title: TF ChIP-seq from whole organism (ENCLB007KOU)

description:
https://www.encodeproject.org/experiments/ENCSR295UVI/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8145-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR295UVI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR735CQR
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB007KOU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG8145-GFP mixed sex embryo (0-10 hours) insertion targeting D. melanogaster nom

tag: antibody

value: nom

tag: biosample encode accession

tag: collection date

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8145

value: pooled male and female

value: embryonic

value: 0-10 hour

tag: lab

tag: source

value: Kevin White

value: ENCBS131LNN at ENCODE; https://www.encodeproject.org/ENCBS131LNN/


title: TF ChIP-seq from whole organism (ENCLB302OTZ)

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/ENCSR296MRL/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG17385-eGFP fusion proteins.
experiment encode accession: ENCSR296MRL
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR174KFQ
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB302OTZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

library_source: genomic

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

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strain CG17385-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG17385

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 CG17385

tag: Sex

tag: dev stage

tag: age

value: 0-24 hour

value: Kevin White, UChicago

tag: link

value: ENCBS710WUG at ENCODE; https://www.encodeproject.org/ENCBS710WUG/


title: LSL rep2

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
The genome of Lactuca sativa (version: Lsativa_467_v5) from JGI (Joint Genome Institute, Berkeley, USA) was used as the reference genome for RNA-seq analysis. The cleaned reads of each sample were mapped individually to the reference sequences using the STAR package
The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2) (Anders et al., 2015), samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates, choose and count uniquely mapped reads for gene expression analysis
The counted reads of each gene were analyzed by a DESeq2-based R pipeline. Differentially expressed (DE) genes were analyzed in a pairwise comparison between genotypes 60814 and ‘Okeechobee’ samples. Transcripts per million (TPM) counts were averaged across biological replicates and genes were filtered for moderate expression (TPM ≥ 100) in at least one genotype.
Assembly: Arabidopsis thaliana , version: Lsativa_467_v5
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

molecule: total RNA

organism: Lactuca sativa

source_name: leaf

growth_protocol: Lettuce plants were grown in 4-inch pots in a growth chamber maintained with a 16 h day light cycle at 22 ºC.

extract_protocol: Upon reaching maturity, RNA was extracted using the Nucleospin RNA Plant and Fungi kit (Machery-Nagel, Düren, Germany) with on-column DNase treatment, and initial quantification and quality was checked on a NanoDrop OneC spectrophotometer

treatment_protocol: Three romaine lettuces (Lactuca sativa var. Longifolia) grown in Belle Glade, FL were selected for leaf tissue histological analysis, including the commercial cultivars ‘Manatee’, and ‘Okeechobee’ and an experimental breeding line named 60184. These accessions were selected from a larger set of romaine accessions based on genotypic variability in their shelf life

tag: tissue

value: leaf

tag: location

value: Belle Glade, FL

tag: tissue type

value: mature

tag: genotype

value: Okeechobee (LSL)


title: TF ChIP-seq from whole organism (ENCLB195OXG)

description:
https://www.encodeproject.org/experiments/ENCSR295UVI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8145-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR295UVI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR735CQR
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB195OXG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: nom

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8145

value: ENCBS094UJP at ENCODE; https://www.encodeproject.org/ENCBS094UJP/


title: LSL rep1


title: Vikl-012_SVR_post

city: Kanazawa

first: Kazunori

last: Kawaguchi

address: 13-1 Takara-Machi

department: Gastroenterology

country: Japan

institute: Kanazawa University

data_processing:
Flow cell specified by manufacture were used for sequencing. Read length was 151bp (valid read length was 150bp).
transcribed region was obtained.
Assembly: human NCBI build37.2
Supplementary files format and content: GTF format: transcribed region was included for each sample.

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

extract_protocol:
total RNA was isolated from PBMCs, 1.2x10^7 to 2.8x10^ per sample,  collected in PAXgene (Becton Dickinson) using a PAXgene Blood RNA Kit (QIAGEN, Valencia, CA).
RNA libraries for RNA-seq were prepared using TruSeq Standard mRNA Library Prep kit (illumina) following manufacture's protocols. Library length was 310~387bp.

tag: cell type

value: peripheral blood mononuclear cells

tag: treatment

value: ombitasvir/paritaprevir/ritonavir

tag: group


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

city: Castanet-Tolosan

first: Florent

last: Delplace

address: 24 chemin de Borde Rouge

country: France

institute: INRAe

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

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.

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB857VAA)

description:
https://www.encodeproject.org/experiments/ENCSR130GIJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG17829-eGFP fusion proteins.
experiment encode accession: ENCSR130GIJ
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB857VAA
size range: 200-800

source_name: Drosophila melanogaster strain CG17829 mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG17829

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG17829

value: pooled male and female

value: embryonic

value: Kevin White

value: ENCBS832OMC at ENCODE; https://www.encodeproject.org/ENCBS832OMC/


title: Control ChIP-seq from whole organism (ENCLB144LIN)

description:
https://www.encodeproject.org/experiments/ENCSR130OWB/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG6765-eGFP fusion proteins.
experiment encode accession: ENCSR130OWB
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB144LIN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG6765-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG6765

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG6765

value: 0-24 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: ENCBS597AGW at ENCODE; https://www.encodeproject.org/ENCBS597AGW/


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


title: Vikl-012_SVR_pre

value: peripheral blood mononuclear cells


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


title: TF ChIP-seq from whole organism (ENCLB984APN)

description:
https://www.encodeproject.org/experiments/ENCSR295CRU/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing MESR4-eGFP fusion proteins.
experiment encode accession: ENCSR295CRU
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR943ZYI
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB984APN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain MESR4-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster MESR4

tag: antibody

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to MESR4

tag: Sex

tag: dev stage

value: ENCBS844WZY at ENCODE; https://www.encodeproject.org/ENCBS844WZY/


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

tag: tissue

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)


title: Vikl-009_SVR_post

value: ombitasvir/paritaprevir/ritonavir


title: ISL rep3

value: leaf

tag: location

value: Belle Glade, FL

tag: tissue type

value: mature

value: Manatee (ISL)


title: Vikl-009_SVR_pre

tag: cell type


title: Vikl-010_SVR_post

tag: treatment


title: ISL rep1

tag: genotype


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

tag: time

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB275WUA)

description:
https://www.encodeproject.org/experiments/ENCSR295CRU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing MESR4-eGFP fusion proteins.
experiment encode accession: ENCSR295CRU
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR943ZYI
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB275WUA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

tag: biosample encode accession

value: not applicable

value: pooled male and female

value: embryonic

tag: age

value: Kevin White

tag: link

value: ENCBS707RXO at ENCODE; https://www.encodeproject.org/ENCBS707RXO/


title: LSL rep3

value: Okeechobee (LSL)


title: TF ChIP-seq from whole organism (ENCLB971SWY)

description:
https://www.encodeproject.org/experiments/ENCSR028DHQ/
***************
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: ENCSR028DHQ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR137DAC
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB971SWY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG12299 embryo (0-24 hours) insertion targeting D. melanogaster CG12299

tag: collection date

tag: geographic location

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12299

value: not collected

value: 0-24 hour

value: Kevin White, UChicago

value: ENCBS162OPS at ENCODE; https://www.encodeproject.org/ENCBS162OPS/


title: ZT91 Senescent bio rep 1

city: Melbourne

first: Christopher

middle: Robert

last: Buckley

state: VIC

address: School of BioSciences, Level 3, Building 184, The University of Melbourne

