflowJ_07

description:
Testing MM285 Array on low input DNA
205333480137_R05C01


title: TF ChIP-seq from whole organism (ENCLB242XQM)

description:
https://www.encodeproject.org/experiments/ENCSR325UBZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Su(H)-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR325UBZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR624TOZ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB242XQM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Su(H)

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Su(H)

value: pooled male and female

value: embryonic

value: 0-24 hour

value: ENCBS824YIG at ENCODE; https://www.encodeproject.org/ENCBS824YIG/


title: Control ChIP-seq from whole organism (ENCLB418KJA)

description:
https://www.encodeproject.org/experiments/ENCSR389KDY/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR389KDY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB418KJA
size range: 150-350

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS414AJZ at ENCODE; https://www.encodeproject.org/ENCBS414AJZ/


title: NIH3T3_EZdirect_0.5ng_WorkflowI_07

description:
Testing MM285 Array on low input DNA
205333480137_R04C01


title: NIH3T3_EZkit_0.5ng_WorkflowJ_07

description:
Testing MM285 Array on low input DNA
205333480137_R03C01


title: Control ChIP-seq from whole organism (ENCLB080NLD)

description:
https://www.encodeproject.org/experiments/ENCSR696TMF/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 worms.
experiment encode accession: ENCSR696TMF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB080NLD
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP178 (unc-119(ed3) III; wgIs178) mixed sex L2 larva insertion targeting C. elegans skn-1

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

value: L2 larva

value: Michael Snyder

value: ENCBS008QTQ at ENCODE; https://www.encodeproject.org/ENCBS008QTQ/


title: Control ChIP-seq from whole organism (ENCLB362YSQ)

description:
https://www.encodeproject.org/experiments/ENCSR323PMD/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing NC2β-eGFP fusion proteins.
experiment encode accession: ENCSR323PMD
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB362YSQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain NC2beta-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster NC2beta

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to NC2beta

value: Kevin White, UChicago

value: Kevin White

value: ENCBS697NXT at ENCODE; https://www.encodeproject.org/ENCBS697NXT/


title: NIH3T3_EZkit_0.5ng_WorkflowG_06

description:
Testing MM285 Array on low input DNA
205333490033_R06C02


title: NIH3T3_EZgold_250ng_WorkflowC_07

description:
A NIH3T3 standard, passge number 3, EZ gold kit
205333480137_R01C01

source_name: NIH3T3 ATCC, P3


title: Control ChIP-seq from whole organism (ENCLB668CWA)

description:
https://www.encodeproject.org/experiments/ENCSR040UNE/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing crp-eGFP fusion proteins.
experiment encode accession: ENCSR040UNE
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB668CWA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

value: pooled male and female

value: embryonic

value: 0-16 hour

value: ENCBS389DPR at ENCODE; https://www.encodeproject.org/ENCBS389DPR/


title: NIH3T3_EZkit_2ng_WorkflowG_06

description:
Testing MM285 Array on low input DNA
205333490033_R05C02

value: 2 ng


title: TF ChIP-seq from whole organism (ENCLB248QRS)

description:
https://www.encodeproject.org/experiments/ENCSR696OWC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-elt-3 in L3 larva worms.
experiment encode accession: ENCSR696OWC
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR149QCW
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB248QRS
size range: 150-350

source_name: Caenorhabditis elegans strain OP75 (unc-119(ed3) III; wgIs75) mixed sex L3 larva insertion targeting C. elegans elt-3

value: L3 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS149CKR at ENCODE; https://www.encodeproject.org/ENCBS149CKR/


title: TF ChIP-seq from whole organism (ENCLB295JJK)

description:
https://www.encodeproject.org/experiments/ENCSR325UBZ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Su(H)-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR325UBZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR624TOZ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB295JJK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Su(H)

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Su(H)

value: 0-24 hour

value: ENCBS702FHJ at ENCODE; https://www.encodeproject.org/ENCBS702FHJ/


title: NIH3T3_EZkit_0.5ng_WorkflowH_06_rep

description:
Testing MM285 Array on low input DNA
205333490033_R04C02


title: TF ChIP-seq from whole organism (ENCLB235LWX)

description:
https://www.encodeproject.org/experiments/ENCSR151WSI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG30403-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR151WSI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR635FXZ
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB235LWX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG30403-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG30403

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG30403

value: Kevin White, UChicago

value: Kevin White

value: ENCBS011NDS at ENCODE; https://www.encodeproject.org/ENCBS011NDS/


title: NIH3T3_EZkit_0.5ng_WorkflowH_06

description:
Testing MM285 Array on low input DNA
205333490033_R03C02


title: Control ChIP-seq from whole organism (ENCLB594YMD)

description:
https://www.encodeproject.org/experiments/ENCSR573YEK/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 worms.
experiment encode accession: ENCSR573YEK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB594YMD
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP177 (unc-119(ed3) III; wgIs177) mixed sex L2 larva insertion targeting C. elegans egl-27

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to EGL-27

value: pooled male and female

value: L2 larva

value: Michael Snyder

value: ENCBS543HKQ at ENCODE; https://www.encodeproject.org/ENCBS543HKQ/


title: NIH3T3_EZkit_0.5ng_WorkflowF_06

description:
Testing MM285 Array on low input DNA
205333490033_R01C02


title: TF ChIP-seq from whole organism (ENCLB161IYT)

description:
https://www.encodeproject.org/experiments/ENCSR696OWC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-elt-3 in L3 larva worms.
experiment encode accession: ENCSR696OWC
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR149QCW
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB161IYT
size range: 150-350

value: L3 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS883WJB at ENCODE; https://www.encodeproject.org/ENCBS883WJB/


title: NIH3T3_EZkit_0.5ng_WorkflowK_21Cycle_06

description:
Testing MM285 Array on low input DNA
205333490033_R06C01


title: NIH3T3_EZkit_0.5ng_WorkflowK_16Cycle_06

description:
Testing MM285 Array on low input DNA
205333490033_R05C01


title: Control ChIP-seq from whole organism (ENCLB736DNI)

description:
https://www.encodeproject.org/experiments/ENCSR573YEK/
***************
biological replicate number: 3
technical replicate number: 1
description: Input ChIP-seq in L2 worms.
experiment encode accession: ENCSR573YEK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB736DNI
fragmentation methods: sonication (generic microtip)

value: whole organism

value: whole organisms

value: ENCBS449KEH at ENCODE; https://www.encodeproject.org/ENCBS449KEH/


title: TF ChIP-seq from whole organism (ENCLB491XPN)

description:
https://www.encodeproject.org/experiments/ENCSR151WSI/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG30403-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR151WSI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR635FXZ
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB491XPN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG30403

value: embryonic

value: 0-24 hour

value: ENCBS034NAQ at ENCODE; https://www.encodeproject.org/ENCBS034NAQ/


title: Control ChIP-seq from whole organism (ENCLB283KLJ)

description:
https://www.encodeproject.org/experiments/ENCSR325OBK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG2116-eGFP fusion proteins.
experiment encode accession: ENCSR325OBK
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-12-13
lab: Kevin White, UChicago
library encode accession: ENCLB283KLJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG2116-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG2116

