title: 20220307_M41_WT_13Gy_FLASH_5M_2626

city: Orsay

first: Anouk

last: Sesink

address: Rue Henri Becquerel

institute: Institut Curie

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values and matrix files

source_name: Lung

growth_protocol: Lungs were collected 5 months following radiotherapy and drug treatment

extract_protocol:
The trachea of the mouse was perfused with 1.5 ml of 50 U/ml dispase using, followed by 0.5 ml of 1% agarose. Lungs were minced using a scalpel to create small pieces and added into 3 ml of 1× DPBS MgCl2+and CaCl2+. Then 320 µl of 25 U/ml elastase were added and the suspension was homogenized at 37 °C using orbital shaking. The suspension was treated with 1× DPBS containing 10% fetal bovine serum (FBS) and 20 µl of 0,5 M EDTA pH 8 and filtered through 100 µm nylon cell strainer. The cells were treated with 37.5 µl of 10 mg/ml DNase I on ice, filtered through a 40 μm nylon cell strainer, centrifuged, resuspended in red blood cell (RBC) lysis buffer and incubated at RT before inhibition of the lysis using PF10 supplementation. After centrifugation, the pellet was resuspended in 1 ml of 1× DPBS containing 0.02% bovine serum albumin (BSA). Concentration of the samples was adjusted to 1 million cells/ml in 1× DPBS containing 0,02% BSA.
Library was performed according to the manufacter's instructions (single cell 3' v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beats into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Mice were irradiated after 2 consecutive days of AsiDNA injections (100mg/kg), followed by a third day with AsiDNA injection (200mg/kg) and FLASH/CONV irradiation.

value: Lung

value: FLASH IR


title: Control ChIP-seq from whole organism (ENCLB738YXG)

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/ENCSR768IJB/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Hsf-eGFP fusion proteins.
experiment encode accession: ENCSR768IJB
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB738YXG
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 Hsf-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Hsf

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: note

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

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

tag: age

value: 0-24 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS739SZT at ENCODE; https://www.encodeproject.org/ENCBS739SZT/


title: 20220307_M41_WT_13Gy_CONV_AsiDNA_5M_2620

country: France

description: 10x Genomics

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment

value: AsiDNA CONV IR


title: TF ChIP-seq from whole organism (ENCLB679SZP)

description:
https://www.encodeproject.org/experiments/ENCSR746LWS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-mml-1 in L3 larva worms.
experiment encode accession: ENCSR746LWS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR626WOI
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB679SZP
size range: 150-350

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP198 (unc-119(ed3) III; wgIs198) mixed sex L3 larva insertion targeting C. elegans mml-1

extract_protocol: not provided

tag: antibody

value: L3 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS478RST at ENCODE; https://www.encodeproject.org/ENCBS478RST/


title: TF ChIP-seq from whole organism (ENCLB275QYH)

description:
https://www.encodeproject.org/experiments/ENCSR648DJA/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Sry-delta-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR648DJA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR974LPR
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB275QYH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: Sry-δ

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

value: ENCBS863HRD at ENCODE; https://www.encodeproject.org/ENCBS863HRD/


title: TF ChIP-seq from whole organism (ENCLB710LRM)

description:
https://www.encodeproject.org/experiments/ENCSR648YVN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG3163-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR648YVN
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR340PDD
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB710LRM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG3163-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG3163

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG3163

value: ENCBS212OLX at ENCODE; https://www.encodeproject.org/ENCBS212OLX/


title: 20220307_M41_WT_13Gy_CONV_5M_2644

description: 10x Genomics

value: Lung

value: CONV IR


title: Control ChIP-seq from whole organism (ENCLB700GXI)

description:
https://www.encodeproject.org/experiments/ENCSR942LEY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG10654-eGFP fusion proteins.
experiment encode accession: ENCSR942LEY
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB700GXI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS786GVL at ENCODE; https://www.encodeproject.org/ENCBS786GVL/


title: Kidney, Foxp1-deficient 3

city: Camperdown

first: RENHUA

last: SONG

state: NSW

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

country: Australia

institute: Centenary Institute

library_source: transcriptomic

data_processing:
Illumina HiSeq xten/NovaSeq 6000 sequencer
The raw paired-end reads were quality checked by FastQC (https://github.com/s-andrews/FastQC) and trimmed to remove adaptor sequences and low-quality reads using Trimmomatic with the default setting.
Then clean reads were mapped to the mouse reference genome GRCm38.86 using the STAR aligner. Only uniquely mapped reads were selected by SAMtools to minimize the rate of false positives.
Deeptools was used to generate a bigwig format to facilitate visualization of the reads coverage and comparison among different samples.
To identify differential expression genes (DEGs) between two different conditions, the raw read count file generated by featureCounts was used as an input for DESeq2, followed by standard differential expression analysis. Genes with Q value≤ 0.05 and |log2FC|>1 (DESeq2) were considered to be significantly different expressed genes.
Gene Ontology (GO) functional-enrichment analysis was performed using the R package clusterProfiler to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with all the expressed genes as background.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the raw read count file generated by featureCounts
Supplementary files format and content: bigwig files to view the data

source_name: Kidney

growth_protocol: Neonatal littermate control (Cdh16Cre;Foxp1fl/+;RiboTag) and Foxp1-deficient (Cdh16Cre;Foxp1fl/fl;RiboTag) animals were used for polysomes isolation analysis. Mice after hypothermic anaesthesia were perfused with PBS. The kidneys were quickly removed, homogenized in 400μl polysome buffer (50mM Tris, pH 7.5, 100mM KCl, 12mM MgCl2, 1% Nonidet P-40, 1mM DTT, 200U/ml RNasin (N2615; Promega), 1 mg/ml heparin, 100μg/ml cyclohexamide, and 1 x protease inhibitor (Roche; 04693132001)) using pellet pestles.

extract_protocol:
The total RNA quality was determined by 2100 Bioanalyzer (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Samples were then centrifuged at 10,000g for 10 min to collect a post-mitochondrial supernatant. 25μl of washed anti-HA antibody-conjugated magnetic beads (Thermo ScientificTM; 88836) was added to the supernatant and incubated on an orbital shaker at 4°C overnight. The following day, samples were washed four times for 5 min in high salt buffer (50 mM Tris, pH 7.5, 300 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 100 μg/mL cycloheximide) in a magnet on ice. After washing, the beads were resuspended in 500ul TRIzol® Reagent for total RNA isolation according the manufacturer’s instructions (Invitrogen).

value: Kidney

tag: cell line

tag: cell type

value: kidney tubular cells

tag: genotype

value: chronic acid load

tag: rip antibody

value: anti-HA antibody


title: Control ChIP-seq from whole organism (ENCLB805XRX)

description:
https://www.encodeproject.org/experiments/ENCSR622TPD/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR622TPD
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB805XRX
size range: 150-350

source_name: Caenorhabditis elegans strain OP114 (unc-119(tm4063) III; wgIs114) mixed sex L1 larva insertion targeting C. elegans F16B12.6

