title: Mint-ChIP-seq from HCT116 (ENCLB848THD)

description:
https://www.encodeproject.org/experiments/ENCSR790WQH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR790WQH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR873HRN
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB848THD

tag: line

value: cell line

value: 48 year

value: male

tag: health state

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS403YHB at ENCODE; https://www.encodeproject.org/ENCBS403YHB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: TF ChIP-seq from whole organism (ENCLB096ZHX)

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/ENCSR266NAT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ELT-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR266NAT
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR091ZYU
encode release date: 2016-09-29
lab: Valerie Reinke, Yale
library encode accession: ENCLB096ZHX
fragmentation methods: sonication (generic microtip)

library_source: genomic

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

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP56 (unc-119(ed3) III; wgIs56) hermaphrodite late embryo 4 hours post synchronization using egg bleaching insertion targeting C. elegans elt-2

tag: antibody

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: note

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

tag: Sex

value: hermaphrodite

tag: dev stage

value: late embryonic

tag: age

value: unknown

tag: lab

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

tag: link

value: ENCBS924LDQ at ENCODE; https://www.encodeproject.org/ENCBS924LDQ/


title: TF ChIP-seq from whole organism (ENCLB291XYB)

description:
https://www.encodeproject.org/experiments/ENCSR150QNB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR150QNB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR357JFV
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB291XYB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strain Eip74EF-GFP mixed sex embryo (8-16 hours) whole organism stably expressing C-terminal eGFP-tagged Eip74EF

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Eip74EF

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS484IWH at ENCODE; https://www.encodeproject.org/ENCBS484IWH/


title: TF ChIP-seq from whole organism (ENCLB184HYV)

description:
https://www.encodeproject.org/experiments/ENCSR122TLF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing sdz-12-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR122TLF
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR742BIV
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB184HYV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP670 (unc-119(tm4063); wgIs670 [sdz-12::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex L4 larva (71 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans sdz-12

value: whole organism

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SDZ-12.

value: L4 larva

value: 71 hour

value: L1 larva starved after bleaching

value: ENCBS019MYX at ENCODE; https://www.encodeproject.org/ENCBS019MYX/


title: Control ChIP-seq from whole organism (ENCLB477RVJ)

description:
https://www.encodeproject.org/experiments/ENCSR194XZB/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing CEH-24-eGFP fusion proteins.
experiment encode accession: ENCSR194XZB
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB477RVJ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP673 (unc-119 (tm4063) III; wgIs673) mixed sex late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans ceh-24

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-24

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS630XEP at ENCODE; https://www.encodeproject.org/ENCBS630XEP/


title: TF ChIP-seq from whole organism (ENCLB072QTI)

description:
https://www.encodeproject.org/experiments/ENCSR359GJP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F13H6.1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR359GJP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR095HSC
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB072QTI
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP471 (unc-119(tm4063) III; wgIs471) hermaphrodite L2 larva 22 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans bcl-11

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F13H6.1

value: hermaphrodite

value: L2 larva

value: hour

value: ENCBS571SIJ at ENCODE; https://www.encodeproject.org/ENCBS571SIJ/


title: Mint-ChIP-seq from Calu3 (ENCLB793NZB)

description:
https://www.encodeproject.org/experiments/ENCSR433FAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR433FAZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR372VUZ
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB793NZB

organism: Homo sapiens

source_name: Homo sapiens Calu3 cell line

tag: line

value: cell line

value: 25 year

value: male

value: Lung adenocarcinoma

value: adult

value: Bradley Bernstein, Broad

value: Mats Ljungman

value: ENCBS827USO at ENCODE; https://www.encodeproject.org/ENCBS827USO/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: TF ChIP-seq from whole organism (ENCLB621VIR)

description:
https://www.encodeproject.org/experiments/ENCSR150QNB/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR150QNB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR357JFV
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB621VIR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Eip74EF

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS402ADD at ENCODE; https://www.encodeproject.org/ENCBS402ADD/


title: Mint-ChIP-seq from Calu3 (ENCLB076WLS)

description:
https://www.encodeproject.org/experiments/ENCSR433FAZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR433FAZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR372VUZ
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB076WLS

value: cell line

value: 25 year

tag: health state


title: Control ChIP-seq from whole organism (ENCLB892WVA)

description:
https://www.encodeproject.org/experiments/ENCSR095MXI/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing RPC-1-eGFP fusion proteins.
experiment encode accession: ENCSR095MXI
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2019-01-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB892WVA
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain JK1107 (glp-1(q224) III) hermaphrodite young adult whole organism

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

value: hermaphrodite

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS661PLM at ENCODE; https://www.encodeproject.org/ENCBS661PLM/


title: TF ChIP-seq from whole organism (ENCLB420KDH)

description:
https://www.encodeproject.org/experiments/ENCSR227BSJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR227BSJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR792YVU
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB420KDH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG11504 mixed sex embryo (0-18 hours) insertion targeting D. melanogaster CG11504

tag: antibody

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG11504

value: 0-18 hour

value: ENCBS745OYK at ENCODE; https://www.encodeproject.org/ENCBS745OYK/


title: TF ChIP-seq from whole organism (ENCLB367HSU)

description:
https://www.encodeproject.org/experiments/ENCSR115ZDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing sup-37-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR115ZDZ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR823XQM
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB367HSU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP611 (unc-119(tm4063); wgIs611 [sup-37::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex L1 larva (6 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans sup-37

tag: biosample encode accession

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SUP-37.

value: pooled male and female

value: L1 larva

value: 6 hour

value: L1 larva starved after bleaching

value: ENCBS161JWN at ENCODE; https://www.encodeproject.org/ENCBS161JWN/


title: Control ChIP-seq from whole organism (ENCLB493LMW)

description:
https://www.encodeproject.org/experiments/ENCSR251RZP/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing NHR-47-eGFP fusion proteins.
experiment encode accession: ENCSR251RZP
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB493LMW
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP481 (unc-119(tm4063) III; wgIs481) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans nhr-47

tag: collection date

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-47

value: hermaphrodite

value: hour

value: ENCBS696TAZ at ENCODE; https://www.encodeproject.org/ENCBS696TAZ/


title: TF ChIP-seq from whole organism (ENCLB616SDF)

description:
https://www.encodeproject.org/experiments/ENCSR224YOT/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing bigmax-eGFP fusion proteins.
experiment encode accession: ENCSR224YOT
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR797ZUO
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB616SDF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: bigmax

tag: geographic location

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS782UCX at ENCODE; https://www.encodeproject.org/ENCBS782UCX/


title: Mint-ChIP-seq from HCT116 (ENCLB890FFF)

description:
https://www.encodeproject.org/experiments/ENCSR633PSA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR633PSA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR608WUK
encode release date: 2022-07-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB890FFF

