title: Control ChIP-seq from whole organism (ENCLB669WKE)

description:
https://www.encodeproject.org/experiments/ENCSR564PVU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing HLHm7-eGFP fusion proteins.
experiment encode accession: ENCSR564PVU
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB669WKE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain HLHm7-GFP mixed sex embryo (0-16 hours) insertion targeting D. melanogaster E(spl)m7-HLH

value: whole organism

tag: biosample encode accession

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to HLHm7

value: pooled male and female

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS275BXE at ENCODE; https://www.encodeproject.org/ENCBS275BXE/


title: brain; Sleep; CFC; DG_sup; rep5

status: Public on Feb 27 2024

type: SRA

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

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: other

organism: Mus musculus

source_name: brain

extract_protocol:
Samples were incubated with the following target panels for the Nanostring GeoMx DSP: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA (Lot# MWTA12001). 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

value: Sleep;CFC

tag: region

tag: slide

tag: roi

tag: molecule type

value: targeted RNA


title: brain; SD; CFC; DG_inf; rep6

value: SD;CFC


title: TF ChIP-seq from whole organism (ENCLB257NUL)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR411YUA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-77 in L1 larva worms.
experiment encode accession: ENCSR411YUA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR912HOD
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB257NUL
size range: 150-350

library_source: genomic

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

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP353 (unc-119(tm4063) III; wgIs353) mixed sex L1 larva insertion targeting C. elegans nhr-77

extract_protocol: not provided

tag: antibody

value: whole organisms

value: not applicable

tag: geographic location

tag: encode accession

tag: Sex

tag: dev stage

value: L1 larva

tag: age

value: unknown

tag: lab

value: Michael Snyder, Stanford

tag: source

value: CGC

tag: link

value: ENCBS700LMM at ENCODE; https://www.encodeproject.org/ENCBS700LMM/


title: Control ChIP-seq from whole organism (ENCLB144USP)

description:
https://www.encodeproject.org/experiments/ENCSR565WHH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing rgr-eGFP fusion proteins.
experiment encode accession: ENCSR565WHH
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB144USP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

organism: Drosophila melanogaster

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

value: whole organism

tag: biosample encode accession

tag: note

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

value: pooled male and female

value: wandering third instar larva

value: ENCBS085YNL at ENCODE; https://www.encodeproject.org/ENCBS085YNL/


title: brain; SD; CFC; Hilus; rep6

tag: tissue

value: Hilus


title: Control ChIP-seq from whole organism (ENCLB449KJL)

description:
https://www.encodeproject.org/experiments/ENCSR866WVF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG1832-eGFP fusion proteins.
experiment encode accession: ENCSR866WVF
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-12-15
lab: Kevin White, UChicago
library encode accession: ENCLB449KJL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG1832-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Clamp

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG1832

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS572WXZ at ENCODE; https://www.encodeproject.org/ENCBS572WXZ/


title: TF ChIP-seq from whole organism (ENCLB684HJJ)

description:
https://www.encodeproject.org/experiments/ENCSR411YUA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-77 in L1 larva worms.
experiment encode accession: ENCSR411YUA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR912HOD
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB684HJJ
size range: 150-350

value: whole organisms

value: not applicable

value: L1 larva

value: ENCBS188ILF at ENCODE; https://www.encodeproject.org/ENCBS188ILF/


title: TF ChIP-seq from whole organism (ENCLB343SOM)

description:
https://www.encodeproject.org/experiments/ENCSR412CSG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-ceh-30 in late embryonic worms.
experiment encode accession: ENCSR412CSG
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR643FLY
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB343SOM
size range: 150-350

source_name: Caenorhabditis elegans strain OP120 (unc-119(ed3) III; wgIs120) mixed sex late embryo insertion targeting C. elegans ceh-30

value: late embryonic

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS813HRP at ENCODE; https://www.encodeproject.org/ENCBS813HRP/


title: brain; SD; CFC; DG_inf; rep5

value: brain

tag: treatment

value: SD;CFC

tag: region

value: targeted RNA


title: TF ChIP-seq from whole organism (ENCLB543MCP)

description:
https://www.encodeproject.org/experiments/ENCSR412CSG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-ceh-30 in late embryonic worms.
experiment encode accession: ENCSR412CSG
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR643FLY
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB543MCP
size range: 150-350

value: whole organism

value: pooled male and female

value: ENCBS122TXO at ENCODE; https://www.encodeproject.org/ENCBS122TXO/


title: TF ChIP-seq from whole organism (ENCLB946DYX)

description:
https://www.encodeproject.org/experiments/ENCSR864LDV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10462-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR864LDV
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR778ELF
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB946DYX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG10462-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG10462

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10462

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS522VXK at ENCODE; https://www.encodeproject.org/ENCBS522VXK/


title: brain; SD; CFC; Hilus; rep5

value: Hilus

tag: slide

tag: roi


title: brain; SD; CFC; DG_sup; rep5

tag: molecule type


title: TF ChIP-seq from whole organism (ENCLB965KZT)

description:
https://www.encodeproject.org/experiments/ENCSR864LDV/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10462-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR864LDV
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR778ELF
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB965KZT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organisms

value: not applicable

tag: geographic location

value: ENCBS066NUE at ENCODE; https://www.encodeproject.org/ENCBS066NUE/


title: TF ChIP-seq from whole organism (ENCLB477CJS)

description:
https://www.encodeproject.org/experiments/ENCSR568EBW/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Camta-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR568EBW
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR355TQJ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB477CJS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: Camta

tag: encode accession

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

tag: Sex

value: Hugo Bellen

value: ENCBS871YQU at ENCODE; https://www.encodeproject.org/ENCBS871YQU/


title: TF ChIP-seq from whole organism (ENCLB670CAQ)

description:
https://www.encodeproject.org/experiments/ENCSR412LYV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against ALY-2 in L4 larva worms.
experiment encode accession: ENCSR412LYV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR589NOT
encode release date: 2018-02-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB670CAQ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP217 (unc-119(ed3) III; ddIs172) mixed sex L4 larva insertion targeting C. elegans aly-2

