title: TF ChIP-seq from whole organism (ENCLB867KOT)

description:
https://www.encodeproject.org/experiments/ENCSR679VHT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-skn-1 in L3 larva worms.
experiment encode accession: ENCSR679VHT
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR815AQR
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB867KOT
size range: 150-350

source_name: Caenorhabditis elegans strain OP342 (unc-119(ed3) III; wgIs342) mixed sex L3 larva insertion targeting C. elegans skn-1

value: whole organism

value: whole organisms

value: not applicable

value: pooled male and female

value: L3 larva

value: ENCBS960VCQ at ENCODE; https://www.encodeproject.org/ENCBS960VCQ/


title: Control ChIP-seq from whole organism (ENCLB060PIJ)

status: Public on Feb 27 2024

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR607FMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing madf-5-eGFP fusion proteins.
experiment encode accession: ENCSR607FMZ
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB060PIJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

library_source: genomic

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

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP436 (wgIs436(C01G12.1::TY1 EGFP 3xFLAG(92D06);unc-119(+);unc-119(tm4063)) L4 larva (50 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans madf-5

tag: biosample encode accession

tag: collection date

tag: geographic location

tag: encode accession

tag: Sex

value: not collected

tag: dev stage

value: L4 larva

tag: age

value: 50 hour

tag: lab

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: link

value: ENCBS658ZCL at ENCODE; https://www.encodeproject.org/ENCBS658ZCL/


title: TF ChIP-seq from whole organism (ENCLB141MHJ)

description:
https://www.encodeproject.org/experiments/ENCSR679VHT/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-skn-1 in L3 larva worms.
experiment encode accession: ENCSR679VHT
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR815AQR
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB141MHJ
size range: 150-350

extract_protocol: not provided

tag: antibody

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS703BQO at ENCODE; https://www.encodeproject.org/ENCBS703BQO/


title: Control ChIP-seq from K562 (ENCLB885FXQ)

description:
https://www.encodeproject.org/experiments/ENCSR099EPT/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ELF4 fusion protein.
experiment encode accession: ENCSR099EPT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB885FXQ
size range: 450-650

organism: Homo sapiens

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ELF4

tag: line

value: cell line

tag: note

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ELF4.

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Kevin White

value: ENCBS802FVB at ENCODE; https://www.encodeproject.org/ENCBS802FVB/


title: Control ChIP-seq from K562 (ENCLB269JOZ)

description:
https://www.encodeproject.org/experiments/ENCSR093AOE/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZBTB26 fusion protein.
experiment encode accession: ENCSR093AOE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB269JOZ
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB26

value: not applicable

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB26.

value: ENCBS695DQK at ENCODE; https://www.encodeproject.org/ENCBS695DQK/


title: TF ChIP-seq from whole organism (ENCLB353GWM)

description:
https://www.encodeproject.org/experiments/ENCSR405WRC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing lin-38-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR405WRC
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR727GDS
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB353GWM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12236 (st12236[lin-38::TY1::EGFP::3xFLAG] II) L4 larva (48 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans lin-38

value: whole organism

value: whole organisms

value: not collected

value: L4 larva

value: 48 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS986XDD at ENCODE; https://www.encodeproject.org/ENCBS986XDD/


title: TF ChIP-seq from whole organism (ENCLB257SYW)

description:
https://www.encodeproject.org/experiments/ENCSR537DUM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-sem-4 in L2 larva worms.
experiment encode accession: ENCSR537DUM
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR403WXH
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB257SYW
size range: 150-350

source_name: Caenorhabditis elegans strain OP57 (unc-119(ed3) III; wgIs57) mixed sex L2 larva insertion targeting C. elegans sem-4

value: pooled male and female

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS157CSP at ENCODE; https://www.encodeproject.org/ENCBS157CSP/


title: Control ChIP-seq from K562 (ENCLB861TXS)

description:
https://www.encodeproject.org/experiments/ENCSR730EDP/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZNF75A fusion protein.
experiment encode accession: ENCSR730EDP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB861TXS
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF75A

value: cell line

value: not applicable

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF75A.

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Kevin White

value: ENCBS676HFO at ENCODE; https://www.encodeproject.org/ENCBS676HFO/


title: TF ChIP-seq from whole organism (ENCLB421YJA)

description:
https://www.encodeproject.org/experiments/ENCSR902UTK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing hmg-1.1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR902UTK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR475NQN
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB421YJA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12311 (st12311(TY1::EGFP::3xFLAG::hmg-1.1] II) L4 larva (48 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans hmg-1.1

value: whole organism

value: whole organisms

value: not collected

value: L4 larva

value: 48 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS233ARE at ENCODE; https://www.encodeproject.org/ENCBS233ARE/


title: TF ChIP-seq from whole organism (ENCLB550FID)

description:
https://www.encodeproject.org/experiments/ENCSR405OOH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing egrh-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR405OOH
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR935YYP
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB550FID
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12196 (st12196[egrh-3::TY1::EGFP::3xFLAG] IV) young adult (65 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans egrh-3

value: not applicable

value: young adult

value: 65 hour

value: ENCBS297ONY at ENCODE; https://www.encodeproject.org/ENCBS297ONY/


title: TF ChIP-seq from whole organism (ENCLB203OVH)

description:
https://www.encodeproject.org/experiments/ENCSR537DUM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-sem-4 in L2 larva worms.
experiment encode accession: ENCSR537DUM
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR403WXH
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB203OVH
size range: 150-350

value: pooled male and female

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS520QME at ENCODE; https://www.encodeproject.org/ENCBS520QME/


title: TF ChIP-seq from whole organism (ENCLB484QJB)

description:
https://www.encodeproject.org/experiments/ENCSR902UTK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing hmg-1.1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR902UTK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR475NQN
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB484QJB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not collected

value: ENCBS563DZY at ENCODE; https://www.encodeproject.org/ENCBS563DZY/


title: Control ChIP-seq from whole organism (ENCLB191ZOZ)

description:
https://www.encodeproject.org/experiments/ENCSR902WVK/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing Y48G9A.11-eGFP fusion proteins.
experiment encode accession: ENCSR902WVK
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB191ZOZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12291 (st12291[Y48G9A.11::TY1::EGFP::3xFLAG] III) L4 larva (47.5 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans Y48G9A.11

value: L4 larva

value: 47.5 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS693JGW at ENCODE; https://www.encodeproject.org/ENCBS693JGW/


title: TF ChIP-seq from whole organism (ENCLB197WFZ)

description:
https://www.encodeproject.org/experiments/ENCSR678ZPU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against ATTF-4 in L4 larva worms.
experiment encode accession: ENCSR678ZPU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR948MUA
encode release date: 2017-11-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB197WFZ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP219 (unc-119(ed3) III; wgIs219) mixed sex L4 larva insertion targeting C. elegans attf-4