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: L1 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS322XYS at ENCODE; https://www.encodeproject.org/ENCBS322XYS/


title: Kidney, Foxp1-deficient 2


title: Kidney, Foxp1-deficient 1


title: TF ChIP-seq from whole organism (ENCLB339LNP)

description:
https://www.encodeproject.org/experiments/ENCSR746LWS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-mml-1 in L3 larva worms.
experiment encode accession: ENCSR746LWS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR626WOI
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB339LNP
size range: 150-350

value: not applicable

tag: geographic location

tag: encode accession

value: pooled male and female

value: L3 larva

value: ENCBS128EWN at ENCODE; https://www.encodeproject.org/ENCBS128EWN/


title: TF ChIP-seq from whole organism (ENCLB694JAY)

description:
https://www.encodeproject.org/experiments/ENCSR746LWS/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq against eGFP-mml-1 in L3 larva worms.
experiment encode accession: ENCSR746LWS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR626WOI
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB694JAY
fragmentation methods: sonication (generic microtip)

tag: note

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

tag: Sex

value: Michael Snyder

value: ENCBS758MSG at ENCODE; https://www.encodeproject.org/ENCBS758MSG/


title: Ctrl mouse Tconv CD8+ T cells, rep. 3

city: Lyon

first: Yenkel

last: Grinberg-Bleyer

address: 28 rue Laennec

department: Immunity, viruses and inflammation

institute: Cancer Research Center of Lyon

data_processing:
Bcl files were converted to fastq using Bcl2fastq (2.20.0).
Gene expression was quantified using Salmon (1.1.0) and the annotation of protein coding genes from gencode vm24.
Transcription matrix was done using R package tximport on the salmon results.
Assembly: mm10
Supplementary files format and content: tab delimited file with samples in columns, genes in rows, and estimated raw counts.

molecule: polyA RNA

source_name: Spleen+lymph nodes

extract_protocol:
RNA was isolated with Nucleospin RNA extraction kits (Macherey Nagel)
libraries were prepared using an Illumina TruSeq Library Kit

value: Spleen+lymph nodes

value: CD8+ T cells

value: WT


title: Kidney, neonatal littermate control 2

value: Kidney

value: kidney tubular cells

value: Control

value: vehicle treatment

value: anti-HA antibody


title: Kidney, neonatal littermate control 3


title: Control ChIP-seq from whole organism (ENCLB222XUO)

description:
https://www.encodeproject.org/experiments/ENCSR439VUM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Sox15-eGFP fusion proteins.
experiment encode accession: ENCSR439VUM
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB222XUO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Sox15-GFP mixed sex prepupa insertion targeting D. melanogaster Sox15

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Sox15

tag: dev stage

value: prepupa

tag: age

value: unknown

value: Kevin White, UChicago

value: Kevin White

value: ENCBS485UFN at ENCODE; https://www.encodeproject.org/ENCBS485UFN/


title: Kidney, neonatal littermate control 1


title: Control ChIP-seq from whole organism (ENCLB880MVS)

description:
https://www.encodeproject.org/experiments/ENCSR641VHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing az2-eGFP fusion proteins.
experiment encode accession: ENCSR641VHQ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB880MVS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain az2-GFP mixed sex embryo (0-16 hours) insertion targeting D. melanogaster az2

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to az2

value: pooled male and female

value: embryonic

value: 0-16 hour

tag: lab

tag: source

value: ENCBS834GPC at ENCODE; https://www.encodeproject.org/ENCBS834GPC/


title: Control ChIP-seq from whole organism (ENCLB467BRE)

description:
https://www.encodeproject.org/experiments/ENCSR921YEJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR921YEJ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB467BRE
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP33 (unc-119(ed3) III; wgIs33) mixed sex L3 larva insertion targeting C. elegans nhr-25

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

value: L3 larva

value: Michael Snyder, Stanford

value: Michael Snyder

tag: link

value: ENCBS473XEQ at ENCODE; https://www.encodeproject.org/ENCBS473XEQ/


title: Control ChIP-seq from whole organism (ENCLB290YXE)

description:
https://www.encodeproject.org/experiments/ENCSR622TPD/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR622TPD
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB290YXE
size range: 150-350

value: whole organism

value: whole organisms

value: L1 larva

value: CGC

value: ENCBS367HDY at ENCODE; https://www.encodeproject.org/ENCBS367HDY/


title: LymphNode ATG5 WT

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

data_processing:
FASTQ files were mapped to the reference genome (mm10-2020-A) using the BD Rhapsody Sequence Analysis Pipeline v1.11
Assembly: mm10
Supplementary files format and content: .st.gz files with counts for each sample

source_name: Lymph node

extract_protocol:
tumor draining lymph nodes (inguinal) were isolated and processed following the protocol described in (https://doi.org/10.1016/j.xpro.2022.101267). Single cell suspensions were stained with a Viability dye, CD45, CD31 and Ter119 antibodies for further sorting.
Library was performed according to the manufacter’s instructions (23-24117(02)).

tag: tissue

value: Lymph node

value: WT


title: LymphNode ATG5 KO

value: ATG5 KO


title: TF ChIP-seq from whole organism (ENCLB416JZC)

description:
https://www.encodeproject.org/experiments/ENCSR622QSS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing EFL-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR622QSS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR734SWX
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB416JZC
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL478 hermaphrodite young adult insertion targeting C. elegans efl-1

tag: antibody

value: not applicable

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

value: hermaphrodite

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS035NHH at ENCODE; https://www.encodeproject.org/ENCBS035NHH/


title: B13, HFD.ATM.exos, scRNAseq

city: La Jolla

first: Theresa

last: Rohm

address: 9500 Gilman Dr

institute: UCSD

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
bcl2fastq was used to demultiplex shallow sequenced BCL files into FASTQ files
cellranger count was used to perform alignment, filtering, barcode counting and UMI counting for both shallow sequenced and deep sequenced FASTQ files
Assembly: mm10
Supplementary files format and content: Matrix files

source_name: stromal vascular cells (SVCs)

growth_protocol: Male mice were ordered from Jackson Lab (C57BL/6, Stock 000664)and kept in the animal facility at the University of California, San Diego under SPF conditions.

extract_protocol:
Epididymal fat was isolated, enzymatically digested in a collagen solution, and after red blood cells were lyzed and a cell vaibility of 80-90% confirmed, stromal vascular cells were used for scRNA-seqencing.
Cell suspensions from each mouse were loaded into a single well of a 10× Genomics Chromium Single Cell Controller.

treatment_protocol: 8-week old weight-matched mice were fed 10 weeks a lard-based high-fat diet (HFD: 60% fat; Research Diets) and then treated for the last months of HFD-feeding with Rosigliatzone (3 mg/kg BW/day) or ATM-Exosomes (10^9 Exos/ i.v. injection twice per week).

value: stromal vascular cells (SVCs)

tag: library id

tag: sample id

tag: condition


title: TF ChIP-seq from whole organism (ENCLB148FBS)

description:
https://www.encodeproject.org/experiments/ENCSR763HRS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Ets21C-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR763HRS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR596UEF
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB148FBS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain d.ets6-GFP mixed sex prepupa at white prepupa stage insertion targeting D. melanogaster Ets21C