value: whole organism

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

tag: dev stage

value: L4 larva

tag: age

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS818WDR at ENCODE; https://www.encodeproject.org/ENCBS818WDR/


title: TF ChIP-seq from whole organism (ENCLB727GYR)

description:
https://www.encodeproject.org/experiments/ENCSR715MKQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against NHR-25 in L3 larva worms.
experiment encode accession: ENCSR715MKQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR921YEJ
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB727GYR
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: pooled male and female

value: L3 larva

tag: lab

tag: source

value: ENCBS434WDJ at ENCODE; https://www.encodeproject.org/ENCBS434WDJ/


title: TF ChIP-seq from whole organism (ENCLB322LQV)

description:
https://www.encodeproject.org/experiments/ENCSR559AJG/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Ebx-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR559AJG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR612BYM
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB322LQV
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: E(bx)

value: whole organisms

tag: biosample encode accession

value: not applicable

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

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

tag: link

value: ENCBS208ISG at ENCODE; https://www.encodeproject.org/ENCBS208ISG/


title: brain; Sleep; No_CFC; CA3; rep2

tag: tissue

value: brain

value: targeted RNA


title: TF ChIP-seq from whole organism (ENCLB660CML)

description:
https://www.encodeproject.org/experiments/ENCSR568EBW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Camta-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR568EBW
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR355TQJ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB660CML
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Camta

value: whole organism

tag: collection date

tag: note

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

value: 0-24 hour

value: Hugo Bellen

value: ENCBS388WDR at ENCODE; https://www.encodeproject.org/ENCBS388WDR/


title: brain; Sleep; No_CFC; Hilus; rep4

tag: treatment

tag: region

value: Hilus


title: brain; SD; CFC; DG_sup; rep6

value: SD;CFC

tag: slide

tag: roi


title: brain; Sleep; No_CFC; DG_sup; rep4

tag: molecule type


title: TF ChIP-seq from whole organism (ENCLB063LJY)

description:
https://www.encodeproject.org/experiments/ENCSR559AJG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Ebx-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR559AJG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR612BYM
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB063LJY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: E(bx)

value: whole organisms

value: not applicable

tag: geographic location

value: pooled male and female

value: ENCBS640TGE at ENCODE; https://www.encodeproject.org/ENCBS640TGE/


title: TF ChIP-seq from whole organism (ENCLB647TCL)

description:
https://www.encodeproject.org/experiments/ENCSR715MIV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ELT-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR715MIV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR328LRC
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB647TCL
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP354 (unc-119(tm4063) III; wgIs354) hermaphrodite mixed stage (embryo) insertion targeting C. elegans elt-1

tag: encode accession

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

tag: Sex

value: hermaphrodite

value: mixed stage (embryonic)

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS099QHL at ENCODE; https://www.encodeproject.org/ENCBS099QHL/


title: TF ChIP-seq from whole organism (ENCLB304ZFN)

description:
https://www.encodeproject.org/experiments/ENCSR715MIV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ELT-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR715MIV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR328LRC
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB304ZFN
fragmentation methods: sonication (generic microtip)

value: whole organism

tag: dev stage

tag: age

value: ENCBS842CHE at ENCODE; https://www.encodeproject.org/ENCBS842CHE/


title: brain; Sleep; No_CFC; Hilus; rep3

value: brain

value: targeted RNA


title: brain; Sleep; No_CFC; DG_inf; rep3


title: brain; Sleep; No_CFC; DG_sup; rep3


title: brain; SD; No_CFC; CA1; rep2


title: Control ChIP-seq from whole organism (ENCLB927ASF)

description:
https://www.encodeproject.org/experiments/ENCSR557GAY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG8319-eGFP fusion proteins.
experiment encode accession: ENCSR557GAY
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB927ASF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG8319-GFP mixed sex prepupa insertion targeting D. melanogaster CG8319

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8319

value: prepupa

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS370MSM at ENCODE; https://www.encodeproject.org/ENCBS370MSM/


title: Control ChIP-seq from whole organism (ENCLB502CHT)

description:
https://www.encodeproject.org/experiments/ENCSR555SGB/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing ind-eGFP fusion proteins.
experiment encode accession: ENCSR555SGB
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB502CHT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organisms

tag: biosample encode accession

value: not applicable

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

value: pooled male and female

value: embryonic

value: 0-16 hour

tag: link

value: ENCBS357DPU at ENCODE; https://www.encodeproject.org/ENCBS357DPU/


title: brain; SD; No_CFC; CA3; rep2

tag: tissue


title: TF ChIP-seq from whole organism (ENCLB891ZYT)

description:
https://www.encodeproject.org/experiments/ENCSR559AJG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Ebx-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR559AJG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR612BYM
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB891ZYT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: E(bx)

tag: collection date

tag: note

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

value: ENCBS520MHL at ENCODE; https://www.encodeproject.org/ENCBS520MHL/


title: Control ChIP-seq from whole organism (ENCLB437DZT)

description:
https://www.encodeproject.org/experiments/ENCSR903ZHS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR903ZHS
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB437DZT
size range: 150-350

source_name: Caenorhabditis elegans strain OP217 (unc-119(ed3) III; ddIs172) mixed sex L1 larva insertion targeting C. elegans aly-2

value: whole organism

value: L1 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS879YHP at ENCODE; https://www.encodeproject.org/ENCBS879YHP/


title: brain; SD; No_CFC; DG_inf; rep4

value: brain

tag: treatment

tag: region

value: targeted RNA


title: TF ChIP-seq from whole organism (ENCLB840BWX)

description:
https://www.encodeproject.org/experiments/ENCSR405OOP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-ztf-4 in L1 larva worms.
experiment encode accession: ENCSR405OOP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR520RET
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB840BWX
size range: 150-350

source_name: Caenorhabditis elegans strain OP322 (unc-119(ed3) III; wgIs322) mixed sex L1 larva insertion targeting C. elegans ztf-4

value: whole organisms

value: not applicable

value: ENCBS785NWL at ENCODE; https://www.encodeproject.org/ENCBS785NWL/


title: TF ChIP-seq from whole organism (ENCLB316OGR)