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG2116

value: pooled male and female

value: Kevin White, UChicago

value: Kevin White

value: ENCBS012HDU at ENCODE; https://www.encodeproject.org/ENCBS012HDU/


title: Control ChIP-seq from whole organism (ENCLB747RWV)

description:
https://www.encodeproject.org/experiments/ENCSR696TMF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 worms.
experiment encode accession: ENCSR696TMF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB747RWV
fragmentation methods: sonication (generic microtip)

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

value: L2 larva

value: unknown

value: Michael Snyder

value: ENCBS696BKW at ENCODE; https://www.encodeproject.org/ENCBS696BKW/


title: NIH3T3_EZkit_0.5ng_WorkflowK_13Cycle_06

description:
Testing MM285 Array on low input DNA
205333490033_R04C01


title: Control ChIP-seq from whole organism (ENCLB015HLU)

description:
https://www.encodeproject.org/experiments/ENCSR230GUY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing lilli-eGFP fusion proteins.
experiment encode accession: ENCSR230GUY
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB015HLU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

value: whole organisms

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

value: ENCBS453WZR at ENCODE; https://www.encodeproject.org/ENCBS453WZR/


title: TF ChIP-seq from whole organism (ENCLB228DKS)

description:
https://www.encodeproject.org/experiments/ENCSR151WSI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG30403-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR151WSI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR635FXZ
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB228DKS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG30403

value: embryonic

value: ENCBS125KBR at ENCODE; https://www.encodeproject.org/ENCBS125KBR/


title: NIH3T3_EZkit_2ng_WorkflowF_06

description:
Testing MM285 Array on low input DNA
205333490033_R03C01

value: 2 ng


title: Control ChIP-seq from whole organism (ENCLB557ZOP)

description:
https://www.encodeproject.org/experiments/ENCSR573YEK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 worms.
experiment encode accession: ENCSR573YEK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB557ZOP
fragmentation methods: sonication (generic microtip)

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to EGL-27

value: pooled male and female

value: Michael Snyder, Stanford

value: ENCBS173PVW at ENCODE; https://www.encodeproject.org/ENCBS173PVW/


title: TF ChIP-seq from whole organism (ENCLB934AVJ)

description:
https://www.encodeproject.org/experiments/ENCSR226MOG/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10565-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR226MOG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR837BBL
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB934AVJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG10565-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG10565

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10565

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS111OFG at ENCODE; https://www.encodeproject.org/ENCBS111OFG/


title: NIH3T3_EZkit_0.5ng_WorkflowI_07

description:
Testing MM285 Array on low input DNA
205333480137_R02C01


title: NIH3T3_EZkit_2ng_WorkflowC_06

description:
Testing MM285 Array on low input DNA
205333490033_R02C01


title: TF ChIP-seq from whole organism (ENCLB234FHY)

description:
https://www.encodeproject.org/experiments/ENCSR149KUC/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG12155-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR149KUC
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR089QIZ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB234FHY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG12155-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG12155

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12155

value: ENCBS022GCH at ENCODE; https://www.encodeproject.org/ENCBS022GCH/


title: Control ChIP-seq from whole organism (ENCLB483BXC)

description:
https://www.encodeproject.org/experiments/ENCSR570PSN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR570PSN
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB483BXC
size range: 150-350

source_name: Caenorhabditis elegans strain OP343 (unc-119(ed3) III; wgIs343) mixed sex L2 larva insertion targeting C. elegans gmeb-1

value: not applicable

value: L2 larva

value: unknown

value: CGC

value: ENCBS690ABL at ENCODE; https://www.encodeproject.org/ENCBS690ABL/


title: Control ChIP-seq from whole organism (ENCLB582AWJ)

description:
https://www.encodeproject.org/experiments/ENCSR224PPR/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Elba2-eGFP fusion proteins.
experiment encode accession: ENCSR224PPR
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB582AWJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG9883-GFP mixed sex embryo (0-4 hours) insertion targeting D. melanogaster Elba2

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Elba2

value: pooled male and female

value: embryonic

value: 0-4 hour

value: ENCBS940XSW at ENCODE; https://www.encodeproject.org/ENCBS940XSW/


title: Control ChIP-seq from whole organism (ENCLB730CJV)

description:
https://www.encodeproject.org/experiments/ENCSR570PSN/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR570PSN
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB730CJV
size range: 150-350

value: Michael Snyder, Stanford

value: ENCBS437HUM at ENCODE; https://www.encodeproject.org/ENCBS437HUM/


title: NIH3T3_EZkit_0.5ng_WorkflowK_16Cycle_05

description:
Testing MM285 Array on low input DNA
205243950081_R02C02


title: NIH3T3_EZkit_0.5ng_WorkflowF_06_rep

description:
Testing MM285 Array on low input DNA
205333490033_R02C02


title: NIH3T3_EZkit_250ng_WorkflowC_05

description:
A NIH3T3 standard, passge number 2, EZ kit
205243950081_R01C01


title: TF ChIP-seq from whole organism (ENCLB288TYR)

description:
https://www.encodeproject.org/experiments/ENCSR224OFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing vri-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR224OFQ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR989MAT
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB288TYR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain vri-GFP mixed sex prepupa at white prepupa stage insertion targeting D. melanogaster vri

value: vri

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

value: prepupa

value: Kevin White, UChicago

value: Kevin White

tag: fly synchronization stage

value: white prepupa

value: ENCBS308AUR at ENCODE; https://www.encodeproject.org/ENCBS308AUR/


title: Control ChIP-seq from whole organism (ENCLB053BLR)