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to C05D10.1

value: Michael Snyder

value: ENCBS740FEM at ENCODE; https://www.encodeproject.org/ENCBS740FEM/


title: TF ChIP-seq from whole organism (ENCLB070BBF)

description:
https://www.encodeproject.org/experiments/ENCSR678ZPU/
***************
biological replicate number: 3
technical replicate number: 3
description: ChIP-seq against ATTF-4 in L4 larva worms.
experiment encode accession: ENCSR678ZPU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR948MUA
encode release date: 2017-11-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB070BBF
fragmentation methods: sonication (generic microtip)

value: pooled male and female

value: unknown

value: ENCBS593IKO at ENCODE; https://www.encodeproject.org/ENCBS593IKO/


title: TF ChIP-seq from whole organism (ENCLB275QJO)

description:
https://www.encodeproject.org/experiments/ENCSR404VKP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing php-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR404VKP
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR985THO
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB275QJO
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: 48 hour

value: L1 larva starved after bleaching

value: ENCBS593PSQ at ENCODE; https://www.encodeproject.org/ENCBS593PSQ/


title: TF ChIP-seq from whole organism (ENCLB171JJE)

description:
https://www.encodeproject.org/experiments/ENCSR404VKP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing php-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR404VKP
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR985THO
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB171JJE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not collected

value: ENCBS428KAP at ENCODE; https://www.encodeproject.org/ENCBS428KAP/


title: TF ChIP-seq from whole organism (ENCLB633TLD)

description:
https://www.encodeproject.org/experiments/ENCSR680ZDH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing PAG-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR680ZDH
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR160SNG
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB633TLD
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP154 (unc-119(ed3) III; wgIs154) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans pag-3

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

value: hermaphrodite

value: L1 larva

value: Valerie Reinke, Yale

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS546NCP at ENCODE; https://www.encodeproject.org/ENCBS546NCP/


title: Control ChIP-seq from K562 (ENCLB737XBL)

description:
https://www.encodeproject.org/experiments/ENCSR028MGN/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-HBP1 fusion protein.
experiment encode accession: ENCSR028MGN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB737XBL
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HBP1

value: cell line

tag: biosample encode accession

value: not applicable

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to HBP1.

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS446VDT at ENCODE; https://www.encodeproject.org/ENCBS446VDT/


title: TF ChIP-seq from whole organism (ENCLB856UZA)

description:
https://www.encodeproject.org/experiments/ENCSR405OOH/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing egrh-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR405OOH
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR935YYP
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB856UZA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

tag: collection date

value: not collected

value: young adult

value: 65 hour

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS514WTD at ENCODE; https://www.encodeproject.org/ENCBS514WTD/


title: TF ChIP-seq from whole organism (ENCLB487XMS)

description:
https://www.encodeproject.org/experiments/ENCSR678ZPU/
***************
biological replicate number: 2
technical replicate number: 2
description: ChIP-seq against ATTF-4 in L4 larva worms.
experiment encode accession: ENCSR678ZPU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR948MUA
encode release date: 2017-11-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB487XMS
fragmentation methods: sonication (generic microtip)

value: not applicable

tag: geographic location

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to C05D10.1

value: pooled male and female

value: L4 larva

value: unknown

value: Michael Snyder

value: ENCBS740FEM at ENCODE; https://www.encodeproject.org/ENCBS740FEM/


title: TF ChIP-seq from whole organism (ENCLB274YPO)

description:
https://www.encodeproject.org/experiments/ENCSR405WRC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing lin-38-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR405WRC
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR727GDS
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB274YPO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: encode accession

value: 48 hour

value: Valerie Reinke, Yale

value: ENCBS782TQM at ENCODE; https://www.encodeproject.org/ENCBS782TQM/


title: TF ChIP-seq from whole organism (ENCLB881QDH)

description:
https://www.encodeproject.org/experiments/ENCSR401IFS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing Y75B8A.6-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR401IFS
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR354FZU
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB881QDH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12275 (st12275[Y75B8A.6 ::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 Y75B8A.6

value: whole organism

value: whole organisms

tag: Sex

value: ENCBS509ITC at ENCODE; https://www.encodeproject.org/ENCBS509ITC/


title: LIV23_334

city: Iowa City

first: Aloysius

middle: John

last: Klingelhutz

state: IA

address: 3-604 BSB, 51 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

description:
Male_LIV_counts.csv
LIV52_23_334

library_source: transcriptomic

data_processing:
cDNA library was constructed using the ribosomal depletion methods, and reads were sequenced in 120 bp paired-end sequences per the Illumina 1.9 encoding Novogene protocols
Sample data integrity was examined using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, version 0.11.9) for quality control of fastq files.
Sequence reads were then mapped to the UCSC rn6 rat reference genome using HISAT2
Gene counts were generated from the BAM files using SummarizedExperiments (version 1.28.0) with the UCSC Rattus Norvegicus (rn6) reference genome
Assembly: Rn6
Supplementary files format and content: CSV file includes raw counts for each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver

growth_protocol: 28-day-old male and female Sprague-Dawley rats (Charles River, Wilmington, MA) were allowed to acclimate for 8 days, followed by a 30 min. and a 2 hour training day in the nose-only apparatus. All rats were provided food (sterile Teklad 5% stock diet, Harlan, Madison, WI) and water ad libitum. 24 rats were weighed and assigned to the sham or PCB 52 exposure groups using a random number generator at 39 days of age for males 42 days of age for females to begin PCB 52 exposure.

extract_protocol:
Portions of the liver were rinsed with PBS and placed in a lysing matrix tube containing 1 mL of TRIzol. Sample solutions were then aliquoted to RNeasy spin columns, followed by the QIAGEN RNeasy Kits protocol to clean and isolate RNA from the tissue samples.
mRNA enrichment: poly (A) capture or rRNA removal

treatment_protocol: Animals were exposed for 4 hours daily for 28 days to PCB 52 using a nose-only inhalation system by passing dried, high-efficiency particulate air (HEPA)-filtered air through the PCB 52-coated glass beads at a flow rate of 12 L/min.

tag: tissue

value: Liver

value: Male

tag: strain

value: Sprague-Dawley

tag: treatment

value: PCB 52


title: TF ChIP-seq from whole organism (ENCLB567SER)

description:
https://www.encodeproject.org/experiments/ENCSR402FQJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-100-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR402FQJ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR730XBT
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB567SER
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12233 (st12233[ceh-100::TY1::EGFP::3xFLAG] II) young adult (64 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans ceh-100

value: not applicable

value: not collected

tag: dev stage

value: young adult

tag: age

value: 64 hour

tag: lab

tag: source

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS038VTF at ENCODE; https://www.encodeproject.org/ENCBS038VTF/


title: Control ChIP-seq from K562 (ENCLB815WTJ)

description:
https://www.encodeproject.org/experiments/ENCSR226CLB/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-THRB fusion protein.
experiment encode accession: ENCSR226CLB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-08-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB815WTJ
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens THRB

tag: line

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to THRB.