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

value: ENCBS456GWO at ENCODE; https://www.encodeproject.org/ENCBS456GWO/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: TF ChIP-seq from whole organism (ENCLB092PQM)

description:
https://www.encodeproject.org/experiments/ENCSR115ZDZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing sup-37-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR115ZDZ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR823XQM
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB092PQM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

tag: encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SUP-37.

value: pooled male and female

value: L1 larva

value: 6 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS060REI at ENCODE; https://www.encodeproject.org/ENCBS060REI/


title: Mint-ChIP-seq from HCT116 (ENCLB501UJV)

description:
https://www.encodeproject.org/experiments/ENCSR633PSA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR633PSA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR608WUK
encode release date: 2022-07-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB501UJV

value: cell line

value: 48 year

value: male

value: colorectal carcinoma


title: Control ChIP-seq from whole organism (ENCLB437TTG)

description:
https://www.encodeproject.org/experiments/ENCSR347AVI/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing T07F8.4-eGFP fusion proteins.
experiment encode accession: ENCSR347AVI
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB437TTG
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP478 (unc-119(tm4063) III; wgIs478) hermaphrodite young adult 64 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans T07F8.4

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to T07F8.4

value: hermaphrodite

value: young adult

value: unknown

value: hour

value: ENCBS715YVN at ENCODE; https://www.encodeproject.org/ENCBS715YVN/


title: Control ChIP-seq from whole organism (ENCLB783MVF)

description:
https://www.encodeproject.org/experiments/ENCSR113XIS/
***************
biological replicate number: 3
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ceh-19-eGFP fusion proteins.
experiment encode accession: ENCSR113XIS
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB783MVF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP739 (unc-119(tm4063); wgIs739 [ceh-19::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex late embryo (5 hours) using egg bleaching insertion targeting C. elegans ceh-19

value: whole organism

value: whole organisms

value: not applicable

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

tag: Sex

value: pooled male and female

value: late embryonic

value: 5 hour

value: egg bleaching

value: ENCBS864WGF at ENCODE; https://www.encodeproject.org/ENCBS864WGF/


title: Mint-ChIP-seq from HCT116 (ENCLB711ICT)

description:
https://www.encodeproject.org/experiments/ENCSR562OQT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR562OQT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR873HRN
encode release date: 2022-07-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB711ICT

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: 48 year

value: male

tag: dev stage

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS403YHB at ENCODE; https://www.encodeproject.org/ENCBS403YHB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Control ChIP-seq from whole organism (ENCLB215WJO)

description:
https://www.encodeproject.org/experiments/ENCSR113XIS/
***************
biological replicate number: 2
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ceh-19-eGFP fusion proteins.
experiment encode accession: ENCSR113XIS
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB215WJO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

tag: age

tag: lab

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS139WMD at ENCODE; https://www.encodeproject.org/ENCBS139WMD/


title: TF ChIP-seq from whole organism (ENCLB317CBD)

description:
https://www.encodeproject.org/experiments/ENCSR317XOG/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG30020-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR317XOG
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR555KVU
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB317CBD
size range: 200-800

source_name: Drosophila melanogaster strain CG30020 mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG30020

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG30020

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS417LXD at ENCODE; https://www.encodeproject.org/ENCBS417LXD/


title: TF ChIP-seq from whole organism (ENCLB255ZPB)

description:
https://www.encodeproject.org/experiments/ENCSR345JIR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing SOX-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR345JIR
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR639KBJ
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB255ZPB
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP517 (unc-119(tm4063) III; wgIs517) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans sox-4

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

value: hermaphrodite

value: L1 larva

value: unknown

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

value: hour

value: ENCBS584WVE at ENCODE; https://www.encodeproject.org/ENCBS584WVE/


title: Mint-ChIP-seq from HCT116 (ENCLB338BPU)

description:
https://www.encodeproject.org/experiments/ENCSR562OQT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR562OQT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR873HRN
encode release date: 2022-07-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB338BPU

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link

value: ENCBS403YHB at ENCODE; https://www.encodeproject.org/ENCBS403YHB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: TF ChIP-seq from whole organism (ENCLB115PHR)

description:
https://www.encodeproject.org/experiments/ENCSR220HPB/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR220HPB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR945JMM
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB115PHR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain 8T-GFP mixed sex embryo (0-4 hours) insertion targeting D. melanogaster tll

value: tll

value: whole organism

value: whole organisms

value: not applicable

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

value: pooled male and female

value: embryonic

value: 0-4 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS351GMY at ENCODE; https://www.encodeproject.org/ENCBS351GMY/


title: TF ChIP-seq from whole organism (ENCLB544OGT)

description:
https://www.encodeproject.org/experiments/ENCSR345JIR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing SOX-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR345JIR
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR639KBJ
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB544OGT
fragmentation methods: sonication (generic microtip)

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

value: hermaphrodite

value: L1 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

tag: post synchronization time units

value: hour

value: ENCBS069FMC at ENCODE; https://www.encodeproject.org/ENCBS069FMC/


title: Mint-ChIP-seq from Calu3 (ENCLB915QEV)

description:
https://www.encodeproject.org/experiments/ENCSR223QCG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR223QCG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR372VUZ
encode release date: 2022-08-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB915QEV

tag: line

value: cell line

value: 25 year

value: male

tag: health state

value: Lung adenocarcinoma

value: adult

value: Bradley Bernstein, Broad

value: Mats Ljungman

value: ENCBS827USO at ENCODE; https://www.encodeproject.org/ENCBS827USO/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: TF ChIP-seq from whole organism (ENCLB398YYT)

description:
https://www.encodeproject.org/experiments/ENCSR010MNU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CHD-7-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR010MNU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR778CNK
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB398YYT
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP609 (unc-119(tm4063) III; wgIs609) mixed sex young adult 67 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans chd-7

tag: antibody

value: whole organism

value: whole organisms

tag: biosample encode accession

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CHD-7

value: pooled male and female

value: young adult

value: ENCBS637HEX at ENCODE; https://www.encodeproject.org/ENCBS637HEX/


title: TF ChIP-seq from whole organism (ENCLB531TQY)