description:
https://www.encodeproject.org/experiments/ENCSR569UBF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR569UBF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB053BLR
size range: 150-350

source_name: Caenorhabditis elegans strain OP304 (unc-119(ed3) III; wgIs304) mixed sex L4 larva insertion targeting C. elegans fos-1

value: whole organism

value: whole organisms

value: not applicable

value: L4 larva

value: unknown

value: ENCBS956HKX at ENCODE; https://www.encodeproject.org/ENCBS956HKX/


title: NIH3T3_EZkit_0.5ng_WorkflowD_03

description:
Testing MM285 array on low input DNA with FFPE kit
205243950093_R06C02

source_name: NIH3T3 ATCC, P2


title: NIH3T3_EZkit_1ng_WorkflowD_03

description:
Testing MM285 array on low input DNA with FFPE kit
205243950093_R05C02

value: 1 ng


title: NIH3T3_EZkit_0.5ng_WorkflowB_03

description:
Testing MM285 Array on low input DNA
205243950093_R03C02


title: Control ChIP-seq from whole organism (ENCLB884NNJ)

description:
https://www.encodeproject.org/experiments/ENCSR569UBF/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR569UBF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB884NNJ
size range: 150-350

value: pooled male and female

value: CGC

value: ENCBS384MKJ at ENCODE; https://www.encodeproject.org/ENCBS384MKJ/


title: TF ChIP-seq from whole organism (ENCLB996ZCT)

description:
https://www.encodeproject.org/experiments/ENCSR224OFQ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing vri-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR224OFQ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR989MAT
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB996ZCT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: vri

value: ENCBS139MHZ at ENCODE; https://www.encodeproject.org/ENCBS139MHZ/


title: Control ChIP-seq from whole organism (ENCLB966VRP)

description:
https://www.encodeproject.org/experiments/ENCSR569PKU/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR569PKU
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB966VRP
size range: 150-350

source_name: Caenorhabditis elegans strain OP218 (unc-119(ed3) III; wgIs218) mixed sex L3 larva insertion targeting C. elegans R02D3.7

value: L3 larva

value: Michael Snyder, Stanford

value: ENCBS966ZBN at ENCODE; https://www.encodeproject.org/ENCBS966ZBN/


title: NIH3T3_EZkit_1ng_WorkflowB_03

description:
Testing MM285 Array on low input DNA
205243950093_R02C02


title: NIH3T3_EZkit_50ng_WorkflowB_03

description:
Testing MM285 Array on low input DNA
205243950093_R01C02

value: 50 ng


title: Control ChIP-seq from whole organism (ENCLB011LCZ)

description:
https://www.encodeproject.org/experiments/ENCSR569PKU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR569PKU
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB011LCZ
size range: 150-350

value: ENCBS212YFP at ENCODE; https://www.encodeproject.org/ENCBS212YFP/


title: NIH3T3_EZkit_50ng_WorkflowE_03

description:
Testing MM285 array on low input DNA with FFPE kit
205243950093_R04C01


title: Control ChIP-seq from whole organism (ENCLB090DLH)

description:
https://www.encodeproject.org/experiments/ENCSR320AIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing odsH-eGFP fusion proteins.
experiment encode accession: ENCSR320AIQ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB090DLH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain OdsH-GFP mixed sex prepupa at white prepupa stage insertion targeting D. melanogaster OdsH

value: whole organism

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

value: prepupa

value: Kevin White, UChicago

value: Kevin White

value: white prepupa

value: ENCBS038NRV at ENCODE; https://www.encodeproject.org/ENCBS038NRV/


title: NIH3T3_EZkit_1ng_WorkflowE_03

description:
Testing MM285 array on low input DNA with FFPE kit
205243950093_R05C01

value: 1 ng


title: Control ChIP-seq from whole organism (ENCLB603TRT)

description:
https://www.encodeproject.org/experiments/ENCSR569BKC/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR569BKC
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB603TRT
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP186 (unc-119(ed3) III; wgIs186) mixed sex L4 larva insertion targeting C. elegans unc-39

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to UNC-39

value: pooled male and female

value: L4 larva

value: unknown

value: Michael Snyder

value: ENCBS043SUW at ENCODE; https://www.encodeproject.org/ENCBS043SUW/


title: NIH3T3_EZkit_250ng_WorkflowC_06

description:
A NIH3T3 standard, passge number 3, EZ kit
205333490033_R01C01

source_name: NIH3T3 ATCC, P3


title: TF ChIP-seq from whole organism (ENCLB978LRU)

description:
https://www.encodeproject.org/experiments/ENCSR224OFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing vri-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR224OFQ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR989MAT
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB978LRU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: vri

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

value: ENCBS062MYG at ENCODE; https://www.encodeproject.org/ENCBS062MYG/


title: Control ChIP-seq from whole organism (ENCLB040CZH)

description:
https://www.encodeproject.org/experiments/ENCSR144XHB/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing svp-eGFP fusion proteins.
experiment encode accession: ENCSR144XHB
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB040CZH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain svp-GFP mixed sex prepupa at white prepupa stage insertion targeting D. melanogaster svp

value: whole organism

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

value: prepupa

value: ENCBS516UQQ at ENCODE; https://www.encodeproject.org/ENCBS516UQQ/


title: Control ChIP-seq from whole organism (ENCLB264ZHI)

description:
https://www.encodeproject.org/experiments/ENCSR318AGT/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Esplmgamma-HLH-eGFP fusion proteins.
experiment encode accession: ENCSR318AGT
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB264ZHI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Esplmgamma-HLH-GFP mixed sex embryo (0-16 hours) insertion targeting D. melanogaster E(spl)mgamma-HLH

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

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS731DDS at ENCODE; https://www.encodeproject.org/ENCBS731DDS/


title: NIH3T3_EZkit_50ng_WorkflowD_03

description:
Testing MM285 array on low input DNA with FFPE kit
205243950093_R04C02

value: 50 ng


title: NIH3T3_EZkit_50ng_WorkflowC_03

description:
Testing MM285 Array on low input DNA
205243950093_R01C01


title: Control ChIP-seq from whole organism (ENCLB670CLT)

description:
https://www.encodeproject.org/experiments/ENCSR569BKC/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR569BKC
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB670CLT
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to UNC-39

value: pooled male and female

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: ENCBS868GND at ENCODE; https://www.encodeproject.org/ENCBS868GND/


title: TF ChIP-seq from whole organism (ENCLB926COO)

description:
https://www.encodeproject.org/experiments/ENCSR317SVS/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing acj6-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR317SVS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR691GHG
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB926COO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain acj6-GFP mixed sex prepupa at white prepupa stage insertion targeting D. melanogaster acj6