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

tag: link

value: ENCBS210TBN at ENCODE; https://www.encodeproject.org/ENCBS210TBN/


title: LIV21_087

description:
Male_LIV_counts.csv
LIV52_21_087

value: Liver

value: Male

value: Sprague-Dawley

value: PCB 52


title: TF ChIP-seq from whole organism (ENCLB212XRQ)

description:
https://www.encodeproject.org/experiments/ENCSR402FQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-100-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR402FQJ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR730XBT
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB212XRQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: whole organisms

value: not applicable

value: not collected

value: young adult

value: 64 hour

value: Valerie Reinke, Yale

tag: worm synchronization stage

value: ENCBS066VYX at ENCODE; https://www.encodeproject.org/ENCBS066VYX/


title: TF ChIP-seq from whole organism (ENCLB034PZX)

description:
https://www.encodeproject.org/experiments/ENCSR897ELP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing nhr-120-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR897ELP
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR603CHQ
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB034PZX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP415 (wgIs415(nhr-120::TY1 EGFP 3xFLAG(91C03);unc-119(+);unc-119(tm4063)) young adult (64 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans nhr-120

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS948WWW at ENCODE; https://www.encodeproject.org/ENCBS948WWW/


title: TF ChIP-seq from whole organism (ENCLB031XQR)

description:
https://www.encodeproject.org/experiments/ENCSR678ZPU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against ATTF-4 in L4 larva worms.
experiment encode accession: ENCSR678ZPU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR948MUA
encode release date: 2017-11-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB031XQR
fragmentation methods: sonication (generic microtip)

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to C05D10.1

value: pooled male and female

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS587PZV at ENCODE; https://www.encodeproject.org/ENCBS587PZV/


title: Control ChIP-seq from whole organism (ENCLB386CJW)

description:
https://www.encodeproject.org/experiments/ENCSR401EGA/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing lin-26-eGFP fusion proteins.
experiment encode accession: ENCSR401EGA
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB386CJW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12178 (st12178[lin-26::GFP+ loxP unc-119(+) + loxP]; unc-119(tm4063) III) young adult (64 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elega...

value: whole organism

value: whole organisms

tag: biosample encode accession

value: ENCBS584RPP at ENCODE; https://www.encodeproject.org/ENCBS584RPP/


title: Control ChIP-seq from GM12878 (ENCLB671NRC)

description:
https://www.encodeproject.org/experiments/ENCSR161EAA/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878 immortalized cell line stably expressing C-terminal eGFP-ZBTB11 fusion protein.
experiment encode accession: ENCSR161EAA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB671NRC
size range: 450-650

source_name: Homo sapiens GM12878 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB11

value: cell line

tag: collection date

value: not applicable

value: GM12878 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB11.

value: female

tag: health state

value: adult

value: Kevin White

value: ENCBS026GLW at ENCODE; https://www.encodeproject.org/ENCBS026GLW/


title: TF ChIP-seq from whole organism (ENCLB115RDE)

description:
https://www.encodeproject.org/experiments/ENCSR678ZPU/
***************
biological replicate number: 3
technical replicate number: 2
description: ChIP-seq against ATTF-4 in L4 larva worms.
experiment encode accession: ENCSR678ZPU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR948MUA
encode release date: 2017-11-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB115RDE
fragmentation methods: sonication (generic microtip)

tag: geographic location

tag: encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to C05D10.1

value: ENCBS593IKO at ENCODE; https://www.encodeproject.org/ENCBS593IKO/


title: LIV19_067

description:
Male_LIV_counts.csv
LIV52_19_067

tag: tissue

value: Liver

tag: Sex

value: Male

value: Sprague-Dawley

value: PCB 52


title: TF ChIP-seq from whole organism (ENCLB921WRR)

description:
https://www.encodeproject.org/experiments/ENCSR895UPM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing let-526-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR895UPM
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR635PJA
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB921WRR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12306 (st12306(let-526::TY1::EGFP::3xFLAG] I) young adult (60 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans let-526

value: not collected

value: young adult

value: 60 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS269PMR at ENCODE; https://www.encodeproject.org/ENCBS269PMR/


title: TF ChIP-seq from whole organism (ENCLB533KRM)

description:
https://www.encodeproject.org/experiments/ENCSR536HCJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-23 in L2 larva worms.
experiment encode accession: ENCSR536HCJ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR067SKF
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB533KRM
size range: 150-350

source_name: Caenorhabditis elegans strain OP43 (unc-119(ed3) III; wgIs43) mixed sex L2 larva insertion targeting C. elegans nhr-23

value: whole organism

value: whole organisms

value: not applicable

value: pooled male and female

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS544YQM at ENCODE; https://www.encodeproject.org/ENCBS544YQM/


title: TF ChIP-seq from whole organism (ENCLB413LLW)

description:
https://www.encodeproject.org/experiments/ENCSR895UPM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing let-526-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR895UPM
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR635PJA
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB413LLW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: ENCBS708BZQ at ENCODE; https://www.encodeproject.org/ENCBS708BZQ/


title: LIV17_768

description:
Male_LIV_counts.csv
LIV52_17_768

value: Liver

value: Male

tag: strain

value: Sprague-Dawley

tag: treatment

value: PCB 52


title: Control ChIP-seq from whole organism (ENCLB257UMM)

description:
https://www.encodeproject.org/experiments/ENCSR893THZ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing F33H1.4-eGFP fusion proteins.
experiment encode accession: ENCSR893THZ
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB257UMM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12303 (st12303[F33H1.4::TY1::EGFP::3xFLAG] II) young adult (62.5 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans F33H1.4

value: not collected

tag: dev stage

value: young adult

tag: age

value: 62.5 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS192NTL at ENCODE; https://www.encodeproject.org/ENCBS192NTL/


title: TF ChIP-seq from whole organism (ENCLB559UQE)

description:
https://www.encodeproject.org/experiments/ENCSR536HCJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-23 in L2 larva worms.
experiment encode accession: ENCSR536HCJ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR067SKF
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB559UQE
size range: 150-350

value: whole organism

value: whole organisms

value: not applicable

value: pooled male and female

tag: lab

tag: source

value: ENCBS421BJN at ENCODE; https://www.encodeproject.org/ENCBS421BJN/


title: LIV15_052

description:
Male_LIV_counts.csv
LIV52_15_052


title: Control ChIP-seq from whole organism (ENCLB874FGQ)

description:
https://www.encodeproject.org/experiments/ENCSR893THZ/
***************
biological replicate number: 2
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing F33H1.4-eGFP fusion proteins.
experiment encode accession: ENCSR893THZ
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB874FGQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: L1 larva starved after bleaching

tag: link

value: ENCBS280WDZ at ENCODE; https://www.encodeproject.org/ENCBS280WDZ/


title: Control ChIP-seq from whole organism (ENCLB171NKH)

description:
https://www.encodeproject.org/experiments/ENCSR844JGM/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in young adult worms.
experiment encode accession: ENCSR844JGM
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB171NKH
size range: 150-350