description:
https://www.encodeproject.org/experiments/ENCSR010MNU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CHD-7-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR010MNU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR778CNK
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB531TQY
fragmentation methods: sonication (generic microtip)

tag: collection date

tag: geographic location

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS782ZZX at ENCODE; https://www.encodeproject.org/ENCBS782ZZX/


title: Mint-ChIP-seq from Calu3 (ENCLB041ZPD)

description:
https://www.encodeproject.org/experiments/ENCSR223QCG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR223QCG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR372VUZ
encode release date: 2022-08-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB041ZPD

value: cell line

value: 25 year

value: male

value: Lung adenocarcinoma

value: adult

value: Bradley Bernstein, Broad


title: TF ChIP-seq from whole organism (ENCLB385NKZ)

description:
https://www.encodeproject.org/experiments/ENCSR220HPB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR220HPB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR945JMM
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB385NKZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: tll

value: whole organism

value: whole organisms

value: not applicable

tag: encode accession

tag: note

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

value: embryonic

value: 0-4 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS140VWJ at ENCODE; https://www.encodeproject.org/ENCBS140VWJ/


title: Control ChIP-seq from whole organism (ENCLB064HSH)

description:
https://www.encodeproject.org/experiments/ENCSR317QFT/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing YL-1-eGFP fusion proteins.
experiment encode accession: ENCSR317QFT
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB064HSH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

tag: Sex

value: pooled male and female

tag: dev stage

value: 0-24 hour

value: ENCBS244LIW at ENCODE; https://www.encodeproject.org/ENCBS244LIW/


title: TF ChIP-seq from whole organism (ENCLB273NWN)

description:
https://www.encodeproject.org/experiments/ENCSR081BBL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing DAF-16-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR081BBL
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR332LQE
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB273NWN
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain ZM7247 (daf-16(mu86);daf-2(e1370) III; hpSi4II (Pmyo-3 GFP::daf-16a)) hermaphrodite L4 larva 54 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans daf-16

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to DAF-16

value: hermaphrodite

value: L4 larva

tag: age

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS773BAM at ENCODE; https://www.encodeproject.org/ENCBS773BAM/


title: Control ChIP-seq from whole organism (ENCLB244QHP)

description:
https://www.encodeproject.org/experiments/ENCSR106DTT/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing CEH-48-eGFP fusion proteins.
experiment encode accession: ENCSR106DTT
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB244QHP
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP631 (unc-119(tm4063) III; wgIs631) mixed sex late embryo 3.5 hours post synchronization using egg bleaching insertion targeting C. elegans ceh-48

value: whole organism

value: whole organisms

value: not applicable

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

value: late embryonic

tag: lab

value: egg bleaching

value: ENCBS352YVV at ENCODE; https://www.encodeproject.org/ENCBS352YVV/


title: Control ChIP-seq from whole organism (ENCLB992XKQ)

description:
https://www.encodeproject.org/experiments/ENCSR091ZYU/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ELT-2-eGFP fusion proteins.
experiment encode accession: ENCSR091ZYU
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-09-29
lab: Valerie Reinke, Yale
library encode accession: ENCLB992XKQ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP56 (unc-119(ed3) III; wgIs56) hermaphrodite late embryo 4 hours post synchronization using egg bleaching insertion targeting C. elegans elt-2

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

tag: source

value: ENCBS347BNH at ENCODE; https://www.encodeproject.org/ENCBS347BNH/


title: Control ChIP-seq from whole organism (ENCLB244GHY)

description:
https://www.encodeproject.org/experiments/ENCSR283FJI/
***************
biological replicate number: 6
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ham-2-eGFP fusion proteins.
experiment encode accession: ENCSR283FJI
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB244GHY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP639 (wgIs639 [ham-2::TY1::EGFP::3xFLAG + unc-119(+)];unc-119 (tm4063)) mixed sex mixed stage (embryo) (3 hours) using egg bleaching insertion targeting C. elegans ham-2

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

value: pooled male and female

value: mixed stage (embryonic)

value: 3 hour

tag: worm synchronization stage

value: ENCBS192ZMY at ENCODE; https://www.encodeproject.org/ENCBS192ZMY/


title: TF ChIP-seq from whole organism (ENCLB794UPN)

description:
https://www.encodeproject.org/experiments/ENCSR224YOT/
***************
biological replicate number: 4
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing bigmax-eGFP fusion proteins.
experiment encode accession: ENCSR224YOT
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR797ZUO
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB794UPN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: bigmax

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS791QFF at ENCODE; https://www.encodeproject.org/ENCBS791QFF/


title: TF ChIP-seq from whole organism (ENCLB172CLD)

description:
https://www.encodeproject.org/experiments/ENCSR316FKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing wek-eGFP fusion proteins.
experiment encode accession: ENCSR316FKJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR473QXV
encode release date: 2018-02-06
lab: Kevin White, UChicago
library encode accession: ENCLB172CLD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: wek

value: whole organism

value: whole organisms

value: not applicable

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

value: 0-16 hour

value: ENCBS085DNP at ENCODE; https://www.encodeproject.org/ENCBS085DNP/


title: Mint-ChIP-seq from natural killer cell (ENCLB769DJM)

description:
https://www.encodeproject.org/experiments/ENCSR036TAN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR036TAN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457FTM
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB769DJM

source_name: Homo sapiens male adult (33 years) natural killer primary cell

value: natural killer cell

value: primary cell

value: 33 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS358EEP at ENCODE; https://www.encodeproject.org/ENCBS358EEP/

value: Derived from ENCODE donor ENCDO195VEA; https://www.encodeproject.org/ENCDO195VEA/


title: TF ChIP-seq from whole organism (ENCLB982SLE)

description:
https://www.encodeproject.org/experiments/ENCSR185SVY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ZTF-11-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR185SVY
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR892EIQ
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB982SLE
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP511 (unc-119(tm4063) III; wgIs511) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans ztf-11