description:
https://www.encodeproject.org/experiments/ENCSR715MKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against NHR-25 in L3 larva worms.
experiment encode accession: ENCSR715MKQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR921YEJ
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB316OGR
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: L3 larva

value: Michael Snyder

value: ENCBS271QBM at ENCODE; https://www.encodeproject.org/ENCBS271QBM/


title: Control ChIP-seq from whole organism (ENCLB752UGK)

description:
https://www.encodeproject.org/experiments/ENCSR903ZHS/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR903ZHS
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB752UGK
size range: 150-350

value: ENCBS259ITR at ENCODE; https://www.encodeproject.org/ENCBS259ITR/


title: Control ChIP-seq from whole organism (ENCLB582PEY)

description:
https://www.encodeproject.org/experiments/ENCSR691LGL/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing pdm3-eGFP fusion proteins.
experiment encode accession: ENCSR691LGL
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB582PEY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain pdm3-GFP mixed sex prepupa at white prepupa stage insertion targeting D. melanogaster pdm3

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to pdm3

value: prepupa

value: Kevin White, UChicago

value: Kevin White

tag: fly synchronization stage

value: white prepupa

value: ENCBS835WHP at ENCODE; https://www.encodeproject.org/ENCBS835WHP/


title: brain; SD; No_CFC; Hilus; rep4

value: brain

value: Hilus

tag: slide

tag: roi

tag: molecule type

value: targeted RNA


title: brain; Sleep; No_CFC; CA1; rep2


title: brain; SD; No_CFC; DG_sup; rep4


title: Control ChIP-seq from whole organism (ENCLB785MXQ)

description:
https://www.encodeproject.org/experiments/ENCSR403WXH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR403WXH
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB785MXQ
size range: 150-350

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

value: whole organisms

value: not applicable

tag: geographic location

tag: encode accession

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

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


title: brain; SD; No_CFC; DG_inf; rep3

source_name: brain


title: Control ChIP-seq from whole organism (ENCLB868FXL)

description:
https://www.encodeproject.org/experiments/ENCSR862VRN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Hr39-eGFP fusion proteins.
experiment encode accession: ENCSR862VRN
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB868FXL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Hr39-RC-GFP mixed sex prepupa at white prepupa stage insertion targeting D. melanogaster Hr39

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Hr39

tag: Sex

value: pooled male and female

tag: dev stage

value: ENCBS166APO at ENCODE; https://www.encodeproject.org/ENCBS166APO/


title: brain; SD; No_CFC; Hilus; rep3


title: TF ChIP-seq from whole organism (ENCLB206CYB)

description:
https://www.encodeproject.org/experiments/ENCSR405OOP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-ztf-4 in L1 larva worms.
experiment encode accession: ENCSR405OOP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR520RET
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB206CYB
size range: 150-350

tag: antibody

value: L1 larva

tag: age

tag: lab

value: ENCBS029SWV at ENCODE; https://www.encodeproject.org/ENCBS029SWV/


title: brain; Sleep; No_CFC; DG_inf; rep4


title: Control ChIP-seq from whole organism (ENCLB739ZLS)

description:
https://www.encodeproject.org/experiments/ENCSR691GHG/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing acj6-eGFP fusion proteins.
experiment encode accession: ENCSR691GHG
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB739ZLS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: biosample encode accession

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

value: prepupa

value: Kevin White, UChicago

tag: source

value: Kevin White

value: white prepupa

tag: link

value: ENCBS567PJU at ENCODE; https://www.encodeproject.org/ENCBS567PJU/


title: brain; SD; No_CFC; DG_sup; rep3

tag: tissue

value: brain

value: targeted RNA


title: brain; Sleep; CFC; CA1; rep2

tag: treatment

value: Sleep;CFC


title: Control ChIP-seq from whole organism (ENCLB948WPK)

description:
https://www.encodeproject.org/experiments/ENCSR403WXH/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR403WXH
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB948WPK
size range: 150-350

value: whole organisms

tag: collection date

value: not applicable

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

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


title: brain; Sleep; CFC; CA3; rep2

tag: region


title: brain; Sleep; CFC; DG_inf; rep4

tag: slide


title: TF ChIP-seq from whole organism (ENCLB574OCY)

description:
https://www.encodeproject.org/experiments/ENCSR860FUA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG4854-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR860FUA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR100SUV
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB574OCY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 4000

source_name: Drosophila melanogaster strain CG4854-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG4854

value: whole organism

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG4854

value: pooled male and female

value: embryonic

value: 0-24 hour

value: ENCBS368OQQ at ENCODE; https://www.encodeproject.org/ENCBS368OQQ/


title: Control ChIP-seq from whole organism (ENCLB155VJH)

description:
https://www.encodeproject.org/experiments/ENCSR689PMU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing fd85E-eGFP fusion proteins.
experiment encode accession: ENCSR689PMU
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB155VJH
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: Transgenic D. mel line, stably expressing a C-terminal GFP fused to fd85E-aka FoxP

value: prepupa

value: Kevin White, UChicago

value: Kevin White

value: ENCBS812MVS at ENCODE; https://www.encodeproject.org/ENCBS812MVS/


title: TF ChIP-seq from whole organism (ENCLB466IFG)

description:
https://www.encodeproject.org/experiments/ENCSR403CSJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-ztf-4 in L3 larva worms.
experiment encode accession: ENCSR403CSJ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR787UFX
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB466IFG
size range: 150-350

source_name: Caenorhabditis elegans strain OP322 (unc-119(ed3) III; wgIs322) mixed sex L3 larva insertion targeting C. elegans ztf-4

value: whole organisms

value: not applicable

value: L3 larva

value: ENCBS638RTI at ENCODE; https://www.encodeproject.org/ENCBS638RTI/


title: brain; Sleep; CFC; DG_sup; rep3

value: brain

value: Sleep;CFC

tag: roi

tag: molecule type

value: targeted RNA


title: TF ChIP-seq from whole organism (ENCLB311OXY)