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Ets21C

value: pooled male and female

value: prepupa

value: Kevin White, UChicago

value: Kevin White

tag: fly synchronization stage

value: white prepupa

value: ENCBS958IOT at ENCODE; https://www.encodeproject.org/ENCBS958IOT/


title: D12,  HFD.ROSI.diet, scRNAseq

description: 10x Genomics

tag: cell type


title: TF ChIP-seq from whole organism (ENCLB570DTU)

description:
https://www.encodeproject.org/experiments/ENCSR763HRS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Ets21C-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR763HRS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR596UEF
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB570DTU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

value: ENCBS444TIO at ENCODE; https://www.encodeproject.org/ENCBS444TIO/


title: B6, HFD.ATM.exos, scRNAseq

description: 10x Genomics


title: TF ChIP-seq from whole organism (ENCLB052SUL)

description:
https://www.encodeproject.org/experiments/ENCSR622QSS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing EFL-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR622QSS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR734SWX
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB052SUL
fragmentation methods: sonication (generic microtip)

tag: geographic location

tag: encode accession

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

value: hermaphrodite

value: young adult

value: ENCBS030IZZ at ENCODE; https://www.encodeproject.org/ENCBS030IZZ/


title: C8, ROSI.ATM.exos, scRNAseq

description: 10x Genomics


title: C9, ROSI.ATM.exos, scRNAseq

description: 10x Genomics


title: D11,  HFD.ROSI.diet, scRNAseq

description: 10x Genomics


title: Control ChIP-seq from whole organism (ENCLB938FVR)

description:
https://www.encodeproject.org/experiments/ENCSR744IWP/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR744IWP
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB938FVR
size range: 150-350

source_name: Caenorhabditis elegans strain OP354 (unc-119(tm4063) III; wgIs354) mixed sex L3 larva insertion targeting C. elegans elt-1

tag: Sex

value: L3 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS289FQA at ENCODE; https://www.encodeproject.org/ENCBS289FQA/


title: A3, PBS.Lipo, scRNAseq

description: 10x Genomics

value: stromal vascular cells (SVCs)


title: TF ChIP-seq from whole organism (ENCLB436OVN)

description:
https://www.encodeproject.org/experiments/ENCSR744BON/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing BLMP-1-eGFP fusion proteins.
experiment encode accession: ENCSR744BON
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR276IVY
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB436OVN
fragmentation methods: sonication (generic microtip)

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

value: whole organism

tag: note

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

tag: dev stage

value: L2 larva

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS762OGE at ENCODE; https://www.encodeproject.org/ENCBS762OGE/


title: A1, PBS.Lipo, scRNAseq

description: 10x Genomics


title: Control ChIP-seq from whole organism (ENCLB773MNU)

description:
https://www.encodeproject.org/experiments/ENCSR744IWP/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR744IWP
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB773MNU
size range: 150-350

value: whole organisms

value: not applicable

value: pooled male and female

tag: age

tag: lab

value: ENCBS967IWN at ENCODE; https://www.encodeproject.org/ENCBS967IWN/


title: TF ChIP-seq from whole organism (ENCLB883XWZ)

description:
https://www.encodeproject.org/experiments/ENCSR637FPY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing slou-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR637FPY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR079ERM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB883XWZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: slou

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS113CHT at ENCODE; https://www.encodeproject.org/ENCBS113CHT/


title: TF ChIP-seq from whole organism (ENCLB821SAE)

description:
https://www.encodeproject.org/experiments/ENCSR637FPY/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing slou-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR637FPY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR079ERM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB821SAE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: ENCBS045IFJ at ENCODE; https://www.encodeproject.org/ENCBS045IFJ/


title: TF ChIP-seq from whole organism (ENCLB675VZT)

description:
https://www.encodeproject.org/experiments/ENCSR763HRS/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Ets21C-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR763HRS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR596UEF
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB675VZT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Ets21C

value: prepupa

value: unknown

value: white prepupa

value: ENCBS733RNJ at ENCODE; https://www.encodeproject.org/ENCBS733RNJ/


title: TF ChIP-seq from whole organism (ENCLB430IFC)

description:
https://www.encodeproject.org/experiments/ENCSR744BON/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing BLMP-1-eGFP fusion proteins.
experiment encode accession: ENCSR744BON
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR276IVY
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB430IFC
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: not applicable

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

value: hermaphrodite

value: L2 larva

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS839FGM at ENCODE; https://www.encodeproject.org/ENCBS839FGM/


title: brain; SD; No_CFC; CA3; rep4 [protein expression level]

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

library_source: other

data_processing:
library strategy: GeoMx NGS readout
Raw FASTQ files were processed via Nanostring's NGS pipeline (v1.0) with default parameters. According to the manufacturer, reads are first processed for quality before trimming adapters and merging paired-end reads. The resulting high quality reads are then aligned to the proprietary Readout Tag Sequence-ID (RTS-ID) barcode. PCR duplicates are removed by matching on the Unique Molecular Index (UMI) and output DCC files are then generated for each region of interest (ROI) or area of illumination (AOI).
Processed DCC files were then mapped to protein targets and collapsed into a single count table using the R package GeoMxTools (v 3.3.0) and themanufactor's reference for each of the target panels ( .pkc files).
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes)
Supplementary files format and content: GeoMx pipeline readable digital counts (DCC) - contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target count table are the raw counts of the probes for a given protein target - or in the case that multiple probes were used, the averaged raw counts.

molecule: protein

source_name: brain

extract_protocol:
Samples were incubated with the following target panels for the Nanostring GeoMx DSP: (v1.0) Mouse NGS Protein Core, (v1.0) Mouse NGS Alzheimer's Pathology Extended Protein, (v1.0) Mouse NGS Alzheimer's Pathology Protein, (v1.0) Mouse NGS Autophagy Protein, (v1.0) Mouse NGS Cell Death Protein, (v1.0) Mouse NGS Glial Cell Subtyping Protein, (v1.0) Mouse NGS MAPK Signaling Protein, (v1.0) Mouse NGS Neural Cell Typing Protein, (v1.0) Mouse NGS PI3K/AKT Signaling Protein, (v1.0) Mouse NGS Parkinson's Pathology Protein. For extraction, regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x).
Manufactor's protocol for Nanostring GeoMx DSP with NGS readout; Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed ROIs were pooled and purified prior to sequencing.

tag: tissue

value: brain

tag: treatment

tag: region

tag: slide

tag: roi


title: B4, HFD.ATM.exos, scRNAseq

description: 10x Genomics

tag: cell type

value: stromal vascular cells (SVCs)

tag: library id

tag: sample id

tag: condition


title: brain; SD; No_CFC; CA1; rep6 [protein expression level]


title: TF ChIP-seq from whole organism (ENCLB796MSP)

description:
https://www.encodeproject.org/experiments/ENCSR636TIL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing maf-S-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR636TIL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR843KFW
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB796MSP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: maf-S

value: whole organism

tag: biosample encode accession

tag: collection date

tag: geographic location

tag: encode accession

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

tag: Sex

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS390FWA at ENCODE; https://www.encodeproject.org/ENCBS390FWA/


title: B5, HFD.ATM.exos, scRNAseq

description: 10x Genomics


title: C7, ROSI.ATM.exos, scRNAseq

description: 10x Genomics


title: TF ChIP-seq from whole organism (ENCLB407UUZ)

description:
https://www.encodeproject.org/experiments/ENCSR617FWQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-25 in L2 larva worms.
experiment encode accession: ENCSR617FWQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR566WAD
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB407UUZ
size range: 150-350