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to ZTF-11

value: hermaphrodite

value: L1 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

tag: post synchronization time

value: hour

value: ENCBS719GTM at ENCODE; https://www.encodeproject.org/ENCBS719GTM/


title: TF ChIP-seq from whole organism (ENCLB810BEC)

description:
https://www.encodeproject.org/experiments/ENCSR316FKJ/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing wek-eGFP fusion proteins.
experiment encode accession: ENCSR316FKJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR473QXV
encode release date: 2018-02-06
lab: Kevin White, UChicago
library encode accession: ENCLB810BEC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: wek

value: whole organism

value: whole organisms

value: not applicable

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

value: pooled male and female

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

tag: link

value: ENCBS139DFA at ENCODE; https://www.encodeproject.org/ENCBS139DFA/


title: TF ChIP-seq from whole organism (ENCLB537FUJ)

description:
https://www.encodeproject.org/experiments/ENCSR317XOG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG30020-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR317XOG
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR555KVU
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB537FUJ
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG30020

value: 0-24 hour

value: ENCBS200IFT at ENCODE; https://www.encodeproject.org/ENCBS200IFT/


title: TF ChIP-seq from whole organism (ENCLB205BGU)

description:
https://www.encodeproject.org/experiments/ENCSR081BBL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing DAF-16-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR081BBL
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR332LQE
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB205BGU
fragmentation methods: sonication (generic microtip)

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to DAF-16

value: hermaphrodite

value: L4 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

tag: post synchronization time units

value: ENCBS616VAU at ENCODE; https://www.encodeproject.org/ENCBS616VAU/


title: Control ChIP-seq from whole organism (ENCLB789VCP)

description:
https://www.encodeproject.org/experiments/ENCSR101ZRY/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing FKH-8-eGFP fusion proteins.
experiment encode accession: ENCSR101ZRY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB789VCP
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP652 (unc-119(tm4063) III; wgIs652) mixed sex L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans fkh-8

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to FKH-8

value: pooled male and female

value: L1 larva

value: hour

value: ENCBS297IAL at ENCODE; https://www.encodeproject.org/ENCBS297IAL/


title: Mint-ChIP-seq from natural killer cell (ENCLB626WMZ)

description:
https://www.encodeproject.org/experiments/ENCSR036TAN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR036TAN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457FTM
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB626WMZ

value: natural killer cell

value: primary cell

value: 33 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS358EEP at ENCODE; https://www.encodeproject.org/ENCBS358EEP/

value: Derived from ENCODE donor ENCDO195VEA; https://www.encodeproject.org/ENCDO195VEA/


title: TF ChIP-seq from whole organism (ENCLB422DKV)

description:
https://www.encodeproject.org/experiments/ENCSR185SVY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ZTF-11-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR185SVY
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR892EIQ
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB422DKV
fragmentation methods: sonication (generic microtip)

value: whole organism

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to ZTF-11

value: hermaphrodite

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS309FBS at ENCODE; https://www.encodeproject.org/ENCBS309FBS/


title: Control ChIP-seq from whole organism (ENCLB912WUH)

description:
https://www.encodeproject.org/experiments/ENCSR246FAX/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing SDZ-38-eGFP fusion proteins.
experiment encode accession: ENCSR246FAX
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-07-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB912WUH
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP543 hermaphrodite young adult 64 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans sdz-38

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SDZ-38

value: young adult

value: hour

value: ENCBS585DSE at ENCODE; https://www.encodeproject.org/ENCBS585DSE/


title: Ws-0 infected by S. sclerotiorum rep 3

city: Castanet-Tolosan

first: Florent

last: Delplace

address: 24 chemin de Borde Rouge

country: France

institute: INRAe

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function described in the pipeline https://doi.org/10.5281/zenodo.1400710) using the nf-core framework (https://github.com/nf-core/rnaseq). Raw counts were normalized by edgeR.
Assembly: Arabidopsis thalinia (Araport11), Sclerotinia sclerotiorum strain 1980 (Derbyshire et al., 2017)
Supplementary files format and content: tab-delimited text files includes CPM values for all Samples

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Leaves of 5-week old plants

growth_protocol: Plants were grown in Jiffy pots under controlled conditions at 22°C, with a 9 hour light period at intensity of 120 μmol/m²/s.

extract_protocol:
Samples were ground using glass beads (2.5 mm) and RNA was extracted using NucleoSpin RNA PLUS extraction kits (Macherey-Nagel) following the manufacturer’s protocols. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed at the center of a Petri dish or on the adaxial surface of leaves on 5-week old plants. The border (ring of ~5mm wide) and center of colonies were collected with a scalpel and frozen in liquid nitrogen.

tag: tissue

value: Leaves of 5-week old plants

tag: genotype

tag: treatment

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: Ws-0 infected by S. sclerotiorum rep 2


title: TF ChIP-seq from whole organism (ENCLB824ADD)

description:
https://www.encodeproject.org/experiments/ENCSR002FCO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CEH-36-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR002FCO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR646YCH
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB824ADD
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP620 (unc-119(tm4063) III; wgIs620) mixed sex early embryo 2 hours post synchronization using egg bleaching insertion targeting C. elegans ceh-36

tag: antibody

value: whole organism

tag: biosample encode accession

tag: collection date

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-36

value: pooled male and female

value: early embryonic

value: egg bleaching

value: ENCBS626HPD at ENCODE; https://www.encodeproject.org/ENCBS626HPD/


title: TF ChIP-seq from whole organism (ENCLB935ENA)

description:
https://www.encodeproject.org/experiments/ENCSR002FCO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CEH-36-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR002FCO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR646YCH
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB935ENA
fragmentation methods: sonication (generic microtip)

tag: geographic location

tag: encode accession

tag: note

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS447GRK at ENCODE; https://www.encodeproject.org/ENCBS447GRK/


title: TF ChIP-seq from whole organism (ENCLB183DYU)

description:
https://www.encodeproject.org/experiments/ENCSR219AHM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG9139-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR219AHM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR264BNK
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB183DYU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG9139-GFP mixed sex prepupa (24 hours) insertion targeting D. melanogaster Rabex-5