country: Australia

institute: University of Melbourne

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT91_S_R1

data_processing:
bcl2fastq 2.17. Raw data was filtered as follows: (1) Discard pair-end reads with adapter; (2) Discard pair-end reads when the content of N bases is more than 10% in either read; (3) Discard pair-end reads when the ration of bases of low quality (Q<20) is more than 0.5 in either read.
STAR. Filtered reads were mapped to the T. aestivum cv. Mace (PGSBv2.1) genome sequence and annotation using STAR with default parameters
Cufflinks. Mapped reads were quantified and normalised using the cuffquant and cuffnorm modules of Cufflinks with default parameters
Assembly: Triticum aestivum cv. Mace. Genbank assembly ID:  GCA_903994175.1
Supplementary files format and content: tab-delimited text file includes raw counts for mature samples
Supplementary files format and content: tab-delimited text file includes raw counts for senescent samples
Supplementary files format and content: tab-delimited text file includes fpkm for mature samples
Supplementary files format and content: tab-delimited text file includes fpkm for senescent samples

organism: Triticum aestivum

source_name: whole flag leaf

growth_protocol: Seeds were chilled at 4°C for 48 h and sown in a mix of sterilised potting soil with 4.5 g/L Osmocote 6-9 month slow-release fertiliser. Growth room was set to 12 h light (200-280 µmol m-2 s-1, 20ºC), 12 h dark (15ºC) prior to switch to continuous conditions.

extract_protocol:
Frozen leaf tissue was ground to a fine powder in liquid nitrogen-cooled mortar and pestles. Lysate buffer was added to the tissue (350 µL per 100 mg of tissue) and the mixture was vortexed immediately. RNA was extracted using ISOLATE II RNA Plant Kit (Meridian Bioscience). RNA from two individual leaf samples was equally pooled to provide two replicates for sequencing.
Library preparation and RNA-sequencing was performed by a commercial provider (Azenta). Library preparations were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs; NEB).

treatment_protocol: When plants had concurrently reached the mature and senescent developmental stages, at dawn (Zeitgeber Time 0; ZT0), the growth room was set to continuous light and temperature (20ºC) and whole flag leaves from the primary tiller of four plants were collected every 2 h from ZT45 to ZT91 (48 h).

value: whole flag leaf

tag: cultivar

value: Mace

value: Senescent leaf


title: Vikl-010_SVR_pre

value: peripheral blood mononuclear cells

tag: group


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

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: ZT91 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT91_S_R2


title: Control ChIP-seq from whole organism (ENCLB487ZHX)

description:
https://www.encodeproject.org/experiments/ENCSR027VEH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG31365-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR027VEH
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB487ZHX
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

value: not applicable

tag: note

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

tag: Sex

value: pooled male and female

tag: lab

tag: source

value: ENCBS869BEE at ENCODE; https://www.encodeproject.org/ENCBS869BEE/


title: Bla-1 infected by S. sclerotiorum rep 4

tag: tissue


title: Vikl-043_SVR_pre

tag: cell type


title: Vikl-078_SVR_post

tag: treatment

value: ombitasvir/paritaprevir/ritonavir


title: Ang-0 infected by S. sclerotiorum rep 4

tag: genotype


title: TF ChIP-seq from whole organism (ENCLB737CBD)

description:
https://www.encodeproject.org/experiments/ENCSR027AMS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG12659-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR027AMS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR142HMN
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB737CBD
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

tag: antibody

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

tag: dev stage

value: embryonic

value: 0-24 hour

value: Kevin White

value: ENCBS964OSN at ENCODE; https://www.encodeproject.org/ENCBS964OSN/


title: ISL rep2

value: leaf

tag: location

value: Belle Glade, FL

tag: tissue type

value: mature

value: Manatee (ISL)


title: ZT91 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT91_M_R2

value: whole flag leaf

value: Mace

value: Mature leaf

tag: time


title: Vikl-078_SVR_pre

value: peripheral blood mononuclear cells


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

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: ZT91 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT91_M_R1


title: Vikl-057_SVR_post

value: ombitasvir/paritaprevir/ritonavir


title: ZT89 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT89_S_R2

value: Senescent leaf


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


title: ZT89 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT89_S_R1


title: Vikl-057_SVR_pre


title: TF ChIP-seq from whole organism (ENCLB222YIT)

description:
https://www.encodeproject.org/experiments/ENCSR027AMS/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG12659-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR027AMS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR142HMN
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB222YIT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

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

value: pooled male and female

value: embryonic

tag: age

value: Kevin White, UChicago

tag: link

value: ENCBS849JFV at ENCODE; https://www.encodeproject.org/ENCBS849JFV/


title: TF ChIP-seq from whole organism (ENCLB579LOW)

description:
https://www.encodeproject.org/experiments/ENCSR027AMS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG12659-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR027AMS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR142HMN
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB579LOW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: encode accession

tag: note

tag: Sex

value: 0-24 hour

value: Kevin White

value: ENCBS818YEZ at ENCODE; https://www.encodeproject.org/ENCBS818YEZ/


title: TF ChIP-seq from whole organism (ENCLB366ENP)

description:
https://www.encodeproject.org/experiments/ENCSR128VHN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dsx-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR128VHN
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR122CCQ
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB366ENP
size range: 200-800

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

value: dsx

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

value: prepupa

value: 24 hour

tag: lab

tag: source

value: ENCBS351DHQ at ENCODE; https://www.encodeproject.org/ENCBS351DHQ/


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

tag: tissue

value: Leaves of 5-week old plants

tag: treatment

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: ZT89 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT89_M_R1

value: whole flag leaf

tag: cultivar

value: Mace

value: Mature leaf


title: Uninfected Ws-0 rep 3

tag: genotype

value: Uninfected (LNI)


title: TF ChIP-seq from whole organism (ENCLB023DQE)

description:
https://www.encodeproject.org/experiments/ENCSR028DHQ/
***************
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: ENCSR028DHQ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR137DAC
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB023DQE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12299

value: not collected

tag: dev stage

value: embryonic

value: Kevin White, UChicago

value: ENCBS027LKQ at ENCODE; https://www.encodeproject.org/ENCBS027LKQ/


title: TF ChIP-seq from whole organism (ENCLB654ZQW)

description:
https://www.encodeproject.org/experiments/ENCSR128VHN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dsx-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR128VHN
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR122CCQ
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB654ZQW
size range: 200-800

value: dsx

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

value: pooled male and female

value: prepupa

value: 24 hour

value: Kevin White

value: ENCBS161IOE at ENCODE; https://www.encodeproject.org/ENCBS161IOE/


title: Vikl-104_SVR_pre

tag: cell type

value: peripheral blood mononuclear cells

tag: group


title: Uninfected Ws-0 rep 2

value: Leaves of 5-week old plants

value: Uninfected (LNI)

tag: time

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB178AJY)

description:
https://www.encodeproject.org/experiments/ENCSR128VHN/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dsx-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR128VHN
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR122CCQ
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB178AJY
size range: 200-800