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

value: whole organisms

value: not applicable

tag: dev stage

tag: age

value: unknown

tag: lab

value: Michael Snyder, Stanford

tag: source

value: CGC

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


title: A2, PBS.Lipo, scRNAseq

description: 10x Genomics


title: TF ChIP-seq from whole organism (ENCLB541VLB)

description:
https://www.encodeproject.org/experiments/ENCSR637FPY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing slou-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR637FPY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR079ERM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB541VLB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: slou

tag: note

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

tag: link

value: ENCBS837EGU at ENCODE; https://www.encodeproject.org/ENCBS837EGU/


title: TF ChIP-seq from whole organism (ENCLB866TZW)

description:
https://www.encodeproject.org/experiments/ENCSR423GBK/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing fd85E-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR423GBK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR689PMU
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB866TZW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain fd85E-GFP mixed sex prepupa insertion targeting D. melanogaster FoxP

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to fd85E-aka FoxP

value: prepupa

value: ENCBS154NVI at ENCODE; https://www.encodeproject.org/ENCBS154NVI/


title: TF ChIP-seq from whole organism (ENCLB416COX)

description:
https://www.encodeproject.org/experiments/ENCSR617FWQ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-25 in L2 larva worms.
experiment encode accession: ENCSR617FWQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR566WAD
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB416COX
fragmentation methods: sonication (generic microtip)

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

value: pooled male and female

value: L2 larva

value: Michael Snyder

value: ENCBS120TLG at ENCODE; https://www.encodeproject.org/ENCBS120TLG/


title: brain; Sleep; No_CFC; hilus; rep6 [protein expression level]

tag: tissue

value: brain

tag: treatment

tag: region

value: hilus

tag: slide

tag: roi


title: Control ChIP-seq from whole organism (ENCLB095ROF)

description:
https://www.encodeproject.org/experiments/ENCSR921EWW/
***************
biological replicate number: 1
technical replicate number: 2
description: This is the ChIP-seq control of transgenic worms expressing DPL-1-eGFP fusion proteins.
experiment encode accession: ENCSR921EWW
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB095ROF
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL507 hermaphrodite young adult insertion targeting C. elegans dpl-1

value: whole organisms

tag: biosample encode accession

value: not applicable

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

value: hermaphrodite

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS881PZH at ENCODE; https://www.encodeproject.org/ENCBS881PZH/


title: D10, HFD.ROSI.diet, scRNAseq

description: 10x Genomics

tag: cell type

value: stromal vascular cells (SVCs)

tag: library id

tag: sample id

tag: condition


title: TF ChIP-seq from whole organism (ENCLB878GNA)

description:
https://www.encodeproject.org/experiments/ENCSR617FWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-25 in L2 larva worms.
experiment encode accession: ENCSR617FWQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR566WAD
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB878GNA
size range: 150-350

value: whole organism

tag: collection date

tag: geographic location

tag: encode accession

tag: Sex

tag: dev stage

value: Michael Snyder, Stanford

value: CGC

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


title: TF ChIP-seq from whole organism (ENCLB151MHY)

description:
https://www.encodeproject.org/experiments/ENCSR636TIL/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing maf-S-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR636TIL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR843KFW
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB151MHY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: maf-S

tag: note

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

value: pooled male and female

value: embryonic

tag: age

value: 0-24 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS728MUJ at ENCODE; https://www.encodeproject.org/ENCBS728MUJ/


title: TF ChIP-seq from whole organism (ENCLB646CAX)

description:
https://www.encodeproject.org/experiments/ENCSR932STL/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Elba2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR932STL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR224PPR
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB646CAX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organisms

value: not applicable

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

value: 0-4 hour

tag: link

value: ENCBS876BXH at ENCODE; https://www.encodeproject.org/ENCBS876BXH/


title: brain; SD; No_CFC; DG_sup; rep4 [protein expression level]

tag: tissue

value: brain

tag: treatment

tag: region

tag: slide

tag: roi


title: Control ChIP-seq from whole organism (ENCLB155FIB)

description:
https://www.encodeproject.org/experiments/ENCSR635FXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG30403-eGFP fusion proteins.
experiment encode accession: ENCSR635FXZ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB155FIB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

tag: biosample encode accession

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

value: ENCBS881OAU at ENCODE; https://www.encodeproject.org/ENCBS881OAU/


title: TF ChIP-seq from whole organism (ENCLB111EGM)

description:
https://www.encodeproject.org/experiments/ENCSR921BPO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against UNC-55 in LE worms.
experiment encode accession: ENCSR921BPO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR538KZZ
encode release date: 2017-11-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB111EGM
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain NC1639 ([wdIs49 (pttr39::UNC-55a::GFP; dpy-20+) III) mixed sex late embryo insertion targeting C. elegans unc-55

tag: collection date

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to UNC-55

value: late embryonic

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS846YIL at ENCODE; https://www.encodeproject.org/ENCBS846YIL/


title: brain; SD; CFC; hilus; rep8 [protein expression level]

value: SD;CFC

value: hilus


title: brain; Sleep; No_CFC; DG_inf; rep6 [protein expression level]


title: Control ChIP-seq from whole organism (ENCLB876JDC)

description:
https://www.encodeproject.org/experiments/ENCSR921EWW/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing DPL-1-eGFP fusion proteins.
experiment encode accession: ENCSR921EWW
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB876JDC
fragmentation methods: sonication (generic microtip)

value: whole organisms

tag: geographic location

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

value: hermaphrodite

value: young adult

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS881PZH at ENCODE; https://www.encodeproject.org/ENCBS881PZH/


title: TF ChIP-seq from whole organism (ENCLB462RSY)

description:
https://www.encodeproject.org/experiments/ENCSR423GBK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing fd85E-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR423GBK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR689PMU
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB462RSY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to fd85E-aka FoxP

value: pooled male and female

value: prepupa

value: Kevin White, UChicago

value: Kevin White

value: ENCBS907OKL at ENCODE; https://www.encodeproject.org/ENCBS907OKL/


title: brain; Sleep; No_CFC; DG_sup; rep6 [protein expression level]

value: brain


title: brain; SD; CFC; DG_sup; rep8 [protein expression level]

value: SD;CFC


title: TF ChIP-seq from whole organism (ENCLB109EHX)

description:
https://www.encodeproject.org/experiments/ENCSR422PMR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG33213-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR422PMR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR702YWZ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB109EHX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG33213-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG33213

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG33213

tag: Sex

value: embryonic

value: 0-24 hour

value: ENCBS009RIT at ENCODE; https://www.encodeproject.org/ENCBS009RIT/


title: brain; Sleep; No_CFC; CA3; rep6 [protein expression level]


title: brain; Sleep; No_CFC; CA1; rep6 [protein expression level]


title: brain; Sleep; No_CFC; DG_sup; rep5 [protein expression level]


title: Control ChIP-seq from whole organism (ENCLB200PZF)

description:
https://www.encodeproject.org/experiments/ENCSR921EWW/
***************
biological replicate number: 1
technical replicate number: 3
description: This is the ChIP-seq control of transgenic worms expressing DPL-1-eGFP fusion proteins.
experiment encode accession: ENCSR921EWW
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB200PZF
fragmentation methods: sonication (generic microtip)

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

value: hermaphrodite

tag: dev stage

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke


title: TF ChIP-seq from whole organism (ENCLB973LJW)

description:
https://www.encodeproject.org/experiments/ENCSR748DHJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing tio-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR748DHJ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR508AYF
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB973LJW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

value: tio

value: whole organism

value: not applicable

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

value: pooled male and female

value: ENCBS645OMM at ENCODE; https://www.encodeproject.org/ENCBS645OMM/


title: brain; SD; CFC; CA1; rep8 [protein expression level]

value: brain

value: SD;CFC


title: brain; SD; CFC; DG_inf; rep7 [protein expression level]


title: brain; Sleep; No_CFC; CA1; rep5 [protein expression level]


title: TF ChIP-seq from whole organism (ENCLB211QBV)

description:
https://www.encodeproject.org/experiments/ENCSR422PMR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG33213-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR422PMR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR702YWZ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB211QBV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG33213