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

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS888TAD at ENCODE; https://www.encodeproject.org/ENCBS888TAD/


title: Control ChIP-seq from whole organism (ENCLB020BZW)

description:
https://www.encodeproject.org/experiments/ENCSR892OFS/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing Y105C5A.15-eGFP fusion proteins.
experiment encode accession: ENCSR892OFS
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB020BZW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP773 (wgIs773(Y105C5A.15::TY1 EGFP 3xFLAG(P000011_H09_13N06);unc-119(+));unc-119 (tm4063)) L4 larva (48 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans Y105C5A.15

value: not collected

value: L4 larva

value: 48 hour

value: ENCBS910PAB at ENCODE; https://www.encodeproject.org/ENCBS910PAB/


title: LIV13_790

description:
Male_LIV_counts.csv
LIV52_13_790

value: Liver

value: Male

value: Sprague-Dawley

value: PCB 52


title: Control ChIP-seq from whole organism (ENCLB162VPQ)

description:
https://www.encodeproject.org/experiments/ENCSR844JGM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in young adult worms.
experiment encode accession: ENCSR844JGM
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB162VPQ
size range: 150-350

value: whole organism

value: whole organisms

value: not applicable

value: young adult

value: ENCBS267HHO at ENCODE; https://www.encodeproject.org/ENCBS267HHO/


title: Control ChIP-seq from whole organism (ENCLB463IQH)

description:
https://www.encodeproject.org/experiments/ENCSR399IYX/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing dmd-8-eGFP fusion proteins.
experiment encode accession: ENCSR399IYX
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB463IQH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP775 (wgIs775(dmd-8::TY1 EGFP 3xFLAG(p_wTRG5_insertion_c_0094G03);unc-119(+));unc-119 (tm4063)) L4 larva (48.5 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans dmd-8

value: 48.5 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS306ERO at ENCODE; https://www.encodeproject.org/ENCBS306ERO/


title: LIV11_288

description:
Male_LIV_counts.csv
LIV52_11_288

value: Sham


title: TF ChIP-seq from whole organism (ENCLB594LRT)

description:
https://www.encodeproject.org/experiments/ENCSR396REY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing klf-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR396REY
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR981DZS
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB594LRT
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

tag: antibody

value: not collected

value: midembryonic

value: 1.5 hour

value: egg bleaching

value: ENCBS996BGS at ENCODE; https://www.encodeproject.org/ENCBS996BGS/


title: LIV9_341

description:
Male_LIV_counts.csv
LIV52_9_341

value: Liver

value: Male

value: Sprague-Dawley


title: TF ChIP-seq from whole organism (ENCLB740YLH)

description:
https://www.encodeproject.org/experiments/ENCSR396ONU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing C17E4.6-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR396ONU
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR268WXK
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB740YLH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12293 (st12293[C17E4.6::TY1::EGFP::3xFLAG] I) young adult (62 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans C17E4.6

value: whole organism

value: whole organisms

value: not applicable

value: 62 hour

tag: worm synchronization stage

value: ENCBS635JEY at ENCODE; https://www.encodeproject.org/ENCBS635JEY/


title: TF ChIP-seq from whole organism (ENCLB010KUD)

description:
https://www.encodeproject.org/experiments/ENCSR401IFS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing Y75B8A.6-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR401IFS
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR354FZU
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB010KUD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: L4 larva

value: 48 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS587YFG at ENCODE; https://www.encodeproject.org/ENCBS587YFG/


title: TF ChIP-seq from whole organism (ENCLB343WIR)

description:
https://www.encodeproject.org/experiments/ENCSR396REY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing klf-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR396REY
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR981DZS
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB343WIR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not collected

value: midembryonic

value: ENCBS258NDI at ENCODE; https://www.encodeproject.org/ENCBS258NDI/


title: Control ChIP-seq from whole organism (ENCLB299FQF)

description:
https://www.encodeproject.org/experiments/ENCSR588YLV/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing saeg-2-eGFP fusion proteins.
experiment encode accession: ENCSR588YLV
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB299FQF
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: L1 larva starved after bleaching

value: ENCBS473NMZ at ENCODE; https://www.encodeproject.org/ENCBS473NMZ/


title: TF ChIP-seq from whole organism (ENCLB280QXW)

description:
https://www.encodeproject.org/experiments/ENCSR897ELP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing nhr-120-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR897ELP
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR603CHQ
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB280QXW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: young adult

value: 64 hour

value: ENCBS832HPB at ENCODE; https://www.encodeproject.org/ENCBS832HPB/


title: TF ChIP-seq from whole organism (ENCLB342BYF)

description:
https://www.encodeproject.org/experiments/ENCSR372GNV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against EGL-27 in L1 worms.
experiment encode accession: ENCSR372GNV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR090ETP
encode release date: 2018-04-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB342BYF
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP177 (unc-119(ed3) III; wgIs177) mixed sex L1 larva insertion targeting C. elegans egl-27

value: whole organism

value: whole organisms

tag: note

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

value: pooled male and female

value: L1 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS893WGH at ENCODE; https://www.encodeproject.org/ENCBS893WGH/


title: TF ChIP-seq from whole organism (ENCLB408JKS)

description:
https://www.encodeproject.org/experiments/ENCSR372GNV/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq against EGL-27 in L1 worms.
experiment encode accession: ENCSR372GNV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR090ETP
encode release date: 2018-04-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB408JKS
fragmentation methods: sonication (generic microtip)

tag: biosample encode accession

value: not applicable

value: ENCBS733ELZ at ENCODE; https://www.encodeproject.org/ENCBS733ELZ/


title: TF ChIP-seq from whole organism (ENCLB742LXW)

description:
https://www.encodeproject.org/experiments/ENCSR396ONU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing C17E4.6-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR396ONU
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR268WXK
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB742LXW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: collection date

value: not collected

value: 62 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS226SXY at ENCODE; https://www.encodeproject.org/ENCBS226SXY/


title: Control ChIP-seq from whole organism (ENCLB641PHL)

description:
https://www.encodeproject.org/experiments/ENCSR395YHD/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing D1046.2-eGFP fusion proteins.
experiment encode accession: ENCSR395YHD
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB641PHL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP397 (wgIs397(D1046.2::TY1 EGFP 3xFLAG(91F09);unc-119(+);unc-119(tm4063)) L4 larva (50 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans D1046.2

value: L4 larva

value: 50 hour

value: L1 larva starved after bleaching

value: ENCBS019TBL at ENCODE; https://www.encodeproject.org/ENCBS019TBL/


title: LIV7_347

description:
Male_LIV_counts.csv
LIV52_7_347

source_name: Liver

value: Liver

value: Male

value: Sprague-Dawley

value: Sham


title: TF ChIP-seq from whole organism (ENCLB430TFS)

description:
https://www.encodeproject.org/experiments/ENCSR702JCF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing lin-26-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR702JCF
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR401EGA
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB430TFS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: young adult

value: 64 hour

value: ENCBS256LZM at ENCODE; https://www.encodeproject.org/ENCBS256LZM/


title: TF ChIP-seq from whole organism (ENCLB040HZW)

description:
https://www.encodeproject.org/experiments/ENCSR702JCF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing lin-26-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR702JCF
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR401EGA
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB040HZW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