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG9139

tag: Sex

tag: dev stage

value: prepupa

tag: age

value: 24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS998BRW at ENCODE; https://www.encodeproject.org/ENCBS998BRW/


title: Wa-1 infected by S. sclerotiorum rep 3

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: Mint-ChIP-seq from GM23338 (ENCLB000SZR)

description:
https://www.encodeproject.org/experiments/ENCSR695NNR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human GM23338.
experiment encode accession: ENCSR695NNR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB000SZR
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

source_name: Homo sapiens GM23338 cell line

tag: line

value: cell line

tag: description

value: PGP-1 iPSCs provided by the George Church lab at HMS. purity 100%

value: male

value: adult

value: 53 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Paola Arlotta

value: ENCBS299FWQ at ENCODE; https://www.encodeproject.org/ENCBS299FWQ/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: TF ChIP-seq from whole organism (ENCLB333WOT)

description:
https://www.encodeproject.org/experiments/ENCSR219AHM/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG9139-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR219AHM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR264BNK
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB333WOT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG9139

value: pooled male and female

value: prepupa

tag: link

value: ENCBS028NHW at ENCODE; https://www.encodeproject.org/ENCBS028NHW/


title: TF ChIP-seq from whole organism (ENCLB796ODZ)

description:
https://www.encodeproject.org/experiments/ENCSR219AHM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG9139-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR219AHM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR264BNK
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB796ODZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: 24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS782KWQ at ENCODE; https://www.encodeproject.org/ENCBS782KWQ/


title: TF ChIP-seq from whole organism (ENCLB356RBG)

description:
https://www.encodeproject.org/experiments/ENCSR182IGG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NHR-232-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR182IGG
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR169GCJ
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB356RBG
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP489 (unc-119(tm4063) III; wgIs489) hermaphrodite late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans nhr-232

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-232

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS140NKH at ENCODE; https://www.encodeproject.org/ENCBS140NKH/


title: Control ChIP-seq from whole organism (ENCLB668XCM)

description:
https://www.encodeproject.org/experiments/ENCSR064VSR/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing UNC-86-eGFP fusion proteins.
experiment encode accession: ENCSR064VSR
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB668XCM
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP476 (unc-119(tm4063) III; wgIs476) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans unc-86

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to UNC-86

value: L1 larva

value: L1 larva starved after bleaching

value: ENCBS384HYS at ENCODE; https://www.encodeproject.org/ENCBS384HYS/


title: Mint-ChIP-seq from GM23338 (ENCLB889BPX)

description:
https://www.encodeproject.org/experiments/ENCSR695NNR/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human GM23338.
experiment encode accession: ENCSR695NNR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB889BPX
fragmentation methods: none

tag: antibody

value: cell line

value: PGP-1 iPSCs provided by the George Church lab at HMS. purity 100%

value: male

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS695QJS at ENCODE; https://www.encodeproject.org/ENCBS695QJS/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Wa-1 infected by S. sclerotiorum rep 2

tag: tissue

value: Leaves of 5-week old plants

tag: genotype

tag: treatment

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: Mint-ChIP-seq from GM23338 (ENCLB326RYM)

description:
https://www.encodeproject.org/experiments/ENCSR695NNR/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human GM23338.
experiment encode accession: ENCSR695NNR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB326RYM

tag: biosample encode accession


title: Wa-1 infected by S. sclerotiorum rep 1


title: TF ChIP-seq from whole organism (ENCLB451VJA)

description:
https://www.encodeproject.org/experiments/ENCSR315AML/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Hand-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR315AML
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR102QDH
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB451VJA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Hand-GFP mixed sex embryo (6-24 hours) insertion targeting D. melanogaster Hand

value: Hand

value: whole organism

value: whole organisms

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: note

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

tag: Sex

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS123KJQ at ENCODE; https://www.encodeproject.org/ENCBS123KJQ/


title: Control ChIP-seq from whole organism (ENCLB204XAZ)

description:
https://www.encodeproject.org/experiments/ENCSR178IVN/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing HLH-6-eGFP fusion proteins.
experiment encode accession: ENCSR178IVN
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB204XAZ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain RW10702 hermaphrodite late embryo 3.5 hours post synchronization using egg bleaching insertion targeting C. elegans hlh-6

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to HLH-6

value: hermaphrodite

tag: dev stage

value: late embryonic

tag: age

value: unknown

tag: lab

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: hour

value: ENCBS799WHY at ENCODE; https://www.encodeproject.org/ENCBS799WHY/


title: Van-0 infected by S. sclerotiorum rep 3

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB680SHM)

description:
https://www.encodeproject.org/experiments/ENCSR315AML/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Hand-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR315AML
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR102QDH
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB680SHM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Hand

value: whole organism

value: whole organisms

value: not applicable

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

value: pooled male and female

tag: source

tag: link

value: ENCBS513ARX at ENCODE; https://www.encodeproject.org/ENCBS513ARX/


title: Control ChIP-seq from SK-N-SH (ENCLB527GNI)

description:
https://www.encodeproject.org/experiments/ENCSR017UWW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR017UWW
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB527GNI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens OSR1 treated with 6 uM all-trans-retinoic acid for 48 hours

tag: line

value: SK-N-SH

value: cell line

value: female

tag: health state

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

value: Michael Snyder, Stanford

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS120KUK at ENCODE; https://www.encodeproject.org/ENCBS120KUK/


title: Van-0 infected by S. sclerotiorum rep 2

tag: tissue

value: Leaves of 5-week old plants

tag: genotype

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB683LHA)

description:
https://www.encodeproject.org/experiments/ENCSR055WPE/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing SNPC-4-eGFP fusion proteins.
experiment encode accession: ENCSR055WPE
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB683LHA
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL551 hermaphrodite young adult 60 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans snpc-4

value: whole organism

value: whole organisms

value: not applicable

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

value: hermaphrodite

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS430DMW at ENCODE; https://www.encodeproject.org/ENCBS430DMW/


title: TF ChIP-seq from whole organism (ENCLB949CNB)

description:
https://www.encodeproject.org/experiments/ENCSR316FKJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing wek-eGFP fusion proteins.
experiment encode accession: ENCSR316FKJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR473QXV
encode release date: 2018-02-06
lab: Kevin White, UChicago
library encode accession: ENCLB949CNB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: wek

tag: biosample encode accession

tag: collection date

tag: geographic location

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

value: pooled male and female

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS666GBO at ENCODE; https://www.encodeproject.org/ENCBS666GBO/


title: Control ChIP-seq from HepG2 (ENCLB165CXL)

description:
https://www.encodeproject.org/experiments/ENCSR332CDN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human HepG2
experiment encode accession: ENCSR332CDN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB165CXL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MBNL3

value: cell line

value: not applicable

tag: encode accession

tag: Sex

value: male

value: hepatocellular carcinoma

tag: dev stage

value: child

value: 15 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS260WRS at ENCODE; https://www.encodeproject.org/ENCBS260WRS/


title: TF ChIP-seq from whole organism (ENCLB160KWN)

description:
https://www.encodeproject.org/experiments/ENCSR313TWF/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG31365-eGFP fusion proteins.
experiment encode accession: ENCSR313TWF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR027VEH
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB160KWN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG31365 mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG31365

value: whole organism

value: whole organisms

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG31365

tag: age

value: 0-24 hour

tag: lab

tag: source

value: ENCBS950VOC at ENCODE; https://www.encodeproject.org/ENCBS950VOC/


title: Control ChIP-seq from whole organism (ENCLB219FWC)

description:
https://www.encodeproject.org/experiments/ENCSR169GCJ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing NHR-232-eGFP fusion proteins.
experiment encode accession: ENCSR169GCJ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB219FWC
fragmentation methods: sonication (generic microtip)