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS110OAL at ENCODE; https://www.encodeproject.org/ENCBS110OAL/


title: ZT87 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT87_S_R2

value: whole flag leaf

value: Mace

value: Senescent leaf


title: Vikl-044_SVR_post

value: ombitasvir/paritaprevir/ritonavir


title: TF ChIP-seq from whole organism (ENCLB130EDI)

description:
https://www.encodeproject.org/experiments/ENCSR128VHN/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dsx-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR128VHN
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR122CCQ
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB130EDI
size range: 200-800

value: dsx

tag: encode accession

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

value: pooled male and female

tag: age

value: Kevin White, UChicago

tag: link

value: ENCBS344ZCK at ENCODE; https://www.encodeproject.org/ENCBS344ZCK/


title: ZT87 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT87_S_R1


title: Uninfected Wa-1 rep 3


title: Vikl-044_SVR_pre

value: peripheral blood mononuclear cells


title: Uninfected Ws-0 rep 1

value: Leaves of 5-week old plants


title: TF ChIP-seq from whole organism (ENCLB492EYA)

description:
https://www.encodeproject.org/experiments/ENCSR025MAQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ATbp-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR025MAQ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR082WMZ
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB492EYA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: ATbp

tag: note

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

tag: Sex

value: embryonic

value: 0-14 hour

tag: lab

value: Kevin White

value: ENCBS959QWU at ENCODE; https://www.encodeproject.org/ENCBS959QWU/


title: ZT87 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT87_M_R2

tag: tissue

value: whole flag leaf

tag: treatment

value: Mature leaf


title: TF ChIP-seq from whole organism (ENCLB220KNO)

description:
https://www.encodeproject.org/experiments/ENCSR025MAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ATbp-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR025MAQ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR082WMZ
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB220KNO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

tag: source

value: ENCBS754RCQ at ENCODE; https://www.encodeproject.org/ENCBS754RCQ/


title: ZT87 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT87_M_R1

tag: cultivar

value: Mace


title: ZT89 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT89_M_R2


title: Vikl-086_SVR_post

value: ombitasvir/paritaprevir/ritonavir


title: Vikl-086_SVR_pre


title: Uninfected Wa-1 rep 2

tag: genotype

value: Uninfected (LNI)

value: 24 hours


title: ZT85 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT85_S_R2

value: Senescent leaf


title: Uninfected Van-0 rep 3

value: Leaves of 5-week old plants


title: Uninfected Wa-1 rep 1


title: Vikl-104_SVR_post

tag: cell type

value: peripheral blood mononuclear cells


title: Control ChIP-seq from whole organism (ENCLB594ZAT)

description:
https://www.encodeproject.org/experiments/ENCSR125WOY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing D-eGFP fusion proteins.
experiment encode accession: ENCSR125WOY
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB594ZAT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

value: pooled male and female

tag: dev stage

value: embryonic

value: Kevin White, UChicago

value: ENCBS623YMG at ENCODE; https://www.encodeproject.org/ENCBS623YMG/


title: Uninfected Van-0 rep 2

tag: time


title: Control ChIP-seq from whole organism (ENCLB165QNW)

description:
https://www.encodeproject.org/experiments/ENCSR293DLH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG32006-eGFP fusion proteins.
experiment encode accession: ENCSR293DLH
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB165QNW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG32006-GFP mixed sex prepupa (48 days) insertion targeting D. melanogaster CG32006

tag: biosample encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG32006

value: prepupa

value: 48 day

value: Kevin White

value: ENCBS072RHB at ENCODE; https://www.encodeproject.org/ENCBS072RHB/


title: Vikl-045_SVR_pre

tag: group


title: ZT85 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT85_M_R2

value: whole flag leaf

value: Mace

value: Mature leaf


title: ZT85 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT85_S_R1


title: TF ChIP-seq from whole organism (ENCLB376JYB)

description:
https://www.encodeproject.org/experiments/ENCSR125NWX/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing nmo-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR125NWX
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR072UGA
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB376JYB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

value: nmo

value: whole organism

value: whole organisms

tag: collection date

value: not applicable

tag: geographic location

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

value: 0-24 hour

value: ENCBS088RUU at ENCODE; https://www.encodeproject.org/ENCBS088RUU/


title: TF ChIP-seq from whole organism (ENCLB344PPW)

description:
https://www.encodeproject.org/experiments/ENCSR125NWX/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing nmo-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR125NWX
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR072UGA
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB344PPW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: encode accession

value: pooled male and female

value: embryonic

tag: age

value: Kevin White, UChicago

tag: link

value: ENCBS489RWC at ENCODE; https://www.encodeproject.org/ENCBS489RWC/


title: Vikl-013_SVR_pre

value: peripheral blood mononuclear cells


title: Uninfected Van-0 rep 1

value: Leaves of 5-week old plants

value: Uninfected (LNI)

value: 24 hours


title: Uninfected Se-0 rep 3


title: Control ChIP-seq from whole organism (ENCLB348HOM)

description:
https://www.encodeproject.org/experiments/ENCSR292YZL/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing nau-eGFP fusion proteins.
experiment encode accession: ENCSR292YZL
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB348HOM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain nau-GFP mixed sex embryo (4-24 hours) insertion targeting D. melanogaster nau

tag: note

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

tag: Sex

tag: lab

value: Kevin White

value: ENCBS283KXC at ENCODE; https://www.encodeproject.org/ENCBS283KXC/


title: Vikl-029_SVR_post

tag: treatment

value: ombitasvir/paritaprevir/ritonavir


title: ZT83 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT83_S_R2

tag: tissue

value: whole flag leaf

tag: cultivar

value: Mace

value: Senescent leaf


title: ZT83 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT83_S_R1


title: Uninfected Se-0 rep 2

tag: genotype


title: TF ChIP-seq from whole organism (ENCLB510PQZ)

description:
https://www.encodeproject.org/experiments/ENCSR292WNJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing pfk-eGFP fusion proteins.
experiment encode accession: ENCSR292WNJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR268FFL
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB510PQZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG15812-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG15812

value: pfk

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG15812

tag: dev stage

value: 0-24 hour

tag: source

value: ENCBS212JNR at ENCODE; https://www.encodeproject.org/ENCBS212JNR/


title: Vikl-029_SVR_pre

tag: cell type

value: peripheral blood mononuclear cells


title: Vikl-045_SVR_post

tag: group


title: TF ChIP-seq from whole organism (ENCLB281MJB)

description:
https://www.encodeproject.org/experiments/ENCSR292WNJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing pfk-eGFP fusion proteins.
experiment encode accession: ENCSR292WNJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR268FFL
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB281MJB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

tag: biosample encode accession

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: ENCBS336DHU at ENCODE; https://www.encodeproject.org/ENCBS336DHU/


title: ZT83 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT83_M_R2

value: Mature leaf

tag: time


title: Vikl-015_SVR_post

value: ombitasvir/paritaprevir/ritonavir


title: Uninfected Rub rep 3

value: Leaves of 5-week old plants

value: Rub

value: Uninfected (LNI)

value: 24 hours


title: ZT83 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT83_M_R1

value: whole flag leaf

value: Mace


title: Control ChIP-seq from whole organism (ENCLB533SGI)

description:
https://www.encodeproject.org/experiments/ENCSR022ZVU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Fer1-eGFP fusion proteins.
experiment encode accession: ENCSR022ZVU
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB533SGI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Fer1-GFP mixed sex embryo (6-24 hours) insertion targeting D. melanogaster Fer1

value: whole organism

value: whole organisms

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Fer1

value: Kevin White

value: ENCBS739HVR at ENCODE; https://www.encodeproject.org/ENCBS739HVR/


title: Vikl-015_SVR_pre

source_name: peripheral blood mononuclear cells

value: peripheral blood mononuclear cells


title: Vikl-013_SVR_post


title: Uninfected Rub rep 1

source_name: Leaves of 5-week old plants


title: Uninfected Rub rep 2


title: TF ChIP-seq from whole organism (ENCLB020WFU)

description:
https://www.encodeproject.org/experiments/ENCSR021VXG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10209-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR021VXG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR733CQH
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB020WFU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG10209-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG10209