value: not collected

value: ENCBS081MET at ENCODE; https://www.encodeproject.org/ENCBS081MET/


title: Control ChIP-seq from whole organism (ENCLB041NXC)

description:
https://www.encodeproject.org/experiments/ENCSR596SSR/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing lin-29-eGFP fusion proteins.
experiment encode accession: ENCSR596SSR
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB041NXC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12227 (st12227[lin-29::TY1::EGFP::3xFLAG] II) L4 larva (49 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans lin-29

value: 49 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS658NLW at ENCODE; https://www.encodeproject.org/ENCBS658NLW/


title: LIV5_115

description:
Male_LIV_counts.csv
LIV52_5_115


title: TF ChIP-seq from whole organism (ENCLB546QUE)

description:
https://www.encodeproject.org/experiments/ENCSR372GNV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against EGL-27 in L1 worms.
experiment encode accession: ENCSR372GNV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR090ETP
encode release date: 2018-04-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB546QUE
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: L1 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS214GKU at ENCODE; https://www.encodeproject.org/ENCBS214GKU/


title: LIV3_818

description:
Male_LIV_counts.csv
LIV52_3_818

value: Liver

value: Male

value: Sprague-Dawley

value: Sham


title: TF ChIP-seq from whole organism (ENCLB690OEE)

description:
https://www.encodeproject.org/experiments/ENCSR374VRB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-12 in L3 larva worms.
experiment encode accession: ENCSR374VRB
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR255HJY
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB690OEE
size range: 150-350

source_name: Caenorhabditis elegans strain OP318 (unc-119(ed3) III; wgIs318) mixed sex L3 larva insertion targeting C. elegans nhr-12

value: whole organism

value: whole organisms

value: not applicable

value: L3 larva

value: CGC

value: ENCBS261MLJ at ENCODE; https://www.encodeproject.org/ENCBS261MLJ/


title: TF ChIP-seq from whole organism (ENCLB484ESE)

description:
https://www.encodeproject.org/experiments/ENCSR880OUI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing egl-18-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR880OUI
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR108PJB
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB484ESE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12252 (st12252[egl-18::TY1::EGFP::3xFLAG] IV) young adult (63 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans egl-18

value: not collected

value: young adult

value: 63 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS922JSM at ENCODE; https://www.encodeproject.org/ENCBS922JSM/


title: LIV1_022

description:
Male_LIV_counts.csv
LIV52_1_022

value: Liver


title: Control ChIP-seq from whole organism (ENCLB434LIS)

description:
https://www.encodeproject.org/experiments/ENCSR374KTM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR374KTM
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB434LIS
size range: 150-350

source_name: Caenorhabditis elegans strain OP373 (unc-119(tm4063) III; wgIs373) mixed sex L3 larva insertion targeting C. elegans nhr-67

value: pooled male and female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS104XNE at ENCODE; https://www.encodeproject.org/ENCBS104XNE/


title: TF ChIP-seq from whole organism (ENCLB124FQK)

description:
https://www.encodeproject.org/experiments/ENCSR374VRB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-12 in L3 larva worms.
experiment encode accession: ENCSR374VRB
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR255HJY
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB124FQK
size range: 150-350

value: whole organism

value: whole organisms

value: ENCBS430RON at ENCODE; https://www.encodeproject.org/ENCBS430RON/


title: TF ChIP-seq from whole organism (ENCLB041EJW)

description:
https://www.encodeproject.org/experiments/ENCSR584KIA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-58-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR584KIA
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR138QCE
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB041EJW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP808 (wgIs808(ceh-58::TY1 EGFP 3xFLAG(p_wTRG5_insertion_c_0091_2F06);unc-119(+));unc-119 (tm4063)) young adult (65 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ceh-58

value: not applicable

value: 65 hour

value: ENCBS173MVJ at ENCODE; https://www.encodeproject.org/ENCBS173MVJ/


title: LIV24_332

description:
Female_LIV_counts.csv
LIV52_24_333

value: Female

value: Sprague-Dawley

value: PCB 52


title: TF ChIP-seq from whole organism (ENCLB580TLR)

description:
https://www.encodeproject.org/experiments/ENCSR699MPC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing hmg-20-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR699MPC
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR556YDQ
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB580TLR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12240 (st12240[hmg-20::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 hmg-20

value: not collected

value: young adult

value: 64 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS464DJD at ENCODE; https://www.encodeproject.org/ENCBS464DJD/


title: Control ChIP-seq from whole organism (ENCLB690XBV)

description:
https://www.encodeproject.org/experiments/ENCSR374KTM/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR374KTM
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB690XBV
size range: 150-350

value: pooled male and female

value: L3 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS459SFV at ENCODE; https://www.encodeproject.org/ENCBS459SFV/


title: TF ChIP-seq from whole organism (ENCLB178NHU)

description:
https://www.encodeproject.org/experiments/ENCSR699MPC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing hmg-20-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR699MPC
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR556YDQ
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB178NHU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

value: L1 larva starved after bleaching

value: ENCBS539OYS at ENCODE; https://www.encodeproject.org/ENCBS539OYS/


title: LIV22_359

description:
Female_LIV_counts.csv
LIV52_22_359

value: Liver

value: Female

value: Sprague-Dawley

value: PCB 52


title: LIV20_591

description:
Female_LIV_counts.csv
LIV52_20_591


title: TF ChIP-seq from whole organism (ENCLB677TZO)

description:
https://www.encodeproject.org/experiments/ENCSR697DHN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing Y56A3A.18-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR697DHN
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR326VJX
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB677TZO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12265 (st12265[Y56A3A.18 ::TY1::EGFP::3xFLAG] III) young adult (63 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans Y56A3A.18

value: not collected

value: young adult

value: 63 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS436IHE at ENCODE; https://www.encodeproject.org/ENCBS436IHE/


title: TF ChIP-seq from whole organism (ENCLB797WTJ)

description:
https://www.encodeproject.org/experiments/ENCSR282AJX/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-zag-1 in L2 larva worms.
experiment encode accession: ENCSR282AJX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR143YHO
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB797WTJ
size range: 150-350

source_name: Caenorhabditis elegans strain OP83 (unc-119(ed3) III; wgIs83) mixed sex L2 larva insertion targeting C. elegans zag-1

value: pooled male and female

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS453TQN at ENCODE; https://www.encodeproject.org/ENCBS453TQN/


title: TF ChIP-seq from whole organism (ENCLB267PKC)

description:
https://www.encodeproject.org/experiments/ENCSR873YHI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing aptf-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR873YHI
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR836ZQN
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB267PKC
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: whole organisms

value: not applicable

value: 64 hour

value: L1 larva starved after bleaching

value: ENCBS557XKQ at ENCODE; https://www.encodeproject.org/ENCBS557XKQ/


title: LIV18_771

description:
Female_LIV_counts.csv
LIV52_18_771

value: Liver

value: Female

value: Sprague-Dawley

value: PCB 52


title: TF ChIP-seq from whole organism (ENCLB285MYS)