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to acj6

value: prepupa

value: white prepupa

value: ENCBS698RKC at ENCODE; https://www.encodeproject.org/ENCBS698RKC/


title: NIH3T3_EZkit_0.5ng_WorkflowK_21Cycle_05

description:
Testing MM285 Array on low input DNA
205243950081_R03C02


title: NIH3T3_EZkit_0.5ng_WorkflowE_03

description:
Testing MM285 array on low input DNA with FFPE kit
205243950093_R06C01


title: Kidney, Foxp1KspKO mice, ChIP

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

data_processing:
Illumina HiSeq xten/NovaSeq 6000 sequencer
The raw paired-end reads were quality checked by FastQC (https://github.com/s-andrews/FastQC) and trimmed to remove adaptor sequences and low-quality reads using Trimmomatic with the default setting.
ChIP-seq reads were aligned to the reference genome GRCm38.86 using the bowtie2 software and only uniquely and non-duplicate mapped reads were used to perform the downstream analysis.
To examine the reproducibility of the ChIP–seq experiments, Deeptools was used to generate a bigwig format to facilitate visualization of the reads coverage and comparison among different samples including input samples.
The number of reads overlapping a region between 3kb upstream and 3kb downstream of the TSS of each gene were calculated by the R package Rsamtools (https://bioconductor.org/packages/Rsamtools).  Promoter counts of each gene were used to identify genes bound by Foxp1 (Pvalue <0.05) using the normalizeChIPtoInput function in the R package edgeR.
Average coverage plots and heatmaps for the binding genes were made using ngs.plot. Differential binding analysis between control and Foxp1-deficent conditions was conducted using the R package edgeR.The motifs analysis was used the regulatory sequence analysis tools (RSAT) peak-motifs. All the bigwig files of ChIP-seq and RiboTag RNA-seq were visualized using the Integrative Genomics Viewer (IGV).
Assembly: mm10
Supplementary files format and content: tab-delimited excel file includes the significant enrichment relative to the control
Supplementary files format and content: bigwig files to view the data

source_name: Kidney

growth_protocol: Neonatal littermate control and Foxp1KspKO mice were hypothermic anesthetized then perfused with PBS. The kidneys were quickly removed to a 0.5ml DMEM/F12 solution containing 2 g/L collagenase IV (Sigma; C5138) and Benzonase nuclease (Millipore; E1014, 1:2000), digested for 20 min at 37°C with gentle agitation.

extract_protocol:
cells were lysed and the chromatin was sheared to a size range of 150 to 300 bp using the sonicator (Diagenode, Bioruptor Pico). For each IP to be performed, aliquot 30μL magnetic Protein G beads (Invitrogen; 1003D) were used to preclear the chromatin, and incubated at 4℃ overnight with the previously characterized Foxp1 polyclonal antibody or control rabbit IgG (2729S; Cell Signaling).
Immune complexes were handled according to the manufacturer’s protocol. Reverse cross-linked immunoprecipitated chromatin was extracted using QIAquick PCR Purification Kit. The library was quantified using the QubitTM dsDNA HS Assay Kit (Invitrogen; Q32851) by QubitTM Fluorometer, inspected with Agilent bioanalyzer and StepOnePlus Real-Time PCR.

treatment_protocol: The digestive system neutralization with DMEM/F12 contain 10% FBS. After centrifugation the kidney digest was re-suspension then washed through a 40um sieves (FALCON; 352340) to collect kidney tubular cells. The ChIP assay was carried out as previously described.

tag: tissue

value: Kidney

value: kidney tubular cells

tag: genotype

tag: chip antibody

value: previously characterized Foxp1 polyclonal antibody (PMID:14516685)


title: TF ChIP-seq from whole organism (ENCLB513RTR)

description:
https://www.encodeproject.org/experiments/ENCSR568VIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-snpc-4 in mixed stage (embryonic) worms.
experiment encode accession: ENCSR568VIQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR201EHF
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB513RTR
size range: 150-350

source_name: Caenorhabditis elegans strain OP179 (unc-119(ed3) III; wgIs179) mixed sex mixed stage (embryo) insertion targeting C. elegans snpc-4

value: mixed stage (embryonic)

value: CGC

value: ENCBS112WGD at ENCODE; https://www.encodeproject.org/ENCBS112WGD/


title: NIH3T3_EZkit_0.5ng_WorkflowC_03

description:
Testing MM285 Array on low input DNA
205243950093_R03C01

tag: cell type


title: TF ChIP-seq from whole organism (ENCLB574NAW)

description:
https://www.encodeproject.org/experiments/ENCSR317SVS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing acj6-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR317SVS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR691GHG
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB574NAW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: biosample encode accession

value: not applicable

value: Kevin White, UChicago

value: Kevin White

value: ENCBS158JYT at ENCODE; https://www.encodeproject.org/ENCBS158JYT/


title: Kidney, Foxp1KspKO mice, Input


title: TF ChIP-seq from whole organism (ENCLB081VUG)

description:
https://www.encodeproject.org/experiments/ENCSR568VIQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-snpc-4 in mixed stage (embryonic) worms.
experiment encode accession: ENCSR568VIQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR201EHF
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB081VUG
size range: 150-350

tag: collection date

value: pooled male and female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS440BHS at ENCODE; https://www.encodeproject.org/ENCBS440BHS/


title: TF ChIP-seq from whole organism (ENCLB070CXX)

description:
https://www.encodeproject.org/experiments/ENCSR317SVS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing acj6-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR317SVS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR691GHG
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB070CXX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to acj6

value: prepupa

value: white prepupa

value: ENCBS553ICZ at ENCODE; https://www.encodeproject.org/ENCBS553ICZ/


title: Kidney, Neonatal littermate control, Input

value: Kidney

value: kidney tubular cells

value: Control


title: Control ChIP-seq from whole organism (ENCLB723RRJ)

description:
https://www.encodeproject.org/experiments/ENCSR567JAU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in mixed stage (embryonic) worms.
experiment encode accession: ENCSR567JAU
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB723RRJ
size range: 150-350