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10209

value: pooled male and female

value: embryonic

tag: age

value: 0-24 hour

value: Kevin White, UChicago

tag: link

value: ENCBS643OYY at ENCODE; https://www.encodeproject.org/ENCBS643OYY/


title: ZT81 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT81_S_R2

tag: treatment

value: Senescent leaf


title: Vikl-040_SVR_post

value: ombitasvir/paritaprevir/ritonavir


title: ZT85 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT85_M_R1

tag: tissue

value: whole flag leaf

value: Mature leaf


title: ZT81 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT81_S_R1

tag: cultivar

value: Mace


title: TF ChIP-seq from whole organism (ENCLB708WAU)

description:
https://www.encodeproject.org/experiments/ENCSR021VXG/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10209-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR021VXG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR733CQH
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB708WAU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

tag: Sex

tag: lab

value: ENCBS268SZY at ENCODE; https://www.encodeproject.org/ENCBS268SZY/


title: Vikl-040_SVR_pre


title: Uninfected Ra-0 rep 3

value: Leaves of 5-week old plants

tag: genotype

value: Uninfected (LNI)

value: 24 hours


title: Vikl-085_SVR_post

tag: cell type

value: peripheral blood mononuclear cells


title: ZT81 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT81_M_R2


title: TF ChIP-seq from whole organism (ENCLB487ESU)

description:
https://www.encodeproject.org/experiments/ENCSR021VXG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10209-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR021VXG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR733CQH
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB487ESU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10209

value: pooled male and female

tag: dev stage

tag: source

value: Kevin White

value: ENCBS372KSB at ENCODE; https://www.encodeproject.org/ENCBS372KSB/


title: Vikl-085_SVR_pre

tag: group


title: ZT81 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT81_M_R1

tag: time


title: Uninfected Se-0 rep 1


title: TF ChIP-seq from whole organism (ENCLB702QHB)

description:
https://www.encodeproject.org/experiments/ENCSR199TFG/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing tj-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR199TFG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR414VZP
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB702QHB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain tj-GFP female adult insertion targeting D. melanogaster tj

tag: antibody

value: tj

tag: biosample encode accession

tag: collection date

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

value: female

value: adult

value: unknown

value: Kevin White, UChicago

value: ENCBS482RZK at ENCODE; https://www.encodeproject.org/ENCBS482RZK/


title: ZT79 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT79_S_R2

value: whole flag leaf

value: Mace

value: Senescent leaf


title: Vikl-060_SVR_post

value: ombitasvir/paritaprevir/ritonavir


title: Uninfected Ra-0 rep 2

value: Leaves of 5-week old plants

value: Uninfected (LNI)

value: 24 hours


title: Vikl-060_SVR_pre

value: peripheral blood mononuclear cells


title: Uninfected Pn-0 rep 3


title: Uninfected Pn-0 rep 2


title: ZT79 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT79_S_R1


title: TF ChIP-seq from whole organism (ENCLB010EGP)

description:
https://www.encodeproject.org/experiments/ENCSR199TFG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing tj-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR199TFG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR414VZP
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB010EGP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

tag: geographic location

tag: encode accession

tag: note

value: Kevin White

value: ENCBS836MUB at ENCODE; https://www.encodeproject.org/ENCBS836MUB/


title: Vikl-041_SVR_post

tag: treatment


title: TF ChIP-seq from whole organism (ENCLB529OGF)

description:
https://www.encodeproject.org/experiments/ENCSR292EYZ/
***************
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: ENCSR292EYZ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR119OOH
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB529OGF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain lola-J-GFP mixed sex embryo (0-12 hours) insertion targeting D. melanogaster lola

value: lola

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

value: pooled male and female

value: embryonic

tag: age

value: 0-12 hour

tag: link

value: ENCBS626ZJG at ENCODE; https://www.encodeproject.org/ENCBS626ZJG/


title: ZT79 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT79_M_R1

tag: tissue

value: whole flag leaf

tag: cultivar

value: Mace

value: Mature leaf


title: Uninfected Oy-0 rep 3

value: Leaves of 5-week old plants

tag: genotype

value: Uninfected (LNI)


title: ZT77 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT77_S_R2

value: Senescent leaf


title: Vikl-075_SVR_post

tag: cell type

value: peripheral blood mononuclear cells

value: ombitasvir/paritaprevir/ritonavir


title: Uninfected Oy-0 rep 2

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB132ULZ)

description:
https://www.encodeproject.org/experiments/ENCSR125CNZ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing D19A-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR125CNZ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR863DOB
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB132ULZ
size range: 200-800

source_name: Drosophila melanogaster strain D19A mixed sex embryo (0-20 hours) insertion targeting D. melanogaster D19A

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to D19A

tag: Sex

tag: dev stage

value: 0-20 hour

tag: lab

value: Kevin White, UChicago

value: Kevin White

value: ENCBS648AIP at ENCODE; https://www.encodeproject.org/ENCBS648AIP/


title: TF ChIP-seq from whole organism (ENCLB223KXD)

description:
https://www.encodeproject.org/experiments/ENCSR125CNZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing D19A-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR125CNZ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR863DOB
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB223KXD
size range: 200-800

value: pooled male and female

value: embryonic

tag: source

value: ENCBS465MYP at ENCODE; https://www.encodeproject.org/ENCBS465MYP/


title: Vikl-075_SVR_pre

tag: group


title: Uninfected Ra-0 rep 1

value: Leaves of 5-week old plants

tag: time


title: TF ChIP-seq from whole organism (ENCLB318MDX)

description:
https://www.encodeproject.org/experiments/ENCSR199TFG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing tj-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR199TFG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR414VZP
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB318MDX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: tj

tag: biosample encode accession

tag: collection date

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

value: female

value: adult

value: unknown

value: ENCBS845OFO at ENCODE; https://www.encodeproject.org/ENCBS845OFO/


title: ZT77 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT77_M_R2

source_name: whole flag leaf

value: whole flag leaf

value: Mace

value: Mature leaf


title: NGN2_AroLITE_24h_r3 TT-Slamseq

city: Berlin

first: Alexandre

middle: P

last: Magalhaes

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 AroLITE 24h replicate 3

data_processing:
Raw reads were filtered and trimmed as described above for BulkRNAseq samples. Filtered reads were aligned using STAR v2.7.9a with parameters ‘–outFilterMultimapNmax 50–outReadsUnmapped Fastx’ to the SILVA database69 (downloaded 6 March 2020) to remove rRNA content. Unaligned reads were afterwards reverse-complemented using the seqtk ‘seq’ v 1.3-r106 using the ‘-r’ parameter (https://github.com/lh3/seqtk). Reverse-complemented reads were processed using SLAM-DUNK  with the ‘all’ pipeline v0.4.1 using the ‘-rl 100 -5 0’ parameters with the GENCODE gene annotation v39 as ‘-b’ option. Reads with a ‘T > C’ conversion representing nascent transcription were filtered from the BAM files using alleyoop with the ‘read-separator’ command. Counts per gene were quantified based on the ‘T > C’-converted reads using featureCounts v 2.0.6 97 using -s 1 and -t gene parameters for stranded and gene body counting.
Supplementary files format and content: NGN2_TTslamseq_Counts_gene.csv has the counts on gene body
Library strategy: TT-Slamseq