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-232

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: hour

tag: link

value: ENCBS827UKC at ENCODE; https://www.encodeproject.org/ENCBS827UKC/


title: Van-0 infected by S. sclerotiorum rep 1

tag: tissue

value: Leaves of 5-week old plants

tag: treatment

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB261NSQ)

description:
https://www.encodeproject.org/experiments/ENCSR332LQE/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing DAF-16-eGFP fusion proteins.
experiment encode accession: ENCSR332LQE
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB261NSQ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain ZM7247 (daf-16(mu86);daf-2(e1370) III; hpSi4II (Pmyo-3 GFP::daf-16a)) hermaphrodite L4 larva 54 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans daf-16

value: whole organism

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to DAF-16

value: L4 larva

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

value: ENCBS850YXP at ENCODE; https://www.encodeproject.org/ENCBS850YXP/


title: Mint-ChIP-seq from GM23338 (ENCLB689OKU)

description:
https://www.encodeproject.org/experiments/ENCSR695NNR/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human GM23338.
experiment encode accession: ENCSR695NNR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB689OKU
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

tag: antibody

tag: line

value: cell line

tag: description

value: PGP-1 iPSCs provided by the George Church lab at HMS. purity 100%

value: male

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS299FWQ at ENCODE; https://www.encodeproject.org/ENCBS299FWQ/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: TF ChIP-seq from whole organism (ENCLB810IUH)

description:
https://www.encodeproject.org/experiments/ENCSR312RCJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8216-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR312RCJ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR506NPV
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB810IUH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG8216-GFP mixed sex prepupa (24 days) insertion targeting D. melanogaster spab

value: spab

value: whole organisms

tag: biosample encode accession

tag: collection date

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8216

value: pooled male and female

value: prepupa

value: 24 day

value: Kevin White, UChicago

value: Kevin White

value: ENCBS579WVL at ENCODE; https://www.encodeproject.org/ENCBS579WVL/


title: Ws-0 infected by S. sclerotiorum rep 1

value: Leaves of 5-week old plants

tag: genotype

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB160EIC)

description:
https://www.encodeproject.org/experiments/ENCSR238YNR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing TBX-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR238YNR
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR484UJP
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB160EIC
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP159 (unc-119(ed3) III; wgIs159) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans tbx-2

value: whole organism

value: not applicable

tag: encode accession

tag: note

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

tag: Sex

value: hermaphrodite

tag: dev stage

value: L1 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

tag: post synchronization time units

value: hour

value: ENCBS641MNP at ENCODE; https://www.encodeproject.org/ENCBS641MNP/


title: TF ChIP-seq from whole organism (ENCLB225NYD)

description:
https://www.encodeproject.org/experiments/ENCSR182IGG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NHR-232-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR182IGG
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR169GCJ
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB225NYD
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-232

value: late embryonic

tag: age

tag: lab

tag: source

value: egg bleaching

tag: link

value: ENCBS007NHT at ENCODE; https://www.encodeproject.org/ENCBS007NHT/


title: TF ChIP-seq from whole organism (ENCLB792TFS)

description:
https://www.encodeproject.org/experiments/ENCSR312RCJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8216-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR312RCJ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR506NPV
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB792TFS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: spab

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8216

value: pooled male and female

value: prepupa

value: 24 day

value: Kevin White, UChicago

value: Kevin White

value: ENCBS347WAM at ENCODE; https://www.encodeproject.org/ENCBS347WAM/


title: Se-0 infected by S. sclerotiorum rep 3

tag: tissue

value: Leaves of 5-week old plants

tag: treatment

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB302KHD)

description:
https://www.encodeproject.org/experiments/ENCSR238YNR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing TBX-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR238YNR
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR484UJP
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB302KHD
fragmentation methods: sonication (generic microtip)

tag: antibody

value: whole organism

value: not applicable

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

value: hermaphrodite

value: L1 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

value: hour

value: ENCBS991YBP at ENCODE; https://www.encodeproject.org/ENCBS991YBP/


title: Se-0 infected by S. sclerotiorum rep 2


title: TF ChIP-seq from whole organism (ENCLB497CNO)

description:
https://www.encodeproject.org/experiments/ENCSR143AWF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG18262-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR143AWF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR754KJL
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB497CNO
size range: 200-800

source_name: Drosophila melanogaster strain CG18262 mixed sex embryo (0-16 hours) insertion targeting D. melanogaster CG18262

value: whole organisms

tag: biosample encode accession

tag: collection date

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG18262

value: pooled male and female

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: ENCBS469YZB at ENCODE; https://www.encodeproject.org/ENCBS469YZB/


title: Human fetal heart

city: New York

first: Hina

last: Chaudhry

state: USA

department: Cardiology

institute: Mount Sinai Hospital

data_processing:
One NovaSeq S2 Flowcell 300 Cycles V1.5 was used to achieve the requested 150 million reads per sample and 2x150bp.

Base-calling: bcl2fastq 2.20.0

Alignment: STAR 2.7.3a --twopassMode None --outSAMstrandField intronMotif --sjdbScore 2 --outFilterMismatchNoverReadLmax 0.04 --outReadsUnmapped Fastx --outSAMunmapped Within --outSAMtype BAM Unsorted --outSAMmode Full --outSAMattributes NH HI AS NM MD nM jM jI XS --outSAMattrRGline ID:TD006710 LB:TD006710 PL:ILLUMINA PU:Unknown SM:TD006710 CN:MSSM DS:rnaseq --chimOutType Junctions SeparateSAMold --chimSegmentMin 15 --chimJunctionOverhangMin 15

Sort: samtools 1.11

Count: subread (featureCounts) 1.6.3 -t exon -g gene_id -p -s 2 (for exon.geneID.txt)

Note that the above featureCounts parameters are only valid for the exon.geneID.txt files.
Assembly: mm10
Supplementary files format and content: Data files include per-sample counts (feature counts)

source_name: Fetal heart

extract_protocol:
Human adult and fetal heart total RNA was purchased from Takara, catalog numbers 636532 and 636583, respectively
RNA libraries for RNA-seq were prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit following the manufacturer's protocol
One MiSeq Reagent Nano Kit v2 (300 CYS) was used for pool QC and balancing.