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS043NEM at ENCODE; https://www.encodeproject.org/ENCBS043NEM/


title: brain; Sleep; No_CFC; CA3; rep5 [protein expression level]


title: TF ChIP-seq from whole organism (ENCLB582YVR)

description:
https://www.encodeproject.org/experiments/ENCSR921BPO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against UNC-55 in LE worms.
experiment encode accession: ENCSR921BPO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR538KZZ
encode release date: 2017-11-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB582YVR
fragmentation methods: sonication (generic microtip)

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to UNC-55

value: late embryonic

tag: age

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS740EMH at ENCODE; https://www.encodeproject.org/ENCBS740EMH/


title: TF ChIP-seq from whole organism (ENCLB907BNJ)

description:
https://www.encodeproject.org/experiments/ENCSR748DHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing tio-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR748DHJ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR508AYF
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB907BNJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: tio

value: whole organism

value: not applicable

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

tag: lab

value: ENCBS808BFH at ENCODE; https://www.encodeproject.org/ENCBS808BFH/


title: TF ChIP-seq from whole organism (ENCLB494KWG)

description:
https://www.encodeproject.org/experiments/ENCSR422PMR/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG33213-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR422PMR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR702YWZ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB494KWG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: pooled male and female

value: 0-24 hour

tag: source

value: ENCBS083YRU at ENCODE; https://www.encodeproject.org/ENCBS083YRU/


title: brain; Sleep; No_CFC; hilus; rep5 [protein expression level]

value: brain

value: hilus


title: Control ChIP-seq from whole organism (ENCLB254WDW)

description:
https://www.encodeproject.org/experiments/ENCSR920XFN/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR920XFN
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB254WDW
size range: 150-350

source_name: Caenorhabditis elegans strain OP106 (unc-119(ed3) III; wgIs106) mixed sex L1 larva insertion targeting C. elegans mdl-1

value: L1 larva

value: CGC

tag: link

value: ENCBS494IPJ at ENCODE; https://www.encodeproject.org/ENCBS494IPJ/


title: brain; SD; CFC; hilus; rep7 [protein expression level]

tag: tissue

value: SD;CFC


title: brain; Sleep; No_CFC; DG_inf; rep5 [protein expression level]

tag: treatment


title: TF ChIP-seq from whole organism (ENCLB712WGL)

description:
https://www.encodeproject.org/experiments/ENCSR748ZJA/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Dif-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR748ZJA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR046BPV
encode release date: 2018-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB712WGL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-300

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

value: Dif

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

value: wandering third instar larva

value: unknown

value: Kevin White, UChicago

value: Kevin White

value: ENCBS973ACZ at ENCODE; https://www.encodeproject.org/ENCBS973ACZ/


title: brain; SD; CFC; CA3; rep8 [protein expression level]

tag: region


title: TF ChIP-seq from whole organism (ENCLB065OLH)

description:
https://www.encodeproject.org/experiments/ENCSR740RYL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-lsy-2 in L2 larva worms.
experiment encode accession: ENCSR740RYL
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR582YPQ
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB065OLH
size range: 150-350

source_name: Caenorhabditis elegans strain OP240 (unc-119(ed3) III; wgIs240) mixed sex L2 larva insertion targeting C. elegans lsy-2

value: whole organism

value: whole organisms

value: not applicable

value: L2 larva

value: Michael Snyder, Stanford

value: ENCBS660DYN at ENCODE; https://www.encodeproject.org/ENCBS660DYN/


title: brain; SD; CFC; DG_inf; rep6 [protein expression level]

value: brain

tag: slide


title: TF ChIP-seq from whole organism (ENCLB190KAQ)

description:
https://www.encodeproject.org/experiments/ENCSR629WQT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Trl-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR629WQT
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR161RRC
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB190KAQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: Trl

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

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Hugo Bellen

value: ENCBS458FGR at ENCODE; https://www.encodeproject.org/ENCBS458FGR/


title: brain; Sleep; CFC; hilus; rep6 [protein expression level]

value: Sleep;CFC

value: hilus

tag: roi


title: brain; Sleep; CFC; DG_inf; rep6 [protein expression level]


title: brain; SD; CFC; CA3; rep7 [protein expression level]

value: SD;CFC


title: TF ChIP-seq from whole organism (ENCLB813RAJ)

description:
https://www.encodeproject.org/experiments/ENCSR740RYL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-lsy-2 in L2 larva worms.
experiment encode accession: ENCSR740RYL
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR582YPQ
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB813RAJ
size range: 150-350

value: whole organism

tag: biosample encode accession

value: unknown

value: CGC

value: ENCBS510PZP at ENCODE; https://www.encodeproject.org/ENCBS510PZP/


title: TF ChIP-seq from whole organism (ENCLB660YGO)

description:
https://www.encodeproject.org/experiments/ENCSR629WQT/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Trl-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR629WQT
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR161RRC
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB660YGO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: collection date

value: not applicable

value: Kevin White, UChicago

value: ENCBS216BDG at ENCODE; https://www.encodeproject.org/ENCBS216BDG/


title: Control ChIP-seq from whole organism (ENCLB898MZQ)

description:
https://www.encodeproject.org/experiments/ENCSR920XFN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR920XFN
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB898MZQ
size range: 150-350

tag: geographic location

value: L1 larva

value: Michael Snyder, Stanford

value: ENCBS230HBA at ENCODE; https://www.encodeproject.org/ENCBS230HBA/


title: brain; Sleep; CFC; DG_sup; rep6 [protein expression level]

value: brain


title: Control ChIP-seq from whole organism (ENCLB356DCR)

description:
https://www.encodeproject.org/experiments/ENCSR739VJU/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing dox-1-eGFP fusion proteins.
experiment encode accession: ENCSR739VJU
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2022-12-19
lab: Valerie Reinke, Yale
library encode accession: ENCLB356DCR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12180 (st12180[dox-1::TY1::EGFP::3xFLAG] I) young adult (66 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans dxbp-1

tag: encode accession

value: not collected

value: young adult

value: 66 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: ENCBS800HYC at ENCODE; https://www.encodeproject.org/ENCBS800HYC/


title: brain; Sleep; CFC; CA3; rep6 [protein expression level]

value: Sleep;CFC


title: Control ChIP-seq from whole organism (ENCLB725CWN)

description:
https://www.encodeproject.org/experiments/ENCSR925FBM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing ab-eGFP fusion proteins.
experiment encode accession: ENCSR925FBM
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB725CWN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