source_name: Caenorhabditis elegans strain OP236 (unc-119(ed3) III; wgIs236) mixed sex mixed stage (embryo) insertion targeting C. elegans ztf-11

value: whole organisms

tag: encode accession

value: mixed stage (embryonic)

value: CGC

value: ENCBS517HPJ at ENCODE; https://www.encodeproject.org/ENCBS517HPJ/


title: TF ChIP-seq from whole organism (ENCLB127KYW)

description:
https://www.encodeproject.org/experiments/ENCSR533AOQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing cebp-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR533AOQ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR259MSM
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB127KYW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP331 (wgIs331(C48E7.11::TY1 EGFP 3xFLAG(P000010_F04)); unc-119(+));unc-119(ed3)) young adult (64 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans cebp-2

value: not applicable

tag: Sex

value: not collected

value: young adult

value: 64 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: ENCBS061SAF at ENCODE; https://www.encodeproject.org/ENCBS061SAF/


title: Control ChIP-seq from whole organism (ENCLB164DHJ)

description:
https://www.encodeproject.org/experiments/ENCSR315IPI/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing salr-eGFP fusion proteins.
experiment encode accession: ENCSR315IPI
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB164DHJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain salr-GFP mixed sex prepupa insertion targeting D. melanogaster salr

value: whole organism

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

value: pooled male and female

tag: dev stage

value: prepupa

tag: age

value: unknown

value: Kevin White, UChicago

value: Kevin White

value: ENCBS061JWF at ENCODE; https://www.encodeproject.org/ENCBS061JWF/


title: TF ChIP-seq from whole organism (ENCLB117BQC)

description:
https://www.encodeproject.org/experiments/ENCSR533AOQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing cebp-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR533AOQ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR259MSM
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB117BQC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: lab

tag: source

value: ENCBS487OAZ at ENCODE; https://www.encodeproject.org/ENCBS487OAZ/


title: Control ChIP-seq from whole organism (ENCLB014ITE)

description:
https://www.encodeproject.org/experiments/ENCSR567JAU/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in mixed stage (embryonic) worms.
experiment encode accession: ENCSR567JAU
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB014ITE
size range: 150-350

value: not applicable

value: mixed stage (embryonic)

value: Michael Snyder, Stanford

value: CGC

tag: link

value: ENCBS019AVX at ENCODE; https://www.encodeproject.org/ENCBS019AVX/


title: Control ChIP-seq from whole organism (ENCLB908KVO)

description:
https://www.encodeproject.org/experiments/ENCSR530KZU/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing vab-7-eGFP fusion proteins.
experiment encode accession: ENCSR530KZU
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB908KVO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12267 (st12267[vab-7::TY1::EGFP::3xFLAG] III) L4 larva (47 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans vab-7

value: not collected

value: L4 larva

value: 47 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS461HWE at ENCODE; https://www.encodeproject.org/ENCBS461HWE/


title: NIH3T3_EZkit_1ng_WorkflowC_03

description:
Testing MM285 Array on low input DNA
205243950093_R02C01

value: 1 ng


title: TF ChIP-seq from whole organism (ENCLB487GYM)

description:
https://www.encodeproject.org/experiments/ENCSR526QUI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing tbx-37-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR526QUI
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR288MSH
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB487GYM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12282 (st12282[tbx-37 ::TY1::EGFP::3xFLAG] III) early embryo (0 hours) using egg bleaching whole organism genetically modified (insertion) using CRISPR targeting C. elegans tbx-37

tag: antibody

value: whole organism

value: early embryonic

value: 0 hour

value: egg bleaching

value: ENCBS266AOK at ENCODE; https://www.encodeproject.org/ENCBS266AOK/


title: TF ChIP-seq from whole organism (ENCLB403BPY)

description:
https://www.encodeproject.org/experiments/ENCSR529XPL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing saeg-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR529XPL
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR588YLV
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB403BPY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12230 (st12230[saeg-2::TY1::EGFP::3xFLAG] III) L4 larva (48 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans saeg-2

value: whole organisms

value: not applicable

value: 48 hour

value: ENCBS340JMQ at ENCODE; https://www.encodeproject.org/ENCBS340JMQ/


title: TF ChIP-seq from whole organism (ENCLB795AZL)

description:
https://www.encodeproject.org/experiments/ENCSR313RIH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10654-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR313RIH
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR942LEY
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB795AZL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG10654-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG10654

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10654

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS316ZFX at ENCODE; https://www.encodeproject.org/ENCBS316ZFX/


title: TF ChIP-seq from whole organism (ENCLB417ICC)

description:
https://www.encodeproject.org/experiments/ENCSR567FOP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-ztf-11 in L4 larva worms.
experiment encode accession: ENCSR567FOP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR586FLU
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB417ICC
size range: 150-350

source_name: Caenorhabditis elegans strain OP236 (unc-119(ed3) III; wgIs236) mixed sex L4 larva insertion targeting C. elegans ztf-11

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS153UMG at ENCODE; https://www.encodeproject.org/ENCBS153UMG/


title: TF ChIP-seq from whole organism (ENCLB255NGH)

description:
https://www.encodeproject.org/experiments/ENCSR529XPL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing saeg-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR529XPL
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR588YLV
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB255NGH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not collected

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS445MET at ENCODE; https://www.encodeproject.org/ENCBS445MET/


title: TF ChIP-seq from whole organism (ENCLB602EBE)

description:
https://www.encodeproject.org/experiments/ENCSR313RIH/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10654-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR313RIH
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR942LEY
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB602EBE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10654

value: pooled male and female

value: ENCBS778RCZ at ENCODE; https://www.encodeproject.org/ENCBS778RCZ/


title: TF ChIP-seq from whole organism (ENCLB088NYS)

description:
https://www.encodeproject.org/experiments/ENCSR567FOP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-ztf-11 in L4 larva worms.
experiment encode accession: ENCSR567FOP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR586FLU
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB088NYS
size range: 150-350

value: ENCBS512ZWW at ENCODE; https://www.encodeproject.org/ENCBS512ZWW/


title: TF ChIP-seq from whole organism (ENCLB706OLO)

description:
https://www.encodeproject.org/experiments/ENCSR526QUI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing tbx-37-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR526QUI
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR288MSH
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB706OLO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: early embryonic

value: 0 hour

value: egg bleaching

value: ENCBS033SPK at ENCODE; https://www.encodeproject.org/ENCBS033SPK/


title: Control ChIP-seq from whole organism (ENCLB601SHY)

description:
https://www.encodeproject.org/experiments/ENCSR566WSV/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR566WSV
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB601SHY
size range: 150-350

source_name: Caenorhabditis elegans strain OP228 (unc-119(ed3) III; wgIs228) mixed sex L1 larva insertion targeting C. elegans nhr-237

value: L1 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS059BAL at ENCODE; https://www.encodeproject.org/ENCBS059BAL/


title: TF ChIP-seq from whole organism (ENCLB438WKY)

description:
https://www.encodeproject.org/experiments/ENCSR141ZKI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG1647-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR141ZKI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR987FJM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB438WKY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG1647-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG1647