value: heart

tag: cell type

value: Cardiac cells

tag: developmental stage

value: fetal


title: Human adult heart

source_name: Adult heart

value: adult


title: iPSC derived sensory neurons

city: Singapore

first: Jeremy

last: Pang

address: 61 Biopolis Drive

country: Singapore

institute: A*STAR

description: Libraries were 150PE sequenced on the Illumina Novaseq platform

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed by Celescope pipeline RNA assay with default parameters to generate filtered single-cell gene expression matrix files (https://github.com/singleron-RD/CeleScope).
Assembly: Homo_sapiens_ensembl_99
Supplementary files format and content: Expression Matrix
Supplementary files format and content: Cell Barcodes
Supplementary files format and content: Gene Information

molecule: polyA RNA

source_name: BJ-iPSC

extract_protocol:
For cell detachment, 46-day old hiPSC-SNs were treated with accutase for 8 min at 37°C and transferred into 15 mL falcon tube before topping up with dPBS to 10 mL and centrifuging at 1000 rpm for 3 min. Supernatant was discarded and hiPSC-SNs were dissociated using papain (Worthington Biochemical) according to manufacturer’s instructions. Briefly, papain digestion was carried out at 37°C with constant agitation for 30 min and with manual pipetting done every 10 min. Cells were spun down at 1000 rpm for 3 min and the supernatant was discarded. The reaction was stopped by re-suspension and incubation in diluted DNase/albumin-inhibitor solution at 37°C for 5 min before spinning down the cells again at 1000 rpm for 3 min and discarding the supernatant. Finally, dissociated cells were resuspended into 500 μL Sensory neuron maturation medium to a concentration of ~ 320 cells/μL and filtered through a 40 µm cell strainer to remove any remaining undissociated cell clumps.
The single-cell suspensions were assessed by acridine orange/propidum iodide staining to contain a cell viability of 97.2%. Using the GEXSCOPE kit, the cells were loaded into microwells of a microfluidic SCOPE-chip and lysed to release mRNA hybridizing to unique barcode sequences on the bead in the same well. The hybridized mRNA was reverse transcribed into cDNA and amplified. The resulting amplified cDNA was fragmented, ligated to adaptors and processed to construct a sequencing library compatible with the Illumina sequencing platform.

tag: cell line

value: BJ-iPSC

value: Induced pluripotent stem cell-derived Sensory neurons

tag: genotype

value: wildtype


title: Se-0 infected by S. sclerotiorum rep 1

source_name: Leaves of 5-week old plants

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB743MWU)

description:
https://www.encodeproject.org/experiments/ENCSR313TWF/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG31365-eGFP fusion proteins.
experiment encode accession: ENCSR313TWF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR027VEH
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB743MWU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG31365

tag: Sex

tag: dev stage

tag: age

value: 0-24 hour

value: Kevin White

value: ENCBS616QNE at ENCODE; https://www.encodeproject.org/ENCBS616QNE/


title: TF ChIP-seq from whole organism (ENCLB191LEP)

description:
https://www.encodeproject.org/experiments/ENCSR143AWF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG18262-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR143AWF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR754KJL
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB191LEP
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG18262

value: pooled male and female

value: embryonic

value: 0-16 hour

tag: lab

value: Kevin White, UChicago

tag: source

tag: link

value: ENCBS588UDM at ENCODE; https://www.encodeproject.org/ENCBS588UDM/


title: Rub infected by S. sclerotiorum rep 3

tag: tissue

value: Rub

tag: treatment

tag: time


title: TF ChIP-seq from whole organism (ENCLB088LJZ)

description:
https://www.encodeproject.org/experiments/ENCSR143AWF/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG18262-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR143AWF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR754KJL
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB088LJZ
size range: 200-800

tag: antibody

tag: biosample encode accession

tag: collection date

value: ENCBS139THK at ENCODE; https://www.encodeproject.org/ENCBS139THK/


title: Rub infected by S. sclerotiorum rep 2

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)


title: TF ChIP-seq from whole organism (ENCLB099FVH)

description:
https://www.encodeproject.org/experiments/ENCSR327NRA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing XND-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR327NRA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR040FYF
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB099FVH
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain QP0661 hermaphrodite young adult 50 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans xnd-1

value: whole organism

tag: geographic location

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

value: hermaphrodite

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS766UQZ at ENCODE; https://www.encodeproject.org/ENCBS766UQZ/


title: TF ChIP-seq from whole organism (ENCLB192TSX)

description:
https://www.encodeproject.org/experiments/ENCSR162MNX/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing TBX-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR162MNX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR896VBS
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB192TSX
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP159 (unc-119(ed3) III; wgIs159) hermaphrodite late embryo 3.5 hours post synchronization using egg bleaching insertion targeting C. elegans tbx-2

value: whole organisms

value: not applicable

tag: encode accession

tag: note

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

value: late embryonic

value: egg bleaching

value: ENCBS059THY at ENCODE; https://www.encodeproject.org/ENCBS059THY/


title: Control ChIP-seq from whole organism (ENCLB099FYH)

description:
https://www.encodeproject.org/experiments/ENCSR142HMN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG12659-eGFP fusion proteins.
experiment encode accession: ENCSR142HMN
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2018-02-01
lab: Kevin White, UChicago
library encode accession: ENCLB099FYH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG12659-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG12659

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12659

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS740ROE at ENCODE; https://www.encodeproject.org/ENCBS740ROE/


title: TF ChIP-seq from whole organism (ENCLB832QGN)

description:
https://www.encodeproject.org/experiments/ENCSR162MNX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing TBX-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR162MNX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR896VBS
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB832QGN
fragmentation methods: sonication (generic microtip)
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: whole organism

value: hermaphrodite

tag: age

value: unknown

tag: lab

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS685HJB at ENCODE; https://www.encodeproject.org/ENCBS685HJB/


title: TF ChIP-seq from whole organism (ENCLB916BMY)

description:
https://www.encodeproject.org/experiments/ENCSR233MSN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing TTX-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR233MSN
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR749OUM
encode release date: 2016-09-29
lab: Valerie Reinke, Yale
library encode accession: ENCLB916BMY
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP68 (unc-119(ed3) III; wgIs68) hermaphrodite late embryo 4 hours post synchronization using egg bleaching insertion targeting C. elegans ttx-3