growth_protocol: We adapted our protocol for the differentiation of human iPSCs into neurons by overexpression of NGN2 from 41. ZIP13K2 cells with integrated NGN2 overexpression cassette were cultured on Matrigel (Corning) pre-coated 10 cm culture plates. When cultures reached a confluency of approximately 80%, 2 μg/mL Doxycycline (Sigma) was added to the culture medium to induce expression of the NGN2 transgene. After 24 hours, induced cultures were sorted for mEGFP expressing cells by flow cytometry. Positive cells were seeded on Matrigel pre-coated 96-well microclear plates (Greiner bio-one) in mTeSR+ and 1x Rho-kinase inhibitor at a density of 2x104 cells / cm2. On day 2, mTeSR+ medium was replaced by N2B27 neural cell culture medium supplemented with 5 g/ml human BDNF (biotechne). Differentiation medium was changed every day for a total of 4 days. Living cells were stained with 0.25 g/ml Hoechst and Spy650-TUB (1:2000) (Spirochrome) and incubated in the microscope prior to image acquisition to equilibrate and thermalize all materials

extract_protocol:
Total RNA was extracted with Trizol (Ambion) and 24:1 chloroform:isoamylalcohol (Sigma) while using 0.1 mM dithiothreitol (DTT) in isopropanol precipitation and ethanol washes. For each sample, 50 µg of total RNA was fragmented with Magnesium RNA Fragmentation Module (NEB), and fragmentation buffer was removed from samples with ethanol precipitation in presence of 0.1 mM DTT. RNA was then resuspended in 350 µl RNase-free water, diluted in biotinylation buffer (200 mM HEPES pH 7.5, and 10 mM EDTA) and topped up with 5 µg MTS-Biotin (previously diluted to 50 µg ml–1 in dimethylformamide) to reach a final volume of 500 µl. The biotinylation reaction was incubated for 30 min at room temperature while keeping samples in rotation and protected from light. Unbound biotin was removed with acid-phenol:chloroform extraction (125:24:1, Ambion) and isopropanol precipitation. Biotinylated RNA was resuspended in 100 µl RNase-free water, denatured in 65 °C for 10 min and then cooled on ice for 5 min. The biotinylated RNA was captured with 100 µl µMACS streptavidin beads (Miltenyi) by incubating for 15 min in rotation while keeping samples protected from light. µMACS columns were equilibrated on magnetic stand with nucleic acid equilibration buffer and two times with biotinylation buffer (20 mM HEPES, 1 mM EDTA, pH 8). Beads were transferred to columns and washed three times with wash buffer (100 mM Tris-HCl pH 7.5, 10 mM EDTA, 1 M NaCl and 0.1 % Tween 20), and labeled RNA was eluted twice with a total 200 µl of 100 mM DTT. RNA was cleaned up with RNeasy Minelute columns (Qiagen) and eluted to RNase-free water with 1 mM DTT. 4sU residues of RNA were alkylated with iodoacetamide treatment (10 mM iodoacetamide in 50 mM NaPO4, pH 8 and 50 % DMSO) by incubating samples in 50 °C for 15 min, followed by quenching with 20 mM DTT. RNA samples were purified with ethanol precipitation and treated with Turbo DNase (Invitrogen).
Sequencing libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit and NEBNext Multiplex Oligos (NEB), according to manufacturer’s instructions, except using 8 min incubation time in fragmentation ste

treatment_protocol: To study immediate effects of NGN2 Wild type, AroLITE and AroPERFECT overexpression on ZIP13K2 human iPS cells, cells were treated with doxycycline for 12 or 24 hours and subjected to 15 minutes of 4-Thiouridine (4sU) labeling using 500 µM 4sU

tag: cell line

value: expressing NGN2 AroLITE 24h replicate 3


title: TF ChIP-seq from whole organism (ENCLB783LFM)

description:
https://www.encodeproject.org/experiments/ENCSR125CNZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing D19A-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR125CNZ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR863DOB
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB783LFM
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

tag: geographic location

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to D19A

value: 0-20 hour

value: Kevin White, UChicago

value: ENCBS904XVF at ENCODE; https://www.encodeproject.org/ENCBS904XVF/


title: Uninfected Oy-0 rep 1

tag: tissue

value: Leaves of 5-week old plants

tag: treatment

value: Uninfected (LNI)

value: 24 hours


title: ZT77 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT77_S_R1

tag: cultivar

value: Senescent leaf


title: ZT77 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT77_M_R1


title: Uninfected Nok-3 rep 3

tag: genotype


title: TF ChIP-seq from whole organism (ENCLB521FCM)

description:
https://www.encodeproject.org/experiments/ENCSR292EYZ/
***************
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: ENCSR292EYZ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR119OOH
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB521FCM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: lola

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

tag: Sex

value: pooled male and female

value: embryonic

tag: age

value: 0-12 hour

value: Kevin White

tag: link

value: ENCBS119SXZ at ENCODE; https://www.encodeproject.org/ENCBS119SXZ/


title: TF ChIP-seq from whole organism (ENCLB897KIN)

description:
https://www.encodeproject.org/experiments/ENCSR199FME/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing grau-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR199FME
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR465VBZ
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB897KIN
size range: 200-800

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

value: grau

value: whole organism

value: whole organisms

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

tag: dev stage

value: 0-24 hour

tag: lab

tag: source

value: ENCBS820TTF at ENCODE; https://www.encodeproject.org/ENCBS820TTF/


title: ZT75 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT75_S_R2

value: whole flag leaf

value: Mace

tag: time


title: TF ChIP-seq from whole organism (ENCLB613GIB)

description:
https://www.encodeproject.org/experiments/ENCSR199FME/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing grau-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR199FME
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR465VBZ
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB613GIB
size range: 200-800

tag: antibody

tag: biosample encode accession

value: not applicable

value: Kevin White, UChicago

value: ENCBS134GKB at ENCODE; https://www.encodeproject.org/ENCBS134GKB/


title: Uninfected Pn-0 rep 1

value: Leaves of 5-week old plants

value: Uninfected (LNI)

value: 24 hours


title: Vikl-041_SVR_pre

tag: cell type

value: peripheral blood mononuclear cells

tag: group


title: ZT79 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT79_M_R2

value: Mature leaf


title: NGN2_AroLITE_12h_r3 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 AroLITE 12h replicate 3

tag: cell line

value: expressing NGN2 AroLITE 12h replicate 3


title: TF ChIP-seq from whole organism (ENCLB480HZX)

description:
https://www.encodeproject.org/experiments/ENCSR199FME/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing grau-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR199FME
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR465VBZ
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB480HZX
size range: 200-800

value: grau

tag: collection date

tag: geographic location

tag: encode accession

tag: note

value: pooled male and female

value: embryonic

value: Kevin White

value: ENCBS045MLJ at ENCODE; https://www.encodeproject.org/ENCBS045MLJ/


title: ZT75 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT75_S_R1

tag: tissue

tag: cultivar

tag: treatment

value: Senescent leaf


title: Uninfected Mt-0 rep 3

tag: genotype


title: NGN2_AroLITE_12h_r2 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 AroLITE 12h replicate 2

value: expressing NGN2 AroLITE 12h replicate 2


title: TF ChIP-seq from whole organism (ENCLB579OME)

description:
https://www.encodeproject.org/experiments/ENCSR018VBD/
***************
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: ENCSR018VBD
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR920WVV
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB579OME
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG34367 pupa (24 hours) insertion targeting D. melanogaster CG34367