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

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

value: 0-24 hour

value: Kevin White

value: ENCBS867KUY at ENCODE; https://www.encodeproject.org/ENCBS867KUY/


title: TF ChIP-seq from whole organism (ENCLB981SHP)

description:
https://www.encodeproject.org/experiments/ENCSR629WQT/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Trl-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR629WQT
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR161RRC
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB981SHP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: Trl

value: whole organisms

value: not applicable

tag: note

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

value: Kevin White, UChicago

value: Hugo Bellen

value: ENCBS313KIA at ENCODE; https://www.encodeproject.org/ENCBS313KIA/


title: brain; Sleep; CFC; hilus; rep5 [protein expression level]

value: brain

value: hilus


title: TF ChIP-seq from whole organism (ENCLB976OPU)

description:
https://www.encodeproject.org/experiments/ENCSR738KZF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-ceh-28 in L4 larva worms.
experiment encode accession: ENCSR738KZF
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR784WEG
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB976OPU
size range: 150-350

source_name: Caenorhabditis elegans strain OP241 (unc-119(ed3) III; wgIs241) mixed sex L4 larva insertion targeting C. elegans ceh-28

value: L4 larva

tag: age

value: unknown

tag: lab

value: Michael Snyder, Stanford

value: CGC

value: ENCBS060JCI at ENCODE; https://www.encodeproject.org/ENCBS060JCI/


title: Control ChIP-seq from whole organism (ENCLB987GML)

description:
https://www.encodeproject.org/experiments/ENCSR615EJQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in late embryonic worms.
experiment encode accession: ENCSR615EJQ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB987GML
size range: 150-350

source_name: Caenorhabditis elegans strain OP305 (unc-119(ed3) III; wgIs305) mixed sex late embryo insertion targeting C. elegans nhr-11

value: whole organism

value: pooled male and female

value: late embryonic

tag: source

tag: link

value: ENCBS254EPW at ENCODE; https://www.encodeproject.org/ENCBS254EPW/


title: brain; Sleep; CFC; DG_sup; rep5 [protein expression level]

source_name: brain

tag: tissue

tag: treatment

value: Sleep;CFC


title: brain; Sleep; CFC; CA1; rep6 [protein expression level]

tag: region

tag: slide


title: brain; Sleep; CFC; CA3; rep5 [protein expression level]

tag: roi


title: brain; Sleep; CFC; DG_inf; rep5 [protein expression level]


title: Control ChIP-seq from whole organism (ENCLB955OFW)

description:
https://www.encodeproject.org/experiments/ENCSR615EJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in late embryonic worms.
experiment encode accession: ENCSR615EJQ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB955OFW
size range: 150-350

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

value: ENCBS152YAI at ENCODE; https://www.encodeproject.org/ENCBS152YAI/


title: Control ChIP-seq from whole organism (ENCLB440CMN)

description:
https://www.encodeproject.org/experiments/ENCSR923VFC/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG2120-eGFP fusion proteins.
experiment encode accession: ENCSR923VFC
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB440CMN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG2120-GFP embryo (18-24 hours) insertion targeting D. melanogaster CG2120

tag: geographic location

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG2120

value: not collected

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS647FYQ at ENCODE; https://www.encodeproject.org/ENCBS647FYQ/


title: brain; SD; CFC; DG_sup; rep7 [protein expression level]

value: brain

value: SD;CFC


title: brain; Sleep; CFC; CA1; rep5 [protein expression level]


title: Control ChIP-seq from whole organism (ENCLB008BQK)

description:
https://www.encodeproject.org/experiments/ENCSR624TOZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Su(H)-eGFP fusion proteins.
experiment encode accession: ENCSR624TOZ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB008BQK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

tag: Sex

value: 0-24 hour

value: ENCBS371KOB at ENCODE; https://www.encodeproject.org/ENCBS371KOB/


title: brain; SD; CFC; CA1; rep7 [protein expression level]


title: brain; SD; No_CFC; CA1; rep5 [protein expression level]


title: TF ChIP-seq from whole organism (ENCLB856SCD)

description:
https://www.encodeproject.org/experiments/ENCSR738KZF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-ceh-28 in L4 larva worms.
experiment encode accession: ENCSR738KZF
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR784WEG
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB856SCD
size range: 150-350

value: whole organism

value: pooled male and female

tag: dev stage

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS252YAQ at ENCODE; https://www.encodeproject.org/ENCBS252YAQ/


title: TF ChIP-seq from whole organism (ENCLB907JSX)

description:
https://www.encodeproject.org/experiments/ENCSR621PCK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing gfzf-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR621PCK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR852VMM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB907JSX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

value: gfzf

value: whole organisms

value: not applicable

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

value: ENCBS022PGD at ENCODE; https://www.encodeproject.org/ENCBS022PGD/


title: brain; Sleep; No_CFC; hilus; rep4 [protein expression level]

value: brain

value: hilus


title: Control ChIP-seq from whole organism (ENCLB102GMX)

description:
https://www.encodeproject.org/experiments/ENCSR738KPG/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR738KPG
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB102GMX
size range: 150-350

source_name: Caenorhabditis elegans strain YL424 (unc-119(ed3)III; vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3'UTR, unc-119 (+)]) mixed sex L1 larva insertion targeting C. elegans efl-1

value: L1 larva

value: ENCBS264VNW at ENCODE; https://www.encodeproject.org/ENCBS264VNW/


title: brain; Sleep; No_CFC; DG_inf; rep4 [protein expression level]


title: Control ChIP-seq from whole organism (ENCLB723BEA)

description:
https://www.encodeproject.org/experiments/ENCSR738KPG/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR738KPG
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB723BEA
size range: 150-350

value: ENCBS411FLF at ENCODE; https://www.encodeproject.org/ENCBS411FLF/


title: TF ChIP-seq from whole organism (ENCLB069YSC)

description:
https://www.encodeproject.org/experiments/ENCSR621PCK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing gfzf-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR621PCK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR852VMM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB069YSC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

tag: note

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS269FZT at ENCODE; https://www.encodeproject.org/ENCBS269FZT/


title: brain; Sleep; No_CFC; CA3; rep4 [protein expression level]


title: TF ChIP-seq from whole organism (ENCLB395TVZ)

description:
https://www.encodeproject.org/experiments/ENCSR920BMA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-efl-1 in young adult worms.
experiment encode accession: ENCSR920BMA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR087KJY
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB395TVZ
size range: 150-350

source_name: Caenorhabditis elegans strain YL445 (unc119(ed3)III; vrIs81 [pPIE-1::EFL-1::GFP FLAG: EFL-1 3'UTR, unc-119 (+)]) mixed sex young adult insertion targeting C. elegans efl-1

value: pooled male and female

value: young adult

tag: age

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS770KNS at ENCODE; https://www.encodeproject.org/ENCBS770KNS/


title: TF ChIP-seq from whole organism (ENCLB892FQJ)

description:
https://www.encodeproject.org/experiments/ENCSR920BMA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-efl-1 in young adult worms.
experiment encode accession: ENCSR920BMA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR087KJY
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB892FQJ
size range: 150-350

value: whole organisms

value: not applicable

tag: lab

value: ENCBS930ZKO at ENCODE; https://www.encodeproject.org/ENCBS930ZKO/


title: brain; Sleep; No_CFC; DG_inf; rep3 [protein expression level]

value: brain


title: TF ChIP-seq from whole organism (ENCLB084VXX)

description:
https://www.encodeproject.org/experiments/ENCSR619HLP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8944-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR619HLP
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR111CQR
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB084VXX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG8944-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG8944