description:
https://www.encodeproject.org/experiments/ENCSR282AJX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-zag-1 in L2 larva worms.
experiment encode accession: ENCSR282AJX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR143YHO
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB285MYS
size range: 150-350

value: ENCBS177SWX at ENCODE; https://www.encodeproject.org/ENCBS177SWX/


title: TF ChIP-seq from whole organism (ENCLB951UHS)

description:
https://www.encodeproject.org/experiments/ENCSR576YEP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing C06A6.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR576YEP
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR182GCE
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB951UHS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP810 (wgIs810(C06A6.2::TY1 EGFP 3xFLAG(GlyStock16H04_GlyStock16H04);unc-119(+));unc-119 (tm4063)) young adult (67 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans C06A6.2

value: not collected

value: young adult

value: 67 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS583XXB at ENCODE; https://www.encodeproject.org/ENCBS583XXB/


title: Control ChIP-seq from whole organism (ENCLB177SXW)

description:
https://www.encodeproject.org/experiments/ENCSR280USI/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing T02C12.2-eGFP fusion proteins.
experiment encode accession: ENCSR280USI
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB177SXW
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL497 hermaphrodite young adult insertion targeting C. elegans snpc-3.4

value: whole organism

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to T02C12.2

value: hermaphrodite

value: unknown

value: ENCBS514HMP at ENCODE; https://www.encodeproject.org/ENCBS514HMP/


title: LIV16_873

description:
Female_LIV_counts.csv
LIV52_16_873


title: Control ChIP-seq from whole organism (ENCLB850GTX)

description:
https://www.encodeproject.org/experiments/ENCSR280HHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR280HHQ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB850GTX
size range: 150-350

source_name: Caenorhabditis elegans strain OP228 (unc-119(ed3) III; wgIs228) mixed sex L3 larva insertion targeting C. elegans nhr-237

value: whole organisms

value: not applicable

value: pooled male and female

value: L3 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS881TLH at ENCODE; https://www.encodeproject.org/ENCBS881TLH/


title: TF ChIP-seq from whole organism (ENCLB149UNK)

description:
https://www.encodeproject.org/experiments/ENCSR880OUI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing egl-18-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR880OUI
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR108PJB
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB149UNK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not collected

value: young adult

value: 63 hour

value: L1 larva starved after bleaching

value: ENCBS627YIH at ENCODE; https://www.encodeproject.org/ENCBS627YIH/


title: TF ChIP-seq from whole organism (ENCLB792DDG)

description:
https://www.encodeproject.org/experiments/ENCSR573APS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing pes-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR573APS
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR043EOJ
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB792DDG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12239 (st12239[pes-1::TY1::EGFP::3xFLAG] IV) early embryo (1 hour) using egg bleaching whole organism genetically modified (insertion) using CRISPR targeting C. elegans pes-1

value: whole organism

value: early embryonic

value: 1 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS137HCA at ENCODE; https://www.encodeproject.org/ENCBS137HCA/


title: TF ChIP-seq from whole organism (ENCLB544ADT)

description:
https://www.encodeproject.org/experiments/ENCSR573APS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing pes-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR573APS
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR043EOJ
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB544ADT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: not applicable

value: ENCBS250FDD at ENCODE; https://www.encodeproject.org/ENCBS250FDD/


title: TF ChIP-seq from whole organism (ENCLB729AXG)

description:
https://www.encodeproject.org/experiments/ENCSR584KIA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-58-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR584KIA
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR138QCE
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB729AXG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: 65 hour

value: ENCBS253QKI at ENCODE; https://www.encodeproject.org/ENCBS253QKI/


title: TF ChIP-seq from whole organism (ENCLB137IMI)

description:
https://www.encodeproject.org/experiments/ENCSR576YEP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing C06A6.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR576YEP
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR182GCE
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB137IMI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not collected

value: 67 hour

value: ENCBS794MJJ at ENCODE; https://www.encodeproject.org/ENCBS794MJJ/


title: LIV14_338

description:
Female_LIV_counts.csv
LIV52_14_338

value: Liver

value: Female

value: Sprague-Dawley

value: PCB 52


title: Control ChIP-seq from whole organism (ENCLB071HNO)

description:
https://www.encodeproject.org/experiments/ENCSR569HMX/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ref-1-eGFP fusion proteins.
experiment encode accession: ENCSR569HMX
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB071HNO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12224 (st12224[ref-1::TY1::EGFP::3xFLAG] II) midembryo (3 hours) using egg bleaching whole organism genetically modified (insertion) using CRISPR targeting C. elegans ref-1

value: whole organism

value: midembryonic

value: 3 hour

value: ENCBS482SMI at ENCODE; https://www.encodeproject.org/ENCBS482SMI/


title: Control ChIP-seq from whole organism (ENCLB897BPN)

description:
https://www.encodeproject.org/experiments/ENCSR566ZRE/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing lin-1-eGFP fusion proteins.
experiment encode accession: ENCSR566ZRE
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB897BPN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12212 (st12212[lin-1::TY1::EGFP::3xFLAG] IV) L4 larva (48 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans lin-1

value: L4 larva

value: 48 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS157LVI at ENCODE; https://www.encodeproject.org/ENCBS157LVI/


title: Control ChIP-seq from whole organism (ENCLB602KFL)

description:
https://www.encodeproject.org/experiments/ENCSR868TYN/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing pbrm-1-eGFP fusion proteins.
experiment encode accession: ENCSR868TYN
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB602KFL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12226 (st12226[pbrm-1::TY1::EGFP::3xFLAG] I) young adult (64.5 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans pbrm-1

value: whole organisms

value: not applicable

value: not collected

value: young adult

value: 64.5 hour

value: ENCBS043YXC at ENCODE; https://www.encodeproject.org/ENCBS043YXC/


title: Control ChIP-seq from whole organism (ENCLB811DKP)

description:
https://www.encodeproject.org/experiments/ENCSR280HHQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR280HHQ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB811DKP
size range: 150-350

value: pooled male and female

value: L3 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS543UIR at ENCODE; https://www.encodeproject.org/ENCBS543UIR/


title: TF ChIP-seq from whole organism (ENCLB846EDI)

description:
https://www.encodeproject.org/experiments/ENCSR279EOP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against DMD-4 in L2 larva worms.
experiment encode accession: ENCSR279EOP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR876GLE
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB846EDI
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP418 (unc-119(tm4063) III; wgIs418) mixed sex L2 larva insertion targeting C. elegans dmd-4

value: whole organism

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

value: L2 larva

value: Michael Snyder

value: ENCBS869XXI at ENCODE; https://www.encodeproject.org/ENCBS869XXI/


title: Control ChIP-seq from whole organism (ENCLB206WSS)

description:
https://www.encodeproject.org/experiments/ENCSR581NPL/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing flt-1-eGFP fusion proteins.
experiment encode accession: ENCSR581NPL
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB206WSS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12255 (st12255[flt-1::TY1::EGFP::3xFLAG] I) midembryo (1 hour) using egg bleaching insertion targeting C. elegans baz-2