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG34367

tag: Sex

value: not collected

tag: dev stage

value: pupa

tag: age

value: 24 hour

tag: link

value: ENCBS707USD at ENCODE; https://www.encodeproject.org/ENCBS707USD/


title: ZT75 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT75_M_R2

value: whole flag leaf

value: Mace

tag: time


title: NGN2_AroLITE_12h_r1 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 AroLITE 12h replicate 1

value: expressing NGN2 AroLITE 12h replicate 1


title: Uninfected Mt-0 rep 2

value: Leaves of 5-week old plants

value: Uninfected (LNI)

value: 24 hours


title: ZT75 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT75_M_R1

value: Mature leaf


title: NGN2_AroPERFECT_24h_r3 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 AroPERFECT 24h replicate 3


title: Uninfected Mt-0 rep 1


title: TF ChIP-seq from whole organism (ENCLB196XUU)

description:
https://www.encodeproject.org/experiments/ENCSR018VBD/
***************
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: ENCSR018VBD
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR920WVV
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB196XUU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

tag: biosample encode accession

value: not applicable

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS788TEI at ENCODE; https://www.encodeproject.org/ENCBS788TEI/


title: ZT73 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT73_S_R2

value: Senescent leaf


title: NGN2_AroLITE_24h_r2 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 AroLITE 24h replicate 2

tag: cell line

value: expressing NGN2 AroLITE 24h replicate 2


title: TF ChIP-seq from whole organism (ENCLB903SWW)

description:
https://www.encodeproject.org/experiments/ENCSR290OJD/
***************
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: ENCSR290OJD
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR480YPK
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB903SWW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Stat92E-GFP mixed sex embryo (0-12 hours) whole organism stably expressing C-terminal eGFP-tagged Stat92E

value: whole organism

value: whole organisms

tag: collection date

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Stat92E

value: pooled male and female

value: embryonic

value: 0-12 hour

value: ENCBS970DED at ENCODE; https://www.encodeproject.org/ENCBS970DED/


title: Uninfected Nok-3 rep 2

value: Leaves of 5-week old plants


title: ZT73 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT73_S_R1

value: whole flag leaf

value: Mace


title: Uninfected Nok-3 rep 1

value: Uninfected (LNI)

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB011RET)

description:
https://www.encodeproject.org/experiments/ENCSR290OJD/
***************
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: ENCSR290OJD
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR480YPK
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB011RET
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

tag: encode accession

tag: note

value: Kevin White, UChicago

value: ENCBS350FME at ENCODE; https://www.encodeproject.org/ENCBS350FME/


title: Uninfected Ll-0 rep 3

tag: tissue


title: ZT73 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT73_M_R2

tag: cultivar

tag: treatment

value: Mature leaf


title: NGN2_AroPERFECT_12h_r2 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 AroPERFECT 12h replicate 2


title: NGN2_AroPERFECT_12h_r3 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 AroPERFECT 12h replicate 3


title: Uninfected Ll-0 rep 2

tag: genotype


title: Uninfected Ll-0 rep 1


title: ZT73 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT73_M_R1


title: TF ChIP-seq from whole organism (ENCLB405GBY)

description:
https://www.encodeproject.org/experiments/ENCSR017FMO/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing phol-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR017FMO
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR729AWQ
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB405GBY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: phol

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

tag: Sex

tag: dev stage

value: 0-16 hour

value: Kevin White

value: ENCBS289OKT at ENCODE; https://www.encodeproject.org/ENCBS289OKT/


title: NGN2_AroPERFECT_12h_r1 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 AroPERFECT 12h replicate 1


title: TF ChIP-seq from whole organism (ENCLB268XBF)

description:
https://www.encodeproject.org/experiments/ENCSR017FMO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing phol-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR017FMO
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR729AWQ
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB268XBF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: pooled male and female

value: embryonic

tag: age

tag: link

value: ENCBS597WJG at ENCODE; https://www.encodeproject.org/ENCBS597WJG/


title: Uninfected Kyoto rep 3

value: Leaves of 5-week old plants

value: Kyoto

tag: time


title: NGN2_WT_24h_r3 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 WT 24h replicate 3

value: expressing NGN2 WT 24h replicate 3


title: ZT71 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT71_S_R2

value: whole flag leaf

value: Mace

value: Senescent leaf


title: TF ChIP-seq from whole organism (ENCLB024NWK)

description:
https://www.encodeproject.org/experiments/ENCSR015ZUX/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing E(spl)m-beta-eGFP fusion proteins.
experiment encode accession: ENCSR015ZUX
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR734MCC
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB024NWK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain E(spl)m-beta-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster E(spl)mbeta-HLH

tag: antibody

value: E(spl)mβ-HLH

tag: biosample encode accession

value: not applicable

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

value: 0-24 hour

value: Kevin White, UChicago

value: ENCBS702ISR at ENCODE; https://www.encodeproject.org/ENCBS702ISR/


title: NGN2_WT_24h_r2 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 WT 24h replicate 2

value: expressing NGN2 WT 24h replicate 2


title: ZT71 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT71_S_R1


title: Uninfected Kyoto rep 2

value: Uninfected (LNI)

value: 24 hours


title: NGN2_AroPERFECT_24h_r2 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 AroPERFECT 24h replicate 1


title: TF ChIP-seq from whole organism (ENCLB544EFD)

description:
https://www.encodeproject.org/experiments/ENCSR015ZUX/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing E(spl)m-beta-eGFP fusion proteins.
experiment encode accession: ENCSR015ZUX
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR734MCC
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB544EFD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

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

value: pooled male and female

value: embryonic

tag: lab

tag: source

value: Kevin White

value: ENCBS309TKW at ENCODE; https://www.encodeproject.org/ENCBS309TKW/


title: Uninfected Kyoto rep 1

value: Leaves of 5-week old plants

value: Kyoto


title: ZT71 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT71_M_R2

value: whole flag leaf

value: Mace

value: Mature leaf


title: Uninfected Hs-0 rep 3


title: NGN2_WT_24h_r1 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 WT 24h replicate 1

tag: cell line

value: expressing NGN2 WT 24h replicate 1


title: NGN2_WT_12h_r3 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 WT 12h replicate 3

value: expressing NGN2 WT 12h replicate 3


title: ZT71 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT71_M_R1


title: TF ChIP-seq from whole organism (ENCLB386LFG)

description:
https://www.encodeproject.org/experiments/ENCSR122VFA/
***************
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: ENCSR122VFA
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR392OLY
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB386LFG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain fd3F-GFP embryo (8-18 hours) insertion targeting D. melanogaster fd3F

tag: collection date

value: not applicable

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to fd3F

value: not collected

value: Kevin White, UChicago

value: ENCBS631DSE at ENCODE; https://www.encodeproject.org/ENCBS631DSE/


title: ZT69 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT69_S_R2

value: Senescent leaf


title: Uninfected Hs-0 rep 2

value: Uninfected (LNI)

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB595BYB)

description:
https://www.encodeproject.org/experiments/ENCSR122VFA/
***************
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: ENCSR122VFA
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR392OLY
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB595BYB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

tag: encode accession

tag: note

value: embryonic

value: Kevin White

value: ENCBS607TPP at ENCODE; https://www.encodeproject.org/ENCBS607TPP/


title: TF ChIP-seq from whole organism (ENCLB396BUV)

description:
https://www.encodeproject.org/experiments/ENCSR017FMO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing phol-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR017FMO
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR729AWQ
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB396BUV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: phol