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG1647

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS509QUP at ENCODE; https://www.encodeproject.org/ENCBS509QUP/


title: TF ChIP-seq from whole organism (ENCLB342HVE)

description:
https://www.encodeproject.org/experiments/ENCSR840UYL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing nfya-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR840UYL
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR352ODW
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB342HVE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12238 (st12238[nfya-2::TY1::EGFP::3xFLAG] I) young adult (64 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans nfya-2

value: whole organisms

value: not applicable

value: not collected

value: young adult

value: 64 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS581VTE at ENCODE; https://www.encodeproject.org/ENCBS581VTE/


title: Kidney, Neonatal littermate control, ChIP

tag: tissue

value: Kidney

value: kidney tubular cells

value: Control

value: control rabbit IgG (2729S; Cell Signaling).


title: TF ChIP-seq from whole organism (ENCLB319TQS)

description:
https://www.encodeproject.org/experiments/ENCSR840UYL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing nfya-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR840UYL
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR352ODW
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB319TQS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: ENCBS268VME at ENCODE; https://www.encodeproject.org/ENCBS268VME/


title: TF ChIP-seq from whole organism (ENCLB880ZJC)

description:
https://www.encodeproject.org/experiments/ENCSR521VGM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-40-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR521VGM
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR754LZH
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB880ZJC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP232 (wgIs232(ceh-40::TY1 EGFP FLAG;unc-119);unc-119(ed3)) young adult (76 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ceh-40

value: 76 hour

value: ENCBS096QAU at ENCODE; https://www.encodeproject.org/ENCBS096QAU/


title: TF ChIP-seq from whole organism (ENCLB247EFA)

description:
https://www.encodeproject.org/experiments/ENCSR141ZKI/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG1647-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR141ZKI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR987FJM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB247EFA
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 CG1647

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS959EHJ at ENCODE; https://www.encodeproject.org/ENCBS959EHJ/


title: Control ChIP-seq from whole organism (ENCLB713UJV)

description:
https://www.encodeproject.org/experiments/ENCSR566WSV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR566WSV
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB713UJV
size range: 150-350

value: not applicable

value: L1 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS620FAY at ENCODE; https://www.encodeproject.org/ENCBS620FAY/


title: Control ChIP-seq from whole organism (ENCLB770YAO)

description:
https://www.encodeproject.org/experiments/ENCSR836ZQN/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing aptf-3-eGFP fusion proteins.
experiment encode accession: ENCSR836ZQN
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB770YAO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP765 (wgIs765(aptf-3::TY1 EGFP 3xFLAG(p_wTRG5_single_colony_c_0091_5E12);unc-119(+));unc-119 (tm4063)) young adult (64 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans aptf-3

value: whole organism

value: not collected

value: young adult

value: 64 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS079YNL at ENCODE; https://www.encodeproject.org/ENCBS079YNL/


title: Control ChIP-seq from whole organism (ENCLB931VVJ)

description:
https://www.encodeproject.org/experiments/ENCSR566WAD/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR566WAD
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB931VVJ
size range: 150-350

source_name: Caenorhabditis elegans strain OP33 (unc-119(ed3) III; wgIs33) mixed sex L2 larva insertion targeting C. elegans nhr-25

value: whole organisms

value: pooled male and female

value: L2 larva

value: ENCBS921EMC at ENCODE; https://www.encodeproject.org/ENCBS921EMC/


title: TF ChIP-seq from whole organism (ENCLB805YRD)

description:
https://www.encodeproject.org/experiments/ENCSR141ZKI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG1647-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR141ZKI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR987FJM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB805YRD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG1647

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS805KHG at ENCODE; https://www.encodeproject.org/ENCBS805KHG/


title: TF ChIP-seq from whole organism (ENCLB723EXG)

description:
https://www.encodeproject.org/experiments/ENCSR512EIF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing hsf-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR512EIF
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR919EWZ
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB723EXG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12254 (st12254[hsf-1::TY1::EGFP::3xFLAG] I) young adult (63 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans hsf-1

value: whole organism

value: not collected

value: young adult

value: 63 hour

value: ENCBS011YUA at ENCODE; https://www.encodeproject.org/ENCBS011YUA/


title: TF ChIP-seq from whole organism (ENCLB680LHR)

description:
https://www.encodeproject.org/experiments/ENCSR140RMO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ab-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR140RMO
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR925FBM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB680LHR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: ab

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

value: ENCBS934SMH at ENCODE; https://www.encodeproject.org/ENCBS934SMH/


title: Control ChIP-seq from whole organism (ENCLB275VKF)

description:
https://www.encodeproject.org/experiments/ENCSR566WAD/
***************
biological replicate number: 3
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR566WAD
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB275VKF
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-25

value: pooled male and female

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS181MMG at ENCODE; https://www.encodeproject.org/ENCBS181MMG/


title: Control ChIP-seq from whole organism (ENCLB430MUG)

description:
https://www.encodeproject.org/experiments/ENCSR820XTA/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ZK337.2-eGFP fusion proteins.
experiment encode accession: ENCSR820XTA
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB430MUG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12326 (st12326(ZK337.2::TY1::EGFP::3xFLAG] I) L4 larva (47 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans klu-1

value: not applicable

value: L4 larva

value: 47 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS241PLL at ENCODE; https://www.encodeproject.org/ENCBS241PLL/


title: Control ChIP-seq from whole organism (ENCLB525MLT)

description:
https://www.encodeproject.org/experiments/ENCSR566WAD/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR566WAD
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB525MLT
size range: 150-350