value: whole organisms

value: not applicable

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

tag: source

value: hour

tag: link

value: ENCBS738LHG at ENCODE; https://www.encodeproject.org/ENCBS738LHG/


title: Ra-0 infected by S. sclerotiorum rep 3

tag: tissue

value: Leaves of 5-week old plants

tag: genotype

tag: treatment

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: T8

city: Shanghai

first: Zeng

last: Ye

address: 270 Dongan Road, Xuhui District

country: China

institute: Fudan University Shanghai Cancer Center

description: 10x Genomincs

data_processing:
Sequencing depth was normalized by using CellRanger (version v3.1.0).
We used Seurat package (version 3.0)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: pancreatic neuroendocrine tumor

extract_protocol:
During surgery, immediately after the tissue specimens were isolated, the tissue specimens were cuted and kept in MACS Tissue Storage Solution (Miltenyi Biotec) for further processing. Tissue specimens were processed as described below. Briefly, specimen was first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1 mm3) on ice and enzymatically digested with collagenase I (Worthington) and DNase I (Worthington) for 45 min at 37°C, with agitation. After digestion, specimen was sieved through a 70 µm cell strainer, and centrifuged at 300 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec).
The scRNA-seq libraries and V(D)J libraries were generated using the 10x Genomics Chromium Controller Instrument and Chromium Single Cell 5’ library & gel bead kit, along with the V(D)J enrichment kit (10x Genomics). Briefly, cells were concentrated to 1000 cells/µL and approximately 10,000 cells were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), which resulted in expected mRNA barcoding of 6,000 single-cells for each specimen. After the reverse transcription step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was used to construct 5’ gene expression libraries and TCR and BCR enriched libraries. For 5’ library construction, the amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by a NextSeq2000 sequencer (Illumina) on a 150 bp paired-end run.

value: pancreatic neuroendocrine tumor

value: transcriptomics

value: no


title: H1

description: 10x Genomincs

source_name: liver metastases

value: liver metastases


title: T9

description: 10x Genomincs


title: H2

description: 10x Genomincs


title: TF ChIP-seq from whole organism (ENCLB342KXM)

description:
https://www.encodeproject.org/experiments/ENCSR038HZR/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CoRest-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR038HZR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR073DRW
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB342KXM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

value: CoRest

value: whole organism

tag: biosample encode accession

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

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS023IXI at ENCODE; https://www.encodeproject.org/ENCBS023IXI/


title: Ra-0 infected by S. sclerotiorum rep 2

tag: time


title: TF ChIP-seq from whole organism (ENCLB974YVK)

description:
https://www.encodeproject.org/experiments/ENCSR233MSN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing TTX-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR233MSN
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR749OUM
encode release date: 2016-09-29
lab: Valerie Reinke, Yale
library encode accession: ENCLB974YVK
fragmentation methods: sonication (generic microtip)

value: whole organisms

tag: collection date

value: not applicable

tag: geographic location

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

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

value: hour

value: ENCBS282ILL at ENCODE; https://www.encodeproject.org/ENCBS282ILL/


title: T6

description: 10x Genomincs

value: pancreatic neuroendocrine tumor

value: transcriptomics

value: no


title: TF ChIP-seq from whole organism (ENCLB227DVM)

description:
https://www.encodeproject.org/experiments/ENCSR327NRA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing XND-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR327NRA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR040FYF
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB227DVM
fragmentation methods: sonication (generic microtip)

value: whole organism

tag: encode accession

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

value: young adult

value: L1 larva starved after bleaching

tag: post synchronization time

tag: post synchronization time units

value: ENCBS561CQM at ENCODE; https://www.encodeproject.org/ENCBS561CQM/


title: T5

description: 10x Genomincs


title: Ra-0 infected by S. sclerotiorum rep 1

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB521PWY)

description:
https://www.encodeproject.org/experiments/ENCSR041BTW/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing MXL-1-eGFP fusion proteins.
experiment encode accession: ENCSR041BTW
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB521PWY
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP537 (unc-119(tm4063) III; wgIs537) hermaphrodite young adult 67 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans mxl-1

value: whole organisms

value: not applicable

tag: note

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

tag: Sex

value: hermaphrodite

tag: dev stage

value: unknown

value: ENCBS783IGT at ENCODE; https://www.encodeproject.org/ENCBS783IGT/


title: Pn-0 infected by S. sclerotiorum rep 3


title: T4

description: 10x Genomincs

value: pancreatic neuroendocrine tumor


title: TF ChIP-seq from whole organism (ENCLB245WIL)

description:
https://www.encodeproject.org/experiments/ENCSR310ZJI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR310ZJI
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR381FHL
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB245WIL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain bsh-GFP embryo (10-12 hours) insertion targeting D. melanogaster bsh

value: bsh

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

value: not collected

value: embryonic

tag: age

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS311MGJ at ENCODE; https://www.encodeproject.org/ENCBS311MGJ/


title: TF ChIP-seq from whole organism (ENCLB062QDB)

description:
https://www.encodeproject.org/experiments/ENCSR038HZR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CoRest-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR038HZR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR073DRW
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB062QDB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: CoRest

value: whole organism

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

value: pooled male and female

value: 0-24 hour

tag: link

value: ENCBS371PXV at ENCODE; https://www.encodeproject.org/ENCBS371PXV/


title: Control ChIP-seq from whole organism (ENCLB296HOG)

description:
https://www.encodeproject.org/experiments/ENCSR139WZD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR139WZD
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB296HOG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG8388-GFP mixed sex embryo (0-14 hours) insertion targeting D. melanogaster CG8388

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8388

value: 0-14 hour

value: ENCBS180NHE at ENCODE; https://www.encodeproject.org/ENCBS180NHE/


title: TF ChIP-seq from whole organism (ENCLB881ZZS)

description:
https://www.encodeproject.org/experiments/ENCSR310ZJI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR310ZJI
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR381FHL
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB881ZZS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: bsh

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

value: ENCBS468XJR at ENCODE; https://www.encodeproject.org/ENCBS468XJR/


title: Control ChIP-seq from whole organism (ENCLB955FRV)

description:
https://www.encodeproject.org/experiments/ENCSR040FYF/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing XND-1-eGFP fusion proteins.
experiment encode accession: ENCSR040FYF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB955FRV
fragmentation methods: sonication (generic microtip)

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

value: hermaphrodite

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS942MVY at ENCODE; https://www.encodeproject.org/ENCBS942MVY/