description:
https://www.encodeproject.org/experiments/ENCSR403CSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-ztf-4 in L3 larva worms.
experiment encode accession: ENCSR403CSJ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR787UFX
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB311OXY
size range: 150-350

value: whole organism

tag: geographic location

tag: encode accession

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS938NHK at ENCODE; https://www.encodeproject.org/ENCBS938NHK/


title: TF ChIP-seq from whole organism (ENCLB512ETG)

description:
https://www.encodeproject.org/experiments/ENCSR900CNJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-fos-1 in L2 larva worms.
experiment encode accession: ENCSR900CNJ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR357SUE
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB512ETG
size range: 150-350

source_name: Caenorhabditis elegans strain OP304 (unc-119(ed3) III; wgIs304) mixed sex L2 larva insertion targeting C. elegans fos-1

tag: Sex

value: pooled male and female

tag: dev stage

value: L2 larva

value: ENCBS945EQK at ENCODE; https://www.encodeproject.org/ENCBS945EQK/


title: brain; Sleep; CFC; Hilus; rep4

value: Hilus


title: brain; Sleep; CFC; Hilus; rep3


title: brain; Sleep; CFC; DG_inf; rep3


title: brain; SD; CFC; CA3; rep2

value: SD;CFC


title: brain; Sleep; CFC; DG_sup; rep4


title: TF ChIP-seq from whole organism (ENCLB331TYZ)

description:
https://www.encodeproject.org/experiments/ENCSR860FUA/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG4854-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR860FUA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR100SUV
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB331TYZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 4000

tag: antibody

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG4854

value: embryonic

tag: age

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS977JAU at ENCODE; https://www.encodeproject.org/ENCBS977JAU/


title: brain; SD; CFC; CA1; rep2

value: brain

value: targeted RNA


title: TF ChIP-seq from whole organism (ENCLB302BFL)

description:
https://www.encodeproject.org/experiments/ENCSR855PBX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Mnt-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR855PBX
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR681OTG
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB302BFL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: Mnt

value: whole organism

tag: biosample encode accession

value: not applicable

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

value: female

value: adult

value: unknown

tag: lab

value: ENCBS156ZPY at ENCODE; https://www.encodeproject.org/ENCBS156ZPY/


title: brain; SD; CFC; DG_inf; rep4

value: SD;CFC


title: TF ChIP-seq from whole organism (ENCLB213YTW)

description:
https://www.encodeproject.org/experiments/ENCSR898YRV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-efl-1 in L1 larva worms.
experiment encode accession: ENCSR898YRV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR294SZY
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB213YTW
size range: 150-350

source_name: Caenorhabditis elegans strain YL418 (unc-119(ed3)III; vrIs65[pGES-1::EFL-1::GFP FLAG:EFL-1 3'UTR, unc-119 (+)]) mixed sex L1 larva insertion targeting C. elegans efl-1

value: whole organisms

value: pooled male and female

value: L1 larva

value: Michael Snyder, Stanford

tag: source

value: CGC

tag: link

value: ENCBS823ZKM at ENCODE; https://www.encodeproject.org/ENCBS823ZKM/


title: TF ChIP-seq from whole organism (ENCLB593ZXJ)

description:
https://www.encodeproject.org/experiments/ENCSR900CNJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-fos-1 in L2 larva worms.
experiment encode accession: ENCSR900CNJ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR357SUE
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB593ZXJ
size range: 150-350

value: L2 larva

value: ENCBS532NSF at ENCODE; https://www.encodeproject.org/ENCBS532NSF/


title: brain; SD; CFC; Hilus; rep4

tag: tissue

value: brain

tag: treatment

value: Hilus

value: targeted RNA


title: brain; SD; CFC; DG_sup; rep4

tag: region


title: TF ChIP-seq from whole organism (ENCLB658FDW)

description:
https://www.encodeproject.org/experiments/ENCSR855AGQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ey-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR855AGQ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR266WRF
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB658FDW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: ey

value: whole organism

tag: collection date

value: not applicable

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

value: wandering third instar larva

value: Kevin White, UChicago

value: Kevin White

value: ENCBS301UEW at ENCODE; https://www.encodeproject.org/ENCBS301UEW/


title: TF ChIP-seq from whole organism (ENCLB031XGM)

description:
https://www.encodeproject.org/experiments/ENCSR898YRV/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq against eGFP-efl-1 in L1 larva worms.
experiment encode accession: ENCSR898YRV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR294SZY
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB031XGM
size range: 150-350

value: whole organisms

value: pooled male and female

value: L1 larva

value: unknown

value: ENCBS332TTD at ENCODE; https://www.encodeproject.org/ENCBS332TTD/


title: TF ChIP-seq from whole organism (ENCLB720JUJ)

description:
https://www.encodeproject.org/experiments/ENCSR855AGQ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ey-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR855AGQ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR266WRF
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB720JUJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: note

value: ENCBS612EGK at ENCODE; https://www.encodeproject.org/ENCBS612EGK/


title: brain; SD; CFC; DG_inf; rep3

value: brain

value: SD;CFC

tag: slide

tag: roi


title: TF ChIP-seq from whole organism (ENCLB867VGJ)

description:
https://www.encodeproject.org/experiments/ENCSR711PDS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against ELT-3 in L1 larva worms.
experiment encode accession: ENCSR711PDS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR354PDY
encode release date: 2017-11-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB867VGJ
fragmentation methods: sonication (generic microtip)

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

tag: geographic location

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

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS736FUR at ENCODE; https://www.encodeproject.org/ENCBS736FUR/


title: brain; SD; CFC; Hilus; rep3

value: Hilus

tag: molecule type

value: targeted RNA


title: Control ChIP-seq from whole organism (ENCLB314CIF)

description:
https://www.encodeproject.org/experiments/ENCSR854PLB/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing GATAd-eGFP fusion proteins.
experiment encode accession: ENCSR854PLB
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB314CIF
fragmentation methods: sonication (Bioruptor generic)