value: whole organism

value: CGC

value: ENCBS011MMW at ENCODE; https://www.encodeproject.org/ENCBS011MMW/


title: Control ChIP-seq from whole organism (ENCLB080SUU)

description:
https://www.encodeproject.org/experiments/ENCSR502XCL/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing bed-1-eGFP fusion proteins.
experiment encode accession: ENCSR502XCL
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB080SUU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12201 (st12201[bed-1::TY1::EGFP::3xFLAG] V) young adult (63 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans bed-1

value: whole organisms

value: not collected

value: young adult

value: 63 hour

value: ENCBS343SVC at ENCODE; https://www.encodeproject.org/ENCBS343SVC/


title: Control ChIP-seq from whole organism (ENCLB949CMI)

description:
https://www.encodeproject.org/experiments/ENCSR500UBZ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing F26F4.8-eGFP fusion proteins.
experiment encode accession: ENCSR500UBZ
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB949CMI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP776 (wgIs776(F26F4.8::TY1 EGFP 3xFLAG(p_wTRG5_insertion_c_0092_3C04);unc-119(+));unc-119 (tm4063)) L4 larva (48 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans F26F4.8

value: 48 hour

value: ENCBS576NFG at ENCODE; https://www.encodeproject.org/ENCBS576NFG/


title: Control ChIP-seq from whole organism (ENCLB748PUP)

description:
https://www.encodeproject.org/experiments/ENCSR565HLF/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR565HLF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB748PUP
size range: 150-350

source_name: Caenorhabditis elegans strain OP18 (unc-119(ed3) III; wgIs18) mixed sex L2 larva insertion targeting C. elegans lin-39

value: not applicable

value: pooled male and female

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: ENCBS820NCM at ENCODE; https://www.encodeproject.org/ENCBS820NCM/


title: TF ChIP-seq from whole organism (ENCLB582DMT)

description:
https://www.encodeproject.org/experiments/ENCSR140RMO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ab-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR140RMO
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR925FBM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB582DMT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: ab

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS624IGX at ENCODE; https://www.encodeproject.org/ENCBS624IGX/


title: TF ChIP-seq from whole organism (ENCLB285WQW)

description:
https://www.encodeproject.org/experiments/ENCSR139RDU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG12942-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR139RDU
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR839RAE
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB285WQW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG12942-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG12942

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12942

value: ENCBS891QZW at ENCODE; https://www.encodeproject.org/ENCBS891QZW/


title: Control ChIP-seq from whole organism (ENCLB711XKU)

description:
https://www.encodeproject.org/experiments/ENCSR498NSZ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing snpc-1.2-eGFP fusion proteins.
experiment encode accession: ENCSR498NSZ
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB711XKU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12251 (st12251[snpc-1.2::TY1::EGFP::3xFLAG] III) L4 larva (48 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans snpc-1.2

value: not applicable

value: not collected

value: L4 larva

value: 48 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS872DTQ at ENCODE; https://www.encodeproject.org/ENCBS872DTQ/


title: Control ChIP-seq from whole organism (ENCLB227EBL)

description:
https://www.encodeproject.org/experiments/ENCSR986VZB/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ets-5-eGFP fusion proteins.
experiment encode accession: ENCSR986VZB
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB227EBL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP809 (wgIs809(ets-5::TY1 EGFP 3xFLAG(p_wTRG5_insertion_c_0090_2C01);unc-119(+));unc-119 (tm4063)) L1 larva (6 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ets-5

value: L1 larva

value: 6 hour

value: ENCBS511ELP at ENCODE; https://www.encodeproject.org/ENCBS511ELP/


title: Control ChIP-seq from whole organism (ENCLB537IGC)

description:
https://www.encodeproject.org/experiments/ENCSR563WCK/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in mixed stage (embryonic) worms.
experiment encode accession: ENCSR563WCK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB537IGC
size range: 150-350

source_name: Caenorhabditis elegans strain OP109 (unc-119(ed3) III; wgIs109) mixed sex mixed stage (embryo) insertion targeting C. elegans blmp-1

value: pooled male and female

value: mixed stage (embryonic)

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS408YCA at ENCODE; https://www.encodeproject.org/ENCBS408YCA/


title: TF ChIP-seq from whole organism (ENCLB021LXS)

description:
https://www.encodeproject.org/experiments/ENCSR521VGM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-40-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR521VGM
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR754LZH
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB021LXS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

value: young adult

value: 76 hour

value: ENCBS807PGK at ENCODE; https://www.encodeproject.org/ENCBS807PGK/


title: Control ChIP-seq from whole organism (ENCLB310KTZ)

description:
https://www.encodeproject.org/experiments/ENCSR565HLF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR565HLF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB310KTZ
size range: 150-350

value: L2 larva

value: ENCBS161JKQ at ENCODE; https://www.encodeproject.org/ENCBS161JKQ/


title: TF ChIP-seq from whole organism (ENCLB359XLM)

description:
https://www.encodeproject.org/experiments/ENCSR490IPC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing nhr-42-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR490IPC
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR617WSR
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB359XLM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP351 (wgIs351(nhr-42::TY1 EGFP 3xFLAG(P000009_D03);unc-119(+));unc-119(tm4063)) L4 larva (50 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans nhr-42

value: not collected

value: L4 larva

value: 50 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS343JCY at ENCODE; https://www.encodeproject.org/ENCBS343JCY/


title: TF ChIP-seq from whole organism (ENCLB259YIP)

description:
https://www.encodeproject.org/experiments/ENCSR490IPC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing nhr-42-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR490IPC
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR617WSR
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB259YIP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: ENCBS783QKL at ENCODE; https://www.encodeproject.org/ENCBS783QKL/


title: Control ChIP-seq from whole organism (ENCLB721ZQW)

description:
https://www.encodeproject.org/experiments/ENCSR563WCK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in mixed stage (embryonic) worms.
experiment encode accession: ENCSR563WCK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB721ZQW
size range: 150-350

value: pooled male and female

value: mixed stage (embryonic)

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS715IUI at ENCODE; https://www.encodeproject.org/ENCBS715IUI/


title: TF ChIP-seq from whole organism (ENCLB491PGC)

description:
https://www.encodeproject.org/experiments/ENCSR139RDU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG12942-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR139RDU
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR839RAE
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB491PGC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12942