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8944

tag: source

value: ENCBS709VIY at ENCODE; https://www.encodeproject.org/ENCBS709VIY/


title: brain; Sleep; No_CFC; CA1; rep4 [protein expression level]


title: TF ChIP-seq from whole organism (ENCLB133GXG)

description:
https://www.encodeproject.org/experiments/ENCSR619HLP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8944-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR619HLP
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR111CQR
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB133GXG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: embryonic

tag: link

value: ENCBS234RRM at ENCODE; https://www.encodeproject.org/ENCBS234RRM/


title: brain; Sleep; No_CFC; hilus; rep3 [protein expression level]

tag: tissue

value: hilus


title: brain; SD; No_CFC; CA1; rep4 [protein expression level]

tag: treatment


title: brain; Sleep; No_CFC; DG_sup; rep3 [protein expression level]

tag: region


title: TF ChIP-seq from whole organism (ENCLB568FLT)

description:
https://www.encodeproject.org/experiments/ENCSR619HLP/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8944-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR619HLP
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR111CQR
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB568FLT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS255ZRY at ENCODE; https://www.encodeproject.org/ENCBS255ZRY/


title: Control ChIP-seq from whole organism (ENCLB063KDY)

description:
https://www.encodeproject.org/experiments/ENCSR734SWX/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing EFL-1-eGFP fusion proteins.
experiment encode accession: ENCSR734SWX
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB063KDY
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL478 hermaphrodite young adult insertion targeting C. elegans efl-1

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

value: hermaphrodite

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS498QSO at ENCODE; https://www.encodeproject.org/ENCBS498QSO/


title: brain; Sleep; No_CFC; DG_sup; rep4 [protein expression level]

value: brain

tag: slide


title: brain; Sleep; No_CFC; CA3; rep3 [protein expression level]

tag: roi


title: brain; Sleep; No_CFC; CA1; rep3 [protein expression level]


title: brain; SD; CFC; hilus; rep6 [protein expression level]

value: SD;CFC


title: TF ChIP-seq from whole organism (ENCLB326WSK)

description:
https://www.encodeproject.org/experiments/ENCSR733FVS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against AMA-1 in YA worms.
experiment encode accession: ENCSR733FVS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR029WBT
encode release date: 2018-02-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB326WSK
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL503 (unc-119(ed3) III; vrIs110 [pPIE-1::AMA-1:GFP:FLAG::AMA-1 3'UTR, unc-119 (+)]) mixed sex young adult insertion targeting C. elegans ama-1

value: whole organism

value: whole organisms

tag: biosample encode accession

value: not applicable

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

value: pooled male and female

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS386SRV at ENCODE; https://www.encodeproject.org/ENCBS386SRV/


title: TF ChIP-seq from whole organism (ENCLB831ERO)

description:
https://www.encodeproject.org/experiments/ENCSR733FVS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against AMA-1 in YA worms.
experiment encode accession: ENCSR733FVS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR029WBT
encode release date: 2018-02-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB831ERO
fragmentation methods: sonication (generic microtip)

tag: collection date

value: ENCBS513JTP at ENCODE; https://www.encodeproject.org/ENCBS513JTP/


title: Control ChIP-seq from whole organism (ENCLB508VSQ)

description:
https://www.encodeproject.org/experiments/ENCSR920JDE/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CrebA-eGFP fusion proteins.
experiment encode accession: ENCSR920JDE
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB508VSQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: geographic location

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

value: wandering third instar larva

value: Kevin White, UChicago

value: Hugo Bellen

value: ENCBS168HWH at ENCODE; https://www.encodeproject.org/ENCBS168HWH/


title: brain; SD; CFC; DG_inf; rep5 [protein expression level]


title: TF ChIP-seq from whole organism (ENCLB710TID)

description:
https://www.encodeproject.org/experiments/ENCSR917ZNB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-237 in L1 larva worms.
experiment encode accession: ENCSR917ZNB
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR566WSV
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB710TID
size range: 150-350

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

tag: encode accession

value: L1 larva

value: unknown

value: CGC

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


title: brain; SD; CFC; DG_sup; rep6 [protein expression level]

value: brain

value: SD;CFC


title: brain; SD; CFC; CA3; rep6 [protein expression level]


title: TF ChIP-seq from whole organism (ENCLB968ZIE)

description:
https://www.encodeproject.org/experiments/ENCSR731HHO/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Sox102F-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR731HHO
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR112EFN
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB968ZIE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Sox102F-GFP mixed sex prepupa at white prepupa stage insertion targeting D. melanogaster Sox102F

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Sox102F

tag: Sex

value: prepupa

value: Kevin White

tag: fly synchronization stage

value: white prepupa

value: ENCBS542APE at ENCODE; https://www.encodeproject.org/ENCBS542APE/


title: brain; SD; CFC; CA1; rep6 [protein expression level]


title: brain; SD; CFC; hilus; rep5 [protein expression level]

value: hilus


title: Control ChIP-seq from whole organism (ENCLB406OIJ)

description:
https://www.encodeproject.org/experiments/ENCSR732THT/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in mixed stage (embryonic) worms.
experiment encode accession: ENCSR732THT
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB406OIJ
size range: 150-350

source_name: Caenorhabditis elegans strain OP99 (unc-119(ed3) III; wgIs99) mixed sex mixed stage (embryo) insertion targeting C. elegans nhr-2

value: pooled male and female

tag: dev stage

value: mixed stage (embryonic)

value: Michael Snyder, Stanford

value: ENCBS830PGF at ENCODE; https://www.encodeproject.org/ENCBS830PGF/


title: TF ChIP-seq from whole organism (ENCLB759ANS)

description:
https://www.encodeproject.org/experiments/ENCSR917ZNB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-237 in L1 larva worms.
experiment encode accession: ENCSR917ZNB
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR566WSV
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB759ANS
size range: 150-350

tag: antibody

value: L1 larva

value: unknown

value: CGC

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


title: brain; SD; CFC; DG_sup; rep5 [protein expression level]

value: brain

value: SD;CFC


title: TF ChIP-seq from whole organism (ENCLB273LYJ)

description:
https://www.encodeproject.org/experiments/ENCSR418YJE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG3919-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR418YJE
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR810HCI
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB273LYJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Drosophila melanogaster strain CG3919-GFP mixed sex prepupa insertion targeting D. melanogaster CG3919

value: whole organism

value: whole organisms

value: not applicable

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG3919

tag: age

value: Kevin White, UChicago

value: ENCBS246OQV at ENCODE; https://www.encodeproject.org/ENCBS246OQV/


title: brain; SD; CFC; CA3; rep5 [protein expression level]


title: brain; SD; CFC; CA1; rep5 [protein expression level]


title: TF ChIP-seq from whole organism (ENCLB957PER)

description:
https://www.encodeproject.org/experiments/ENCSR418YJE/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG3919-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR418YJE
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR810HCI
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB957PER
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: prepupa

tag: lab

tag: source

value: Kevin White

value: ENCBS282YKI at ENCODE; https://www.encodeproject.org/ENCBS282YKI/


title: Control ChIP-seq from whole organism (ENCLB859WZS)

description:
https://www.encodeproject.org/experiments/ENCSR732THT/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in mixed stage (embryonic) worms.
experiment encode accession: ENCSR732THT
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB859WZS
size range: 150-350

value: pooled male and female

value: mixed stage (embryonic)

value: Michael Snyder, Stanford

tag: link

value: ENCBS222KDA at ENCODE; https://www.encodeproject.org/ENCBS222KDA/


title: brain; SD; CFC; DG_inf; rep4 [protein expression level]

tag: tissue

tag: treatment


title: Control ChIP-seq from whole organism (ENCLB247CQF)

description:
https://www.encodeproject.org/experiments/ENCSR917RGN/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR917RGN
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB247CQF
size range: 150-350