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

value: pooled male and female

value: 0-16 hour

value: ENCBS410IOT at ENCODE; https://www.encodeproject.org/ENCBS410IOT/


title: ZT69 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT69_S_R1

tag: tissue

value: whole flag leaf

tag: cultivar

value: Mace


title: Uninfected Gy-0 rep 3

value: Leaves of 5-week old plants

tag: genotype

tag: treatment


title: TF ChIP-seq from whole organism (ENCLB425SYD)

description:
https://www.encodeproject.org/experiments/ENCSR014ETB/
***************
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: ENCSR014ETB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR640NJO
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB425SYD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain lola-RI-GFP mixed sex wandering third instar larva whole organism stably expressing C-terminal eGFP-tagged lola

value: lola

value: not applicable

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

tag: Sex

tag: dev stage

value: wandering third instar larva

value: unknown

value: Kevin White, UChicago

value: ENCBS571NMZ at ENCODE; https://www.encodeproject.org/ENCBS571NMZ/


title: NGN2_WT_12h_r1 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 WT 12h replicate 1

value: expressing NGN2 WT 12h replicate 1


title: NGN2_WT_12h_r2 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells expressing NGN2 WT 12h replicate 2

value: expressing NGN2 WT 12h replicate 2


title: ZIP13K2_r2 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells replicate 2


title: TF ChIP-seq from whole organism (ENCLB735WVR)

description:
https://www.encodeproject.org/experiments/ENCSR014ETB/
***************
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: ENCSR014ETB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR640NJO
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB735WVR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

tag: age

value: Kevin White

tag: link

value: ENCBS018EHZ at ENCODE; https://www.encodeproject.org/ENCBS018EHZ/


title: ZT69 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT69_M_R2

value: Mature leaf

tag: time


title: ZT69 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT69_M_R1

value: whole flag leaf


title: TF ChIP-seq from whole organism (ENCLB082RMH)

description:
https://www.encodeproject.org/experiments/ENCSR014ETB/
***************
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: ENCSR014ETB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR640NJO
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB082RMH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

tag: biosample encode accession

value: pooled male and female

value: ENCBS439IJN at ENCODE; https://www.encodeproject.org/ENCBS439IJN/


title: ZIP13K2_r1 TT-Slamseq

description: TT-Slamseq library of ZIP13K2 cells replicate 1


title: Uninfected Gy-0 rep 2

value: Leaves of 5-week old plants

value: Uninfected (LNI)

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB362SQK)

description:
https://www.encodeproject.org/experiments/ENCSR013WUH/
***************
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: ENCSR013WUH
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB362SQK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: not applicable

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

value: not collected

value: embryonic

value: 0-16 hour

tag: lab

tag: source

value: ENCBS895SIM at ENCODE; https://www.encodeproject.org/ENCBS895SIM/


title: Uninfected Gy-0 rep 1


title: ZT67 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT67_S_R2

value: Mace

value: Senescent leaf


title: TF ChIP-seq from whole organism (ENCLB060HZG)

description:
https://www.encodeproject.org/experiments/ENCSR012MXT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Nf-YC-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR012MXT
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR877IXV
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB060HZG
size range: 200-800

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

value: Nf-YC

value: whole organism

value: whole organisms

tag: collection date

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

value: 0-18 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS196YKZ at ENCODE; https://www.encodeproject.org/ENCBS196YKZ/


title: Uninfected Es-0 rep 3

value: Leaves of 5-week old plants

value: Uninfected (LNI)

value: 24 hours


title: ChIPseq NGN2 AroPERFECT input

description: ChIP-seq

data_processing:
Reads were mapped to genome using BWA and samtools was used for SAM to BAM conversion, sorting and indexing. Genome Analysis Toolkit v4 was used to remove duplicated reads. Peak calling was then performed using MACS3 v3.0.0 b1 using the input of the respective sample
genome_build: hg38

extract_protocol:
Cells were detached with Accutase solution (Sigma), washed twice in PBS and fixed in rotation with 1% formaldehyde for 10 minutes at room temperature. Subsequently, the reaction was quenched by addition of glycine leading to a final concentration of 125 mM. Per replicate, three million cells were used as starting material. In brief, we followed the ChIPmentation protocol version 3 for histone marks and transcription factors (Schmidl et al., 2015).  Cells were lysed in lysis buffer 3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% N-laurosylsarcosine) supplemented with 1x cOmplete protease inhibitor cocktail. Afterwards, chromatin was sonicated for 10 minutes using a Covaris E220evolution focused-ultrasonicator with 2% duty cycles, 105 W peak incident power and 200 cycles per burst. Lysates were clarified by centrifugation for 10 minutes at 20,000g. 10% of the clarified lysate was put aside as input control. The remaining lysate was mixed with 50 µL of equilibrated anti-FLAG antibody (Merck, F1804, 1 µg total) coupled to DynabeadsTM Protein G magnetic beads (Invitrogen) and incubated on a 3D-shaker over night at 4oC. The next day, samples were washed twice in TF-wash buffer I (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% sodium dodecyl sulfate, 1% Triton-X-100 and 2 mM EDTA pH 8.0) followed by two washes in TF-wash buffer III (10mM Tris-HCl pH 8.0, 250 mM LiCl, 1% Triton-X-100, 0.7% sodium deoxycholate and 1 mM EDTA pH 8.0) and a final wash with 10 mM Tris-HCl pH 8.0
All samples were tagmented for 5 minutes at 37oC using the Illumina Tagment DNA kit and immediately put on ice. Tagmented chromatin was washed in ice-cold wash buffer I and TET buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA pH 8.0, 0.2% Tween-20) twice each, and reverse-crosslinked for 1h at 55oC and 9h at 65oC in the presence of 300 mM NaCl and proteinase K (Ambion). Subsequently, DNA was purified using AMPureXP beads. Sequencing libraries were amplified using the Kapa HiFi HotStart Ready Mix (Roche) and Nextera custom primers (Illumina) (Buenrostro et al., 2013) for a total of 12 cycles
Paired-end 100 with 50 million fragments per library

tag: cell type

tag: chip antibody

value: anti-FLAG antibody Merck, F1804


title: Uninfected Es-0 rep 2


title: ChIPseq NGN2 AroLITE input

description: ChIP-seq


title: Uninfected Es-0 rep 1


title: TF ChIP-seq from whole organism (ENCLB032TKN)

description:
https://www.encodeproject.org/experiments/ENCSR012MXT/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Nf-YC-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR012MXT
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR877IXV
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB032TKN
size range: 200-800

value: not applicable

tag: geographic location

tag: encode accession

tag: note

value: pooled male and female

value: embryonic

value: ENCBS744FZD at ENCODE; https://www.encodeproject.org/ENCBS744FZD/


title: ZT67 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT67_M_R2

tag: tissue

value: whole flag leaf

tag: cultivar

value: Mace

value: Mature leaf


title: ChIPseq NGN2 48h WT Rep 3

description: ChIP-seq


title: Uninfected Hs-0 rep 1

tag: genotype

tag: treatment


title: Uninfected Ei-2 rep 3


title: ZT67 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT67_M_R1


title: Uninfected Ei-2 rep 2


title: TF ChIP-seq from whole organism (ENCLB697LXU)

description:
https://www.encodeproject.org/experiments/ENCSR288BZG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing SREBP-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR288BZG
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR331EDA
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB697LXU
size range: 200-800

source_name: Drosophila melanogaster strain SREBP mixed sex wandering third instar larva insertion targeting D. melanogaster SREBP

value: whole organism

value: whole organisms

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

tag: Sex

tag: dev stage

value: wandering third instar larva

tag: age

value: unknown

value: ENCBS062EDO at ENCODE; https://www.encodeproject.org/ENCBS062EDO/


title: ZT65 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT65_S_R2

value: Senescent leaf

tag: time


title: ZT65 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT65_S_R1


title: ChIPseq NGN2 WT input

description: ChIP-seq


title: ChIPseq NGN2 48h WT Rep 2

description: ChIP-seq


title: Uninfected Eds-1 rep 4

value: Leaves of 5-week old plants

value: Uninfected (LNI)


title: ZT65 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT65_M_R2


title: TF ChIP-seq from whole organism (ENCLB451WNA)

description:
https://www.encodeproject.org/experiments/ENCSR288BZG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing SREBP-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR288BZG
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR331EDA
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB451WNA
size range: 200-800

tag: antibody

tag: biosample encode accession

value: Kevin White, UChicago

value: Kevin White

tag: link

value: ENCBS050YZO at ENCODE; https://www.encodeproject.org/ENCBS050YZO/


title: ChIPseq NGN2 48h AroPERFECT Rep 3

description: ChIP-seq

value: anti-FLAG antibody Merck, F1804


title: ZT67 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT67_S_R1


title: ZT65 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT65_M_R1


title: Uninfected Ei-2 rep 1

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB889JEH)

description:
https://www.encodeproject.org/experiments/ENCSR122CCQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing dsx-eGFP fusion proteins.
experiment encode accession: ENCSR122CCQ
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB889JEH
size range: 200-800