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS880RTY at ENCODE; https://www.encodeproject.org/ENCBS880RTY/


title: TF ChIP-seq from whole organism (ENCLB823PZS)

description:
https://www.encodeproject.org/experiments/ENCSR985WUI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ctbp-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR985WUI
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR954JXW
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB823PZS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12203 (st12203[ctbp-1::TY1::EGFP::3xFLAG] X) L4 larva (48 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans ctbp-1

value: not collected

value: L4 larva

value: 48 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS584SWE at ENCODE; https://www.encodeproject.org/ENCBS584SWE/


title: Control ChIP-seq from whole organism (ENCLB694VOD)

description:
https://www.encodeproject.org/experiments/ENCSR563NMV/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR563NMV
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB694VOD
size range: 150-350

source_name: Caenorhabditis elegans strain OP367 (unc-119(tm4063) III; wgIs367) mixed sex L1 larva insertion targeting C. elegans lsy-2

value: pooled male and female

value: L1 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS773RPI at ENCODE; https://www.encodeproject.org/ENCBS773RPI/


title: Control ChIP-seq from whole organism (ENCLB703IVQ)

description:
https://www.encodeproject.org/experiments/ENCSR310QLH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Ets65A-eGFP fusion proteins.
experiment encode accession: ENCSR310QLH
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB703IVQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Drosophila melanogaster strain ets3-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Ets65A

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Ets65A

value: embryonic

value: 0-24 hour

value: ENCBS116RDU at ENCODE; https://www.encodeproject.org/ENCBS116RDU/


title: Control ChIP-seq from whole organism (ENCLB232WOE)

description:
https://www.encodeproject.org/experiments/ENCSR997BAA/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing nhr-41-eGFP fusion proteins.
experiment encode accession: ENCSR997BAA
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB232WOE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12221 (st12221[nhr-41::TY1::EGFP::3xFLAG] IV) L4 larva (48.5 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans nhr-41

value: not collected

value: L4 larva

value: 48.5 hour

value: Valerie Reinke, Yale

value: ENCBS644HIA at ENCODE; https://www.encodeproject.org/ENCBS644HIA/


title: TF ChIP-seq from whole organism (ENCLB286TNP)

description:
https://www.encodeproject.org/experiments/ENCSR812MWL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing flt-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR812MWL
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR661MKW
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB286TNP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP797 (wgIs797(flt-1::TY1 EGFP 3xFLAG(Fosmid: flt-1);unc-119(+));unc-119 (tm4063)) early embryo (1 hour) using egg bleaching insertion targeting C. elegans baz-2

value: early embryonic

value: 1 hour

value: Valerie Reinke

value: egg bleaching

value: ENCBS915BII at ENCODE; https://www.encodeproject.org/ENCBS915BII/


title: TF ChIP-seq from whole organism (ENCLB180IGO)

description:
https://www.encodeproject.org/experiments/ENCSR512EIF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing hsf-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR512EIF
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR919EWZ
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB180IGO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: young adult

value: 63 hour

value: L1 larva starved after bleaching

value: ENCBS519BXD at ENCODE; https://www.encodeproject.org/ENCBS519BXD/


title: TF ChIP-seq from whole organism (ENCLB736KQV)

description:
https://www.encodeproject.org/experiments/ENCSR985WUI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ctbp-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR985WUI
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR954JXW
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB736KQV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: not applicable

value: 48 hour

value: ENCBS472UAP at ENCODE; https://www.encodeproject.org/ENCBS472UAP/


title: Control ChIP-seq from whole organism (ENCLB341JQK)

description:
https://www.encodeproject.org/experiments/ENCSR821YZO/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing arid-1-eGFP fusion proteins.
experiment encode accession: ENCSR821YZO
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB341JQK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12194 (st12194[arid-1::TY1::EGFP::3xFLAG] V) L4 larva (47 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans arid-1

value: not collected

value: L4 larva

value: 47 hour

value: ENCBS015XIK at ENCODE; https://www.encodeproject.org/ENCBS015XIK/


title: TF ChIP-seq from whole organism (ENCLB602ZVR)

description:
https://www.encodeproject.org/experiments/ENCSR812MWL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing flt-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR812MWL
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR661MKW
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB602ZVR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: early embryonic

value: 1 hour

value: Valerie Reinke, Yale

value: ENCBS952XNH at ENCODE; https://www.encodeproject.org/ENCBS952XNH/


title: Control ChIP-seq from whole organism (ENCLB351IRS)

description:
https://www.encodeproject.org/experiments/ENCSR985THO/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing php-3-eGFP fusion proteins.
experiment encode accession: ENCSR985THO
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB351IRS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12213 (st12213[php-3::TY1::EGFP::3xFLAG] III) L4 larva (48 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans php-3

value: whole organism

value: Valerie Reinke

value: ENCBS380UFG at ENCODE; https://www.encodeproject.org/ENCBS380UFG/


title: Control ChIP-seq from whole organism (ENCLB529FVR)

description:
https://www.encodeproject.org/experiments/ENCSR981DZS/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing klf-2-eGFP fusion proteins.
experiment encode accession: ENCSR981DZS
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB529FVR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12310 (st12310(TY1::EGFP::3xFLAG::klf-2] II) midembryo (1.5 hours) using egg bleaching whole organism genetically modified (insertion) using CRISPR targeting C. elegans klf-2

value: midembryonic

value: 1.5 hour

value: egg bleaching

value: ENCBS345JMC at ENCODE; https://www.encodeproject.org/ENCBS345JMC/


title: TF ChIP-seq from whole organism (ENCLB167DHM)

description:
https://www.encodeproject.org/experiments/ENCSR216AQL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing vfl-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR216AQL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR004EEK
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB167DHM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: vfl

value: whole organisms

value: not applicable

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

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS783HDO at ENCODE; https://www.encodeproject.org/ENCBS783HDO/


title: TF ChIP-seq from whole organism (ENCLB595HAN)

description:
https://www.encodeproject.org/experiments/ENCSR216AQL/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing vfl-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR216AQL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR004EEK
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB595HAN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: ENCBS367ITO at ENCODE; https://www.encodeproject.org/ENCBS367ITO/


title: TF ChIP-seq from whole organism (ENCLB086UHS)

description:
https://www.encodeproject.org/experiments/ENCSR139RDU/
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biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG12942-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR139RDU
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR839RAE
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB086UHS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12942

value: ENCBS161EDJ at ENCODE; https://www.encodeproject.org/ENCBS161EDJ/