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

value: whole organism

value: not applicable

tag: encode accession

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

tag: Sex

value: wandering third instar larva

value: Kevin White, UChicago

value: ENCBS485HNU at ENCODE; https://www.encodeproject.org/ENCBS485HNU/


title: brain; SD; CFC; DG_sup; rep3


title: brain; Sleep; No_CFC; CA3; rep1


title: brain; Sleep; No_CFC; CA1; rep1


title: TF ChIP-seq from whole organism (ENCLB296JBI)

description:
https://www.encodeproject.org/experiments/ENCSR855PBX/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Mnt-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR855PBX
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR681OTG
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB296JBI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: Mnt

value: whole organisms

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

value: female

tag: dev stage

value: adult

value: unknown

value: Kevin White

value: ENCBS178SMZ at ENCODE; https://www.encodeproject.org/ENCBS178SMZ/


title: Control ChIP-seq from whole organism (ENCLB621HBI)

description:
https://www.encodeproject.org/experiments/ENCSR546LJI/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Pdp1-eGFP fusion proteins.
experiment encode accession: ENCSR546LJI
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB621HBI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Pdp1-MiMIC-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Pdp1

tag: biosample encode accession

value: D. mel line contraining an intronic eGFP exon to create a Pdp1-GFP fusion gene

value: pooled male and female

value: embryonic

tag: age

value: 0-24 hour

value: Hugo Bellen

value: ENCBS983LGN at ENCODE; https://www.encodeproject.org/ENCBS983LGN/


title: brain; Sleep; No_CFC; Hilus; rep2

value: brain

value: Hilus

value: targeted RNA


title: brain; Sleep; No_CFC; DG_inf; rep2


title: brain; Sleep; No_CFC; DG_inf; rep1


title: brain; Sleep; No_CFC; DG_sup; rep2


title: Control ChIP-seq from whole organism (ENCLB202EFA)

description:
https://www.encodeproject.org/experiments/ENCSR685RPG/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing kay-eGFP fusion proteins.
experiment encode accession: ENCSR685RPG
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB202EFA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

value: not applicable

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

tag: lab

value: Kevin White, UChicago

tag: source

value: ENCBS283CEA at ENCODE; https://www.encodeproject.org/ENCBS283CEA/


title: TF ChIP-seq from whole organism (ENCLB612OPP)

description:
https://www.encodeproject.org/experiments/ENCSR898ATP/
***************
biological replicate number: 1
technical replicate number: 2
description: ChIP-seq of transgenic worms expressing K09A11.1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR898ATP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR293HER
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB612OPP
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP372 (unc-119(tm4063) III; wgIs372) hermaphrodite late embryo insertion targeting C. elegans K09A11.1

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to K09A11.1

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: link

value: ENCBS874KTH at ENCODE; https://www.encodeproject.org/ENCBS874KTH/


title: Control ChIP-seq from whole organism (ENCLB368DSS)

description:
https://www.encodeproject.org/experiments/ENCSR543PPU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Antp-eGFP fusion proteins.
experiment encode accession: ENCSR543PPU
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB368DSS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Hugo Bellen

value: ENCBS537EBT at ENCODE; https://www.encodeproject.org/ENCBS537EBT/


title: TF ChIP-seq from whole organism (ENCLB910PXC)

description:
https://www.encodeproject.org/experiments/ENCSR898ATP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing K09A11.1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR898ATP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR293HER
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB910PXC
fragmentation methods: sonication (generic microtip)

value: whole organism

value: not applicable


title: brain; Sleep; No_CFC; DG_sup; rep1

tag: tissue

value: brain

tag: treatment

value: targeted RNA


title: brain; SD; No_CFC; DG_inf; rep2

tag: region


title: brain; SD; No_CFC; CA1; rep1


title: Control ChIP-seq from whole organism (ENCLB115JEV)

description:
https://www.encodeproject.org/experiments/ENCSR685FEO/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Hr96-eGFP fusion proteins.
experiment encode accession: ENCSR685FEO
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB115JEV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Hr96-GFP female adult insertion targeting D. melanogaster Hr96

value: whole organisms

tag: collection date

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Hr96

value: female

value: adult

value: Kevin White, UChicago

value: Kevin White

value: ENCBS601EVD at ENCODE; https://www.encodeproject.org/ENCBS601EVD/


title: brain; SD; No_CFC; CA3; rep1

source_name: brain

tag: slide

tag: roi


title: Control ChIP-seq from whole organism (ENCLB662FIS)

description:
https://www.encodeproject.org/experiments/ENCSR685DWE/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG13123-eGFP fusion proteins.
experiment encode accession: ENCSR685DWE
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB662FIS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG13123-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG13123

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG13123

value: ENCBS368WBQ at ENCODE; https://www.encodeproject.org/ENCBS368WBQ/


title: TF ChIP-seq from whole organism (ENCLB766FYH)

description:
https://www.encodeproject.org/experiments/ENCSR898ATP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing K09A11.1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR898ATP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR293HER
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB766FYH
fragmentation methods: sonication (generic microtip)

tag: encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to K09A11.1

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS337KTQ at ENCODE; https://www.encodeproject.org/ENCBS337KTQ/


title: TF ChIP-seq from whole organism (ENCLB522KIW)

description:
https://www.encodeproject.org/experiments/ENCSR898ATP/
***************
biological replicate number: 2
technical replicate number: 2
description: ChIP-seq of transgenic worms expressing K09A11.1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR898ATP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR293HER
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB522KIW
fragmentation methods: sonication (generic microtip)

value: whole organism

value: not applicable

tag: Sex


title: brain; SD; No_CFC; DG_sup; rep2

value: brain

tag: molecule type

value: targeted RNA


title: Control ChIP-seq from whole organism (ENCLB528JOD)

description:
https://www.encodeproject.org/experiments/ENCSR684NLC/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing gcm2-eGFP fusion proteins.
experiment encode accession: ENCSR684NLC
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB528JOD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain gcm2-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster gcm2