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

tag: collection date

value: not applicable

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

value: pooled male and female

value: prepupa

value: 24 hour

tag: lab

tag: source

value: ENCBS385LST at ENCODE; https://www.encodeproject.org/ENCBS385LST/


title: ChIPseq NGN2 48h AroPERFECT Rep 2

description: ChIP-seq

tag: cell type

tag: chip antibody


title: ChIPseq NGN2 48h WT Rep 1

description: ChIP-seq


title: ZT63 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT63_S_R2

value: whole flag leaf

value: Mace


title: TF ChIP-seq from whole organism (ENCLB049LLZ)

description:
https://www.encodeproject.org/experiments/ENCSR121SPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing crp-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR121SPZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR080DBI
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB049LLZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: crp

value: whole organism

value: whole organisms

tag: geographic location

tag: encode accession

tag: note

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

value: embryonic

value: 0-24 hour

value: ENCBS335RLG at ENCODE; https://www.encodeproject.org/ENCBS335RLG/


title: TF ChIP-seq from whole organism (ENCLB972EUV)

description:
https://www.encodeproject.org/experiments/ENCSR012MXT/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Nf-YC-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR012MXT
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR877IXV
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB972EUV
size range: 200-800

value: Nf-YC

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

value: 0-18 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS407KDI at ENCODE; https://www.encodeproject.org/ENCBS407KDI/


title: ChIPseq NGN2 48h AroPERFECT Rep 1

description: ChIP-seq

value: anti-FLAG antibody Merck, F1804


title: Uninfected Eds-1 rep 3

source_name: Leaves of 5-week old plants

tag: tissue

value: Leaves of 5-week old plants

tag: genotype

value: Uninfected (LNI)

value: 24 hours


title: ChIPseq NGN2 48h AroLITE Rep 3

description: ChIP-seq


title: Uninfected Eds-1 rep 1

tag: treatment


title: TF ChIP-seq from whole organism (ENCLB400HEQ)

description:
https://www.encodeproject.org/experiments/ENCSR121SPZ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing crp-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR121SPZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR080DBI
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB400HEQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: crp

value: not applicable

tag: Sex

value: pooled male and female

tag: dev stage

value: ENCBS838NRT at ENCODE; https://www.encodeproject.org/ENCBS838NRT/


title: ZT63 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT63_S_R1

value: whole flag leaf

tag: cultivar

value: Mace

value: Senescent leaf

tag: time


title: ZT63 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT63_M_R1

value: Mature leaf


title: TF ChIP-seq from whole organism (ENCLB675IJH)

description:
https://www.encodeproject.org/experiments/ENCSR121SPZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing crp-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR121SPZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR080DBI
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB675IJH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: whole organisms

tag: biosample encode accession

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

value: embryonic

tag: age

value: 0-24 hour

value: ENCBS726ZHB at ENCODE; https://www.encodeproject.org/ENCBS726ZHB/


title: ZT63 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT63_M_R2


title: ChIPseq NGN2 48h AroLITE Rep 2

description: ChIP-seq

value: anti-FLAG antibody Merck, F1804


title: TF ChIP-seq from whole organism (ENCLB198FFA)

description:
https://www.encodeproject.org/experiments/ENCSR288BZG/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing SREBP-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR288BZG
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR331EDA
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB198FFA
size range: 200-800

tag: collection date

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

value: wandering third instar larva

value: unknown

tag: lab

value: Kevin White, UChicago

value: Kevin White

tag: link

value: ENCBS539OMD at ENCODE; https://www.encodeproject.org/ENCBS539OMD/


title: Control ChIP-seq from whole organism (ENCLB098TCV)

description:
https://www.encodeproject.org/experiments/ENCSR196IIL/
***************
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: ENCSR196IIL
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB098TCV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain D1 pupa (24 hours) insertion targeting D. melanogaster D1

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to D1

value: not collected

value: pupa

value: 24 hour

tag: source

value: ENCBS926VSU at ENCODE; https://www.encodeproject.org/ENCBS926VSU/


title: ChIPseq NGN2 48h AroLITE Rep 1

description: ChIP-seq

tag: cell type

tag: chip antibody


title: Uninfected Ct-1 rep 3

value: Leaves of 5-week old plants

value: Uninfected (LNI)

value: 24 hours


title: ZT61 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT61_S_R2

value: whole flag leaf

value: Mace

value: Senescent leaf


title: ChIPseq NGN2 24h WT Rep 2

description: ChIP-seq

value: anti-FLAG antibody Merck, F1804


title: TF ChIP-seq from whole organism (ENCLB961PUU)

description:
https://www.encodeproject.org/experiments/ENCSR287NIU/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG11617-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR287NIU
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR072FJD
encode release date: 2017-12-11
lab: Kevin White, UChicago
library encode accession: ENCLB961PUU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG11617-GFP mixed sex adult insertion targeting D. melanogaster CG11617

value: whole organism

value: whole organisms

tag: geographic location

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG11617

value: pooled male and female

value: adult

value: unknown

value: ENCBS134AQE at ENCODE; https://www.encodeproject.org/ENCBS134AQE/


title: Uninfected Ct-1 rep 1

tag: tissue

tag: genotype

tag: treatment


title: ChIPseq NGN2 24h WT Rep 1

description: ChIP-seq


title: ZT61 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT61_M_R2

tag: cultivar

value: Mature leaf


title: Uninfected Ct-1 rep 2

tag: time


title: ZT61 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT61_S_R1


title: Uninfected Col-0 rep 10


title: TF ChIP-seq from whole organism (ENCLB948XGI)

description:
https://www.encodeproject.org/experiments/ENCSR287NIU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG11617-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR287NIU
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR072FJD
encode release date: 2017-12-11
lab: Kevin White, UChicago
library encode accession: ENCLB948XGI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: not applicable

tag: Sex

tag: dev stage

value: Kevin White, UChicago

value: Kevin White

value: ENCBS636TYX at ENCODE; https://www.encodeproject.org/ENCBS636TYX/


title: Control ChIP-seq from whole organism (ENCLB122AVZ)

description:
https://www.encodeproject.org/experiments/ENCSR286HLA/
***************
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: ENCSR286HLA
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB122AVZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG15601 mixed sex embryo (0-14 hours) insertion targeting D. melanogaster CG15601

tag: biosample encode accession

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG15601

value: embryonic

tag: age

value: 0-14 hour

value: ENCBS842UWS at ENCODE; https://www.encodeproject.org/ENCBS842UWS/


title: Uninfected Eds-1 rep 2

value: Leaves of 5-week old plants

value: Uninfected (LNI)

value: 24 hours