value: whole organisms

value: midembryonic

value: 1 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS747AMI at ENCODE; https://www.encodeproject.org/ENCBS747AMI/


title: Control ChIP-seq from whole organism (ENCLB982NEB)

description:
https://www.encodeproject.org/experiments/ENCSR866UWY/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing tra-1-eGFP fusion proteins.
experiment encode accession: ENCSR866UWY
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB982NEB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain DZ840 (tra-1(ez72[biotag::GFP::TEV::3xflag::tra-1]) III) L4 larva (48 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans tra-1

value: not applicable

value: not collected

value: L4 larva

value: 48 hour

value: L1 larva starved after bleaching

value: ENCBS637IFK at ENCODE; https://www.encodeproject.org/ENCBS637IFK/


title: LIV10_638

description:
Female_LIV_counts.csv
LIV52_10_638

source_name: Liver

value: Liver

value: Female

value: Sprague-Dawley

value: Sham


title: TF ChIP-seq from whole organism (ENCLB524ANK)

description:
https://www.encodeproject.org/experiments/ENCSR873YHI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing aptf-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR873YHI
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR836ZQN
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB524ANK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: young adult

value: 64 hour

value: ENCBS139NTQ at ENCODE; https://www.encodeproject.org/ENCBS139NTQ/


title: TF ChIP-seq from whole organism (ENCLB550XYR)

description:
https://www.encodeproject.org/experiments/ENCSR560XDR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing T22C8.4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR560XDR
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR439MOS
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB550XYR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP785 (wgIs785(T22C8.4::TY1 EGFP 3xFLAG(p_wTRG5_single_colony_c_0093_5D01);unc-119(+));unc-119 (tm4063)) midembryo (2 hours) using egg bleaching insertion targeting C. elegans T22C8.4

value: midembryonic

value: 2 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS409YBZ at ENCODE; https://www.encodeproject.org/ENCBS409YBZ/


title: TF ChIP-seq from whole organism (ENCLB483OTM)

description:
https://www.encodeproject.org/experiments/ENCSR697DHN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing Y56A3A.18-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR697DHN
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR326VJX
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB483OTM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

value: not collected

value: 63 hour

value: L1 larva starved after bleaching

value: ENCBS661TXE at ENCODE; https://www.encodeproject.org/ENCBS661TXE/


title: TF ChIP-seq from whole organism (ENCLB369PTF)

description:
https://www.encodeproject.org/experiments/ENCSR279EOP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against DMD-4 in L2 larva worms.
experiment encode accession: ENCSR279EOP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR876GLE
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB369PTF
fragmentation methods: sonication (generic microtip)

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

value: pooled male and female

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS441HII at ENCODE; https://www.encodeproject.org/ENCBS441HII/


title: Control ChIP-seq from whole organism (ENCLB481YKW)

description:
https://www.encodeproject.org/experiments/ENCSR557XRC/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing dmd-6-eGFP fusion proteins.
experiment encode accession: ENCSR557XRC
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB481YKW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RJP5356 (rp168(dmd-6::GFP::AID::TEV::3xFLAG) IV) L4 larva (48 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans dmd-6

value: whole organism

value: whole organisms

value: L4 larva

value: 48 hour

value: ENCBS448RLZ at ENCODE; https://www.encodeproject.org/ENCBS448RLZ/


title: TF ChIP-seq from whole organism (ENCLB780EKY)

description:
https://www.encodeproject.org/experiments/ENCSR560XDR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing T22C8.4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR560XDR
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR439MOS
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB780EKY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

value: midembryonic

value: 2 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS979AUS at ENCODE; https://www.encodeproject.org/ENCBS979AUS/


title: LIV8_012

description:
Female_LIV_counts.csv
LIV52_8_012

value: Liver

value: Female

value: Sprague-Dawley

value: Sham


title: Control ChIP-seq from whole organism (ENCLB932QTS)

description:
https://www.encodeproject.org/experiments/ENCSR276IVY/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing BLMP-1-eGFP fusion proteins.
experiment encode accession: ENCSR276IVY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB932QTS
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP109 (unc-119(ed3) III; wgIs109) hermaphrodite L2 larva insertion targeting C. elegans blmp-1

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

value: hermaphrodite

value: L2 larva

value: unknown

value: ENCBS377CDO at ENCODE; https://www.encodeproject.org/ENCBS377CDO/


title: Control ChIP-seq from whole organism (ENCLB475YJX)

description:
https://www.encodeproject.org/experiments/ENCSR556EFG/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing unc-3-eGFP fusion proteins.
experiment encode accession: ENCSR556EFG
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB475YJX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12259 (st12259[unc-3::TY1::EGFP::3xFLAG] II) late embryo (2.5 hours) using egg bleaching whole organism genetically modified (insertion) using CRISPR targeting C. elegans unc-3

value: whole organism

value: whole organisms

value: not collected

value: late embryonic

value: 2.5 hour

value: ENCBS016ESX at ENCODE; https://www.encodeproject.org/ENCBS016ESX/


title: Control ChIP-seq from whole organism (ENCLB586AWQ)

description:
https://www.encodeproject.org/experiments/ENCSR372VPK/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR372VPK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB586AWQ
size range: 150-350

source_name: Caenorhabditis elegans strain OP62 (unc-119(ed3) III; wgIs62) mixed sex L2 larva insertion targeting C. elegans lin-11

value: not applicable

value: pooled male and female

value: Michael Snyder, Stanford

value: CGC

value: ENCBS160UNT at ENCODE; https://www.encodeproject.org/ENCBS160UNT/


title: LIV6_367

description:
Female_LIV_counts.csv
LIV52_6_367

value: Liver

value: Female

value: Sprague-Dawley

value: Sham


title: TF ChIP-seq from whole organism (ENCLB280NZQ)

description:
https://www.encodeproject.org/experiments/ENCSR383LSY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ztf-23-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR383LSY
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR133XXV
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB280NZQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12279 (st12279[ztf-23 ::TY1::EGFP::3xFLAG] I) midembryo (1.5 hours) using egg bleaching whole organism genetically modified (insertion) using CRISPR targeting C. elegans ztf-23

value: midembryonic

value: 1.5 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS485GGZ at ENCODE; https://www.encodeproject.org/ENCBS485GGZ/


title: LIV4_308

description:
Female_LIV_counts.csv
LIV52_4_308


title: TF ChIP-seq from whole organism (ENCLB350JHF)

description:
https://www.encodeproject.org/experiments/ENCSR555CQS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing rcor-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR555CQS
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR922HTN
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB350JHF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12222 (st12222[rcor-1::TY1::EGFP::3xFLAG] I) young adult (65 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans rcor-1

value: whole organism

value: whole organisms

value: not collected

value: young adult

value: 65 hour

value: L1 larva starved after bleaching

value: ENCBS617IUD at ENCODE; https://www.encodeproject.org/ENCBS617IUD/


title: LIV2_797

description:
Female_LIV_counts.csv
LIV52_2_797

value: Liver


title: TF ChIP-seq from whole organism (ENCLB092EFC)