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to gcm2

value: pooled male and female

tag: dev stage

value: embryonic

value: 0-24 hour

value: ENCBS425QGL at ENCODE; https://www.encodeproject.org/ENCBS425QGL/


title: TF ChIP-seq from whole organism (ENCLB680PSE)

description:
https://www.encodeproject.org/experiments/ENCSR898HZV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-21 in L2 larva worms.
experiment encode accession: ENCSR898HZV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR002EBG
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB680PSE
size range: 150-350

source_name: Caenorhabditis elegans strain OP361 (unc-119(tm4063) III; wgIs361) mixed sex L2 larva insertion targeting C. elegans nhr-21

tag: antibody

tag: biosample encode accession

value: L2 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS934VAT at ENCODE; https://www.encodeproject.org/ENCBS934VAT/


title: brain; SD; No_CFC; DG_inf; rep1


title: Control ChIP-seq from whole organism (ENCLB502EGS)

description:
https://www.encodeproject.org/experiments/ENCSR852VMM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing gfzf-eGFP fusion proteins.
experiment encode accession: ENCSR852VMM
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB502EGS
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

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

tag: age

tag: lab

value: Kevin White, UChicago

value: Kevin White

value: ENCBS784VPK at ENCODE; https://www.encodeproject.org/ENCBS784VPK/


title: TF ChIP-seq from whole organism (ENCLB351YIV)

description:
https://www.encodeproject.org/experiments/ENCSR898HZV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-21 in L2 larva worms.
experiment encode accession: ENCSR898HZV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR002EBG
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB351YIV
size range: 150-350

value: whole organism

value: not applicable

value: unknown

tag: source

tag: link

value: ENCBS658NRN at ENCODE; https://www.encodeproject.org/ENCBS658NRN/


title: brain; SD; No_CFC; Hilus; rep1

tag: tissue

value: brain

tag: treatment

value: Hilus

value: targeted RNA


title: TF ChIP-seq from whole organism (ENCLB398EQN)

description:
https://www.encodeproject.org/experiments/ENCSR711PDS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against ELT-3 in L1 larva worms.
experiment encode accession: ENCSR711PDS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR354PDY
encode release date: 2017-11-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB398EQN
fragmentation methods: sonication (generic microtip)

value: whole organisms

tag: collection date

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

value: pooled male and female

value: L1 larva

value: Michael Snyder

value: ENCBS364VAL at ENCODE; https://www.encodeproject.org/ENCBS364VAL/


title: TF ChIP-seq from whole organism (ENCLB988RFO)

description:
https://www.encodeproject.org/experiments/ENCSR710IDA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-zag-1 in L4 larva worms.
experiment encode accession: ENCSR710IDA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR509HPC
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB988RFO
size range: 150-350

source_name: Caenorhabditis elegans strain OP83 (unc-119(ed3) III; wgIs83) mixed sex L4 larva insertion targeting C. elegans zag-1

value: L4 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS115CLS at ENCODE; https://www.encodeproject.org/ENCBS115CLS/


title: brain; SD; No_CFC; DG_sup; rep1

tag: region


title: TF ChIP-seq from whole organism (ENCLB311KOH)

description:
https://www.encodeproject.org/experiments/ENCSR682NHG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing NC2β-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR682NHG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR323PMD
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB311KOH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

tag: note

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS918HZM at ENCODE; https://www.encodeproject.org/ENCBS918HZM/


title: brain; Sleep; No_CFC; Hilus; rep1

value: brain

value: Hilus

tag: slide

tag: roi

value: targeted RNA


title: brain; Sleep; CFC; CA1; rep1

value: Sleep;CFC


title: brain; Sleep; CFC; CA3; rep1


title: TF ChIP-seq from whole organism (ENCLB919VQX)

description:
https://www.encodeproject.org/experiments/ENCSR682NHG/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing NC2β-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR682NHG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR323PMD
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB919VQX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: not applicable

tag: geographic location

tag: encode accession

value: pooled male and female

value: ENCBS924LCG at ENCODE; https://www.encodeproject.org/ENCBS924LCG/


title: brain; SD; No_CFC; Hilus; rep2

tag: molecule type


title: Control ChIP-seq from whole organism (ENCLB479MCG)

description:
https://www.encodeproject.org/experiments/ENCSR898AMG/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 worms.
experiment encode accession: ENCSR898AMG
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB479MCG
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP231 (unc-119(ed3) III; wgIs231) mixed sex L4 larva insertion targeting C. elegans ZK546.5

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to ZK546.5

tag: Sex

tag: dev stage

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS745TNV at ENCODE; https://www.encodeproject.org/ENCBS745TNV/


title: brain; Sleep; CFC; DG_inf; rep2


title: brain; Sleep; CFC; DG_sup; rep2


title: brain; Sleep; CFC; DG_inf; rep1


title: Control ChIP-seq from whole organism (ENCLB600LIV)

description:
https://www.encodeproject.org/experiments/ENCSR681OTG/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Mnt-eGFP fusion proteins.
experiment encode accession: ENCSR681OTG
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB600LIV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

tag: biosample encode accession

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

value: female

value: adult

value: Kevin White, UChicago

value: ENCBS777EOU at ENCODE; https://www.encodeproject.org/ENCBS777EOU/


title: TF ChIP-seq from whole organism (ENCLB435DPN)

description:
https://www.encodeproject.org/experiments/ENCSR681YMA/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing pho-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR681YMA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR820IUK
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB435DPN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

value: pho

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

value: embryonic

tag: age

value: 0-24 hour

value: Kevin White

value: ENCBS686TXN at ENCODE; https://www.encodeproject.org/ENCBS686TXN/


title: Control ChIP-seq from whole organism (ENCLB172DPR)

description:
https://www.encodeproject.org/experiments/ENCSR680BUH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing ems-eGFP fusion proteins.
experiment encode accession: ENCSR680BUH
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB172DPR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain 16T-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster ems

value: whole organisms

value: not applicable

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

value: pooled male and female

tag: lab

tag: source

value: ENCBS860DMW at ENCODE; https://www.encodeproject.org/ENCBS860DMW/


title: brain; Sleep; CFC; Hilus; rep1

tag: tissue

value: brain

value: Sleep;CFC

value: Hilus

value: targeted RNA


title: brain; Sleep; CFC; Hilus; rep2

tag: treatment


title: TF ChIP-seq from whole organism (ENCLB943UDT)

description:
https://www.encodeproject.org/experiments/ENCSR595DCM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against ZK546.5 in L4 worms.
experiment encode accession: ENCSR595DCM
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR898AMG
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB943UDT
fragmentation methods: sonication (generic microtip)

value: whole organism

tag: collection date

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to ZK546.5

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

tag: link

value: ENCBS936ZRD at ENCODE; https://www.encodeproject.org/ENCBS936ZRD/


title: Control ChIP-seq from whole organism (ENCLB290TTV)

description:
https://www.encodeproject.org/experiments/ENCSR892ECY/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing F49E8.2-eGFP fusion proteins.
experiment encode accession: ENCSR892ECY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB290TTV
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP383 (unc-119(tm4063) III; wgIs383) hermaphrodite young adult 48 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans oef-1