source_name: Caenorhabditis elegans strain OP321 (unc-119(tm4063) III; wgIs321) mixed sex L1 larva insertion targeting C. elegans tlp-1

value: L1 larva

value: unknown

value: CGC

value: ENCBS279QTG at ENCODE; https://www.encodeproject.org/ENCBS279QTG/


title: Control ChIP-seq from whole organism (ENCLB481PXN)

description:
https://www.encodeproject.org/experiments/ENCSR917RGN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR917RGN
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB481PXN
size range: 150-350

value: whole organism

value: ENCBS805JKC at ENCODE; https://www.encodeproject.org/ENCBS805JKC/


title: Control ChIP-seq from whole organism (ENCLB661TFD)

description:
https://www.encodeproject.org/experiments/ENCSR612BYM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Ebx-eGFP fusion proteins.
experiment encode accession: ENCSR612BYM
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB661TFD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organisms

value: not applicable

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

value: embryonic

value: 0-16 hour

value: ENCBS919SYL at ENCODE; https://www.encodeproject.org/ENCBS919SYL/


title: Control ChIP-seq from whole organism (ENCLB581VPY)

description:
https://www.encodeproject.org/experiments/ENCSR917HXG/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR917HXG
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2018-02-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB581VPY
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP337 (unc119(ed3);wgIs377(fkh-10::TY1 EGFP FLAG;unc119)) mixed sex L3 larva insertion targeting C. elegans fkh-10

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

value: L3 larva

value: Michael Snyder

value: ENCBS999BTJ at ENCODE; https://www.encodeproject.org/ENCBS999BTJ/


title: brain; SD; CFC; DG_sup; rep4 [protein expression level]

source_name: brain

value: brain

value: SD;CFC

tag: region

tag: slide


title: brain; SD; CFC; CA1; rep4 [protein expression level]

tag: roi


title: TF ChIP-seq from whole organism (ENCLB141LHR)

description:
https://www.encodeproject.org/experiments/ENCSR741KZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ftz-f1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR741KZZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR576JSM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB141LHR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Drosophila melanogaster strain ftz-f1-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster ftz-f1

tag: biosample encode accession

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to ftz-f1

value: pooled male and female

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS313WAD at ENCODE; https://www.encodeproject.org/ENCBS313WAD/


title: brain; SD; CFC; CA3; rep4 [protein expression level]


title: brain; SD; CFC; hilus; rep3 [protein expression level]

value: hilus


title: Control ChIP-seq from whole organism (ENCLB558OUP)

description:
https://www.encodeproject.org/experiments/ENCSR611YZN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing p53-eGFP fusion proteins.
experiment encode accession: ENCSR611YZN
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB558OUP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain p53-MiMIC-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster p53

value: whole organism

value: whole organisms

value: not applicable

tag: geographic location

tag: encode accession

value: D. mel line contraining an intronic eGFP exon to create a p53-GFP fusion gene

value: Hugo Bellen

value: ENCBS861UXW at ENCODE; https://www.encodeproject.org/ENCBS861UXW/


title: brain; SD; CFC; DG_sup; rep3 [protein expression level]


title: Control ChIP-seq from whole organism (ENCLB241CTA)

description:
https://www.encodeproject.org/experiments/ENCSR609JSK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Xbp1-eGFP fusion proteins.
experiment encode accession: ENCSR609JSK
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB241CTA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Xbp1-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Xbp1

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Xbp1

tag: Sex

value: embryonic

value: ENCBS144YCS at ENCODE; https://www.encodeproject.org/ENCBS144YCS/


title: brain; SD; CFC; CA3; rep3 [protein expression level]

value: brain

value: SD;CFC


title: TF ChIP-seq from whole organism (ENCLB468ZUU)

description:
https://www.encodeproject.org/experiments/ENCSR731HHO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Sox102F-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR731HHO
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR112EFN
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB468ZUU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Sox102F

value: pooled male and female

tag: dev stage

value: prepupa

value: unknown

tag: fly synchronization stage

value: white prepupa

value: ENCBS548EBZ at ENCODE; https://www.encodeproject.org/ENCBS548EBZ/


title: brain; SD; CFC; DG_inf; rep3 [protein expression level]


title: Control ChIP-seq from whole organism (ENCLB072KHE)

description:
https://www.encodeproject.org/experiments/ENCSR729ROL/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in worms.
experiment encode accession: ENCSR729ROL
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB072KHE
size range: 150-350

source_name: Caenorhabditis elegans strain OP215 (unc-119(ed3) III; wgIs215) mixed sex L4/young adult insertion targeting C. elegans W03F9.2

value: whole organism

value: L4/young adult

value: Michael Snyder, Stanford

value: CGC

value: ENCBS197UCS at ENCODE; https://www.encodeproject.org/ENCBS197UCS/


title: brain; SD; CFC; CA1; rep3 [protein expression level]


title: Control ChIP-seq from whole organism (ENCLB104FLN)

description:
https://www.encodeproject.org/experiments/ENCSR722SAA/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG3838-eGFP fusion proteins.
experiment encode accession: ENCSR722SAA
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB104FLN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG3838-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG3838

value: whole organisms

value: not applicable

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG3838

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS488PGK at ENCODE; https://www.encodeproject.org/ENCBS488PGK/


title: brain; Sleep; CFC; hilus; rep4 [protein expression level]

value: brain

value: Sleep;CFC

value: hilus


title: brain; SD; CFC; hilus; rep4 [protein expression level]

value: SD;CFC


title: Control ChIP-seq from whole organism (ENCLB514WRG)

description:
https://www.encodeproject.org/experiments/ENCSR729ROL/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in worms.
experiment encode accession: ENCSR729ROL
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB514WRG
size range: 150-350

value: pooled male and female

tag: age

value: unknown

value: ENCBS361TUA at ENCODE; https://www.encodeproject.org/ENCBS361TUA/


title: TF ChIP-seq from whole organism (ENCLB689DZP)

description:
https://www.encodeproject.org/experiments/ENCSR722RUT/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dpn-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR722RUT
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR278WHS
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB689DZP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

value: dpn

value: whole organism

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

value: embryonic

value: 0-16 hour

tag: lab

value: ENCBS730XEG at ENCODE; https://www.encodeproject.org/ENCBS730XEG/


title: brain; Sleep; CFC; CA3; rep4 [protein expression level]


title: TF ChIP-seq from whole organism (ENCLB518FNB)

description:
https://www.encodeproject.org/experiments/ENCSR613JPW/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing snoo-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR613JPW
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR489LXY
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB518FNB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain snoo-MiMIC mixed sex pupa insertion targeting D. melanogaster Snoo

value: Snoo

value: whole organisms

value: not applicable

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

value: pupa

tag: source

value: Hugo Bellen

tag: link

value: ENCBS341GKC at ENCODE; https://www.encodeproject.org/ENCBS341GKC/


title: TF ChIP-seq from whole organism (ENCLB390LGZ)

description:
https://www.encodeproject.org/experiments/ENCSR722RUT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dpn-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR722RUT
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR278WHS
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB390LGZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Kevin White, UChicago

value: Kevin White

value: ENCBS135HKP at ENCODE; https://www.encodeproject.org/ENCBS135HKP/


title: brain; Sleep; CFC; CA1; rep4 [protein expression level]

tag: tissue

value: brain

tag: treatment

value: Sleep;CFC