description:
https://www.encodeproject.org/experiments/ENCSR272RWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-R02D3.7 in L2 larva worms.
experiment encode accession: ENCSR272RWZ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR883CKA
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB092EFC
size range: 150-350

source_name: Caenorhabditis elegans strain OP218 (unc-119(ed3) III; wgIs218) mixed sex L2 larva insertion targeting C. elegans R02D3.7

value: not applicable

value: pooled male and female

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS584OTT at ENCODE; https://www.encodeproject.org/ENCBS584OTT/


title: TF ChIP-seq from whole organism (ENCLB536RPM)

description:
https://www.encodeproject.org/experiments/ENCSR555CQS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing rcor-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR555CQS
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR922HTN
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB536RPM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS555BJX at ENCODE; https://www.encodeproject.org/ENCBS555BJX/


title: TF ChIP-seq from whole organism (ENCLB405ZUF)

description:
https://www.encodeproject.org/experiments/ENCSR272RWZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-R02D3.7 in L2 larva worms.
experiment encode accession: ENCSR272RWZ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR883CKA
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB405ZUF
size range: 150-350

value: whole organism

value: whole organisms

value: ENCBS657BIX at ENCODE; https://www.encodeproject.org/ENCBS657BIX/


title: LIV12_637

description:
Female_LIV_counts.csv
LIV52_12_637

value: Female

value: Sprague-Dawley

value: Sham


title: TF ChIP-seq from whole organism (ENCLB319IWJ)

description:
https://www.encodeproject.org/experiments/ENCSR383LSY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ztf-23-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR383LSY
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR133XXV
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB319IWJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not collected

value: midembryonic

value: 1.5 hour

value: egg bleaching

value: ENCBS015GBA at ENCODE; https://www.encodeproject.org/ENCBS015GBA/


title: Control ChIP-seq from whole organism (ENCLB970GBX)

description:
https://www.encodeproject.org/experiments/ENCSR863LHP/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing pha-4-eGFP fusion proteins.
experiment encode accession: ENCSR863LHP
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB970GBX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12220 (st12220[pha-4::TY1::EGFP::3xFLAG] V) L4 larva (48 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans pha-4

value: not applicable

value: L4 larva

value: 48 hour

value: L1 larva starved after bleaching

value: ENCBS310AHP at ENCODE; https://www.encodeproject.org/ENCBS310AHP/


title: Control ChIP-seq from whole organism (ENCLB298UAX)

description:
https://www.encodeproject.org/experiments/ENCSR269UEF/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR269UEF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB298UAX
size range: 150-350

source_name: Caenorhabditis elegans strain OP27 (unc-119(ed3) III; wgIs27) mixed sex L2 larva insertion targeting C. elegans mab-5

value: pooled male and female

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS724DXD at ENCODE; https://www.encodeproject.org/ENCBS724DXD/


title: TF ChIP-seq from whole organism (ENCLB617DNY)

description:
https://www.encodeproject.org/experiments/ENCSR687THM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing mcd-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR687THM
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR171HDO
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB617DNY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12215 (st12215[mcd-1::TY1::EGFP::3xFLAG] II) young adult (65 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans mcd-1

value: whole organism

value: whole organisms

value: young adult

value: 65 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS824IFL at ENCODE; https://www.encodeproject.org/ENCBS824IFL/


title: Control ChIP-seq from whole organism (ENCLB172NLS)

description:
https://www.encodeproject.org/experiments/ENCSR841LDV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG7786-eGFP fusion proteins.
experiment encode accession: ENCSR841LDV
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB172NLS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strain CG7786-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG7786

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7786

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS121BEG at ENCODE; https://www.encodeproject.org/ENCBS121BEG/


title: TF ChIP-seq from whole organism (ENCLB390UEJ)

description:
https://www.encodeproject.org/experiments/ENCSR687THM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing mcd-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR687THM
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR171HDO
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB390UEJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not collected

value: L1 larva starved after bleaching

value: ENCBS948QAU at ENCODE; https://www.encodeproject.org/ENCBS948QAU/


title: Control ChIP-seq from whole organism (ENCLB468GIO)

description:
https://www.encodeproject.org/experiments/ENCSR838HNJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG32264-eGFP fusion proteins.
experiment encode accession: ENCSR838HNJ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB468GIO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG32264-GFP mixed sex wandering third instar larva insertion targeting D. melanogaster CG32264

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG32264

value: pooled male and female

value: wandering third instar larva

value: unknown

value: ENCBS672BFD at ENCODE; https://www.encodeproject.org/ENCBS672BFD/


title: Control ChIP-seq from whole organism (ENCLB227IRC)

description:
https://www.encodeproject.org/experiments/ENCSR861BPL/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing sox-2-eGFP fusion proteins.
experiment encode accession: ENCSR861BPL
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB227IRC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12244 (st12244[sox-2::TY1::EGFP::3xFLAG] X.) late embryo (3.5 hours) using egg bleaching whole organism genetically modified (insertion) using CRISPR targeting C. elegans sox-2

value: whole organisms

value: late embryonic

value: 3.5 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS385SLU at ENCODE; https://www.encodeproject.org/ENCBS385SLU/


title: Control ChIP-seq from whole organism (ENCLB995GKW)

description:
https://www.encodeproject.org/experiments/ENCSR269UEF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR269UEF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB995GKW
size range: 150-350

value: not applicable

value: L2 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS290UYK at ENCODE; https://www.encodeproject.org/ENCBS290UYK/


title: Control ChIP-seq from whole organism (ENCLB363WNI)

description:
https://www.encodeproject.org/experiments/ENCSR858MGR/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing Y53F4B.3-eGFP fusion proteins.
experiment encode accession: ENCSR858MGR
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB363WNI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12270 (st12270[Y53F4B.3::TY1::EGFP::3xFLAG] II) young adult (64 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans Y53F4B.3

value: whole organism

value: not collected

value: young adult

value: 64 hour

value: L1 larva starved after bleaching

value: ENCBS507KTI at ENCODE; https://www.encodeproject.org/ENCBS507KTI/


title: Control ChIP-seq from whole organism (ENCLB101HCM)

description:
https://www.encodeproject.org/experiments/ENCSR547IXO/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing cebp-1-eGFP fusion proteins.
experiment encode accession: ENCSR547IXO
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB101HCM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12290 (st12290[cebp-1::TY1::EGFP::3xFLAG] X) young adult (62 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans cebp-1

value: whole organisms

value: 62 hour

value: ENCBS086GKF at ENCODE; https://www.encodeproject.org/ENCBS086GKF/


title: Control ChIP-seq from whole organism (ENCLB456QWL)

description:
https://www.encodeproject.org/experiments/ENCSR556YDQ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing hmg-20-eGFP fusion proteins.
experiment encode accession: ENCSR556YDQ
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB456QWL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12240 (st12240[hmg-20::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 hmg-20

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS389ESS at ENCODE; https://www.encodeproject.org/ENCBS389ESS/