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F49E8-2

value: hermaphrodite

value: young adult

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS964ERD at ENCODE; https://www.encodeproject.org/ENCBS964ERD/


title: brain; Sleep; CFC; DG_sup; rep1

value: brain

value: Sleep;CFC

tag: region

tag: slide

tag: roi


title: brain; SD; CFC; CA3; rep1

value: SD;CFC

tag: molecule type

value: targeted RNA


title: TF ChIP-seq from whole organism (ENCLB591RFX)

description:
https://www.encodeproject.org/experiments/ENCSR710IDA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-zag-1 in L4 larva worms.
experiment encode accession: ENCSR710IDA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR509HPC
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB591RFX
size range: 150-350

value: whole organism

value: whole organisms

tag: biosample encode accession

value: not applicable

tag: geographic location

tag: encode accession

tag: Sex

value: pooled male and female

tag: dev stage

value: L4 larva

value: CGC

value: ENCBS910DKO at ENCODE; https://www.encodeproject.org/ENCBS910DKO/


title: brain; SD; CFC; DG_inf; rep2

tag: tissue


title: Control ChIP-seq from whole organism (ENCLB672ZPF)

description:
https://www.encodeproject.org/experiments/ENCSR535ZRZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing her-eGFP fusion proteins.
experiment encode accession: ENCSR535ZRZ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB672ZPF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

value: embryonic

tag: age

value: 0-24 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS256ZVR at ENCODE; https://www.encodeproject.org/ENCBS256ZVR/


title: brain; SD; CFC; DG_sup; rep2

value: brain

tag: treatment


title: Control ChIP-seq from whole organism (ENCLB599OLP)

description:
https://www.encodeproject.org/experiments/ENCSR883CKA/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR883CKA
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB599OLP
size range: 150-350

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

tag: collection date

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

tag: link

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


title: TF ChIP-seq from whole organism (ENCLB035AOQ)

description:
https://www.encodeproject.org/experiments/ENCSR595DCM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against ZK546.5 in L4 worms.
experiment encode accession: ENCSR595DCM
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR898AMG
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB035AOQ
fragmentation methods: sonication (generic microtip)

tag: antibody

value: whole organism

value: whole organisms

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to ZK546.5

value: Michael Snyder

value: ENCBS472LQI at ENCODE; https://www.encodeproject.org/ENCBS472LQI/


title: brain; SD; CFC; DG_inf; rep1

value: SD;CFC

tag: region

tag: slide

value: targeted RNA


title: brain; SD; CFC; Hilus; rep2

value: Hilus

tag: roi

tag: molecule type


title: brain; SD; CFC; CA1; rep1


title: Control ChIP-seq from whole organism (ENCLB113CZE)

description:
https://www.encodeproject.org/experiments/ENCSR278WHS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing dpn-eGFP fusion proteins.
experiment encode accession: ENCSR278WHS
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB113CZE
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: biosample encode accession

value: not applicable

tag: geographic location

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

value: pooled male and female

value: embryonic

value: 0-16 hour

value: ENCBS827NDH at ENCODE; https://www.encodeproject.org/ENCBS827NDH/


title: brain; SD; CFC; DG_sup; rep1

value: brain


title: Control ChIP-seq from whole organism (ENCLB049EHI)

description:
https://www.encodeproject.org/experiments/ENCSR883CKA/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR883CKA
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB049EHI
size range: 150-350

tag: encode accession

tag: Sex

value: L2 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

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


title: Control ChIP-seq from whole organism (ENCLB017ZDG)

description:
https://www.encodeproject.org/experiments/ENCSR537BJC/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Bab2-eGFP fusion proteins.
experiment encode accession: ENCSR537BJC
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB017ZDG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain bab2-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster bab2

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Bab2

tag: dev stage

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS830TRJ at ENCODE; https://www.encodeproject.org/ENCBS830TRJ/


title: brain; SD; CFC; Hilus; rep1

tag: tissue

value: SD;CFC

value: Hilus

value: targeted RNA


title: TF ChIP-seq from whole organism (ENCLB592EYQ)

description:
https://www.encodeproject.org/experiments/ENCSR273JZM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing crc-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR273JZM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR479BNA
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB592EYQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: crc

value: not applicable

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

value: pooled male and female

value: embryonic

tag: age

tag: lab

value: Hugo Bellen

value: ENCBS355HXQ at ENCODE; https://www.encodeproject.org/ENCBS355HXQ/


title: Control ChIP-seq from whole organism (ENCLB629AJV)

description:
https://www.encodeproject.org/experiments/ENCSR898AMG/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L4 worms.
experiment encode accession: ENCSR898AMG
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB629AJV
fragmentation methods: sonication (generic microtip)

value: whole organism

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to ZK546.5

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

tag: source

value: Michael Snyder

value: ENCBS209TKB at ENCODE; https://www.encodeproject.org/ENCBS209TKB/


title: Gene Expression WT 17 days

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description:
10x Genomics
count_table.csv
metadata.csv

library_source: transcriptomic

data_processing:
Raw sequencing data were demultiplexed, aligned to the mouse genome (mm10) and UMI-collapsed using CellRanger.
Assembly: mm10
Supplementary files format and content: CSV gene counts
Supplementary files format and content: CSV metadata

molecule: total RNA

source_name: beta cell graft

extract_protocol:
Cells were  lysed in droplets using the 10X Chromium instrument.
10x Genomics 3' single cell RNA sequencing protocol v3.1 & Cell hashing protocol (https://citeseq.files.wordpress.com/2019/02/cell_hashing_protocol_190213.pdf)

value: beta cell graft

tag: cell line

tag: cell type

value: beta cell

tag: genotype

value: Wild type

tag: treatment

value: syngenic autoreactive splenocytes


title: Gene Expression WT 10 days


title: TF ChIP-seq from whole organism (ENCLB955LKC)

description:
https://www.encodeproject.org/experiments/ENCSR399PUK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-snpc-4 in L3 larva worms.
experiment encode accession: ENCSR399PUK
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR613HUF
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB955LKC
size range: 150-350

source_name: Caenorhabditis elegans strain OP179 (unc-119(ed3) III; wgIs179) mixed sex L3 larva insertion targeting C. elegans snpc-4

tag: antibody

value: whole organisms

tag: collection date

value: not applicable

value: L3 larva

value: CGC

tag: link

value: ENCBS133NAH at ENCODE; https://www.encodeproject.org/ENCBS133NAH/


title: Gene Expression KO 17 days

value: Rnls mutant


title: TF ChIP-seq from whole organism (ENCLB900VZZ)

description:
https://www.encodeproject.org/experiments/ENCSR399PUK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-snpc-4 in L3 larva worms.
experiment encode accession: ENCSR399PUK
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR613HUF
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB900VZZ
size range: 150-350

value: whole organism

value: pooled male and female

value: ENCBS813ARE at ENCODE; https://www.encodeproject.org/ENCBS813ARE/


title: Control ChIP-seq from whole organism (ENCLB322KEV)

description:
https://www.encodeproject.org/experiments/ENCSR269HSO/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG11762-eGFP fusion proteins.
experiment encode accession: ENCSR269HSO
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB322KEV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG11762-GFP mixed sex prepupa insertion targeting D. melanogaster ouib

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG11762

value: prepupa

value: unknown

value: Kevin White, UChicago

value: Kevin White

value: ENCBS835HGK at ENCODE; https://www.encodeproject.org/ENCBS835HGK/


title: Gene Expression KO 10 days

value: beta cell graft

value: beta cell


title: Bulk RNAseq MYOD1 WT Rep 3

city: Berlin

first: Alexandre

middle: P

last: Magalhaes

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Bulk RNA-seq

data_processing:
Reads were mapped to a genome using STAR aligner. Count read tables were generated by the same program
genome_build: mm39

molecule: polyA RNA

extract_protocol:
C2C12 induced cells  were harvested following the Direct-zolTM RNA MicroPrep Kit (Zymo Research) standard protocol
1 μg of RNA of each sample was used as input for library preparation using the KAPA Stranded mRNA-Seq Kit (Roche) following the manufacturer’s instructions. Unique Dual-Indexed Set-B (UDI; KAPA biosystems) adapters were ligated and the library was amplified for 8 cycles
Paired-end 100 with 50 million fragments per library


title: TF ChIP-seq from whole organism (ENCLB330DUQ)

description:
https://www.encodeproject.org/experiments/ENCSR269HHK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing kay-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR269HHK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR331XEF
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB330DUQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain kay-GFP male adult insertion targeting D. melanogaster kay

value: kay

value: whole organisms

tag: biosample encode accession

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

value: male

value: adult

value: ENCBS437GJH at ENCODE; https://www.encodeproject.org/ENCBS437GJH/


title: Bulk RNAseq MYOD1 WT Rep 2

description: Bulk RNA-seq


title: TF ChIP-seq from whole organism (ENCLB383BTV)

description:
https://www.encodeproject.org/experiments/ENCSR592DAH/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-F16B12.6 in L1 larva worms.
experiment encode accession: ENCSR592DAH
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR622TPD
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB383BTV
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: not applicable

tag: geographic location

value: L1 larva

value: Michael Snyder, Stanford

value: CGC

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


title: TF ChIP-seq from whole organism (ENCLB781RCO)

description:
https://www.encodeproject.org/experiments/ENCSR592DAH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-F16B12.6 in L1 larva worms.
experiment encode accession: ENCSR592DAH
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR622TPD
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB781RCO
size range: 150-350

tag: encode accession

value: pooled male and female

value: unknown

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


title: Bulk RNAseq MYOD1 WT Rep 1

description: Bulk RNA-seq


title: Bulk RNAseq MYOD1  AroPerfect-C Rep 2

description: Bulk RNA-seq


title: Bulk RNAseq MYOD1  AroPerfect-C Rep 3

description: Bulk RNA-seq


title: Control ChIP-seq from whole organism (ENCLB133GFR)

description:
https://www.encodeproject.org/experiments/ENCSR589YYN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR589YYN
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB133GFR
size range: 150-350

source_name: Caenorhabditis elegans strain OP186 (unc-119(ed3) III; wgIs186) mixed sex L2 larva insertion targeting C. elegans unc-39

tag: Sex

value: L2 larva

value: ENCBS874ILT at ENCODE; https://www.encodeproject.org/ENCBS874ILT/


title: TF ChIP-seq from whole organism (ENCLB099SSW)

description:
https://www.encodeproject.org/experiments/ENCSR269HHK/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing kay-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR269HHK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR331XEF
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB099SSW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: kay

tag: dev stage

value: Kevin White, UChicago

value: Kevin White

value: ENCBS502XST at ENCODE; https://www.encodeproject.org/ENCBS502XST/


title: Control ChIP-seq from whole organism (ENCLB025YRX)

description:
https://www.encodeproject.org/experiments/ENCSR266WRF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing ey-eGFP fusion proteins.
experiment encode accession: ENCSR266WRF
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB025YRX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organisms

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

value: wandering third instar larva

value: ENCBS001SVK at ENCODE; https://www.encodeproject.org/ENCBS001SVK/


title: Bulk RNAseq MYOD1 AroPerfect Rep 3

description: Bulk RNA-seq


title: Control ChIP-seq from whole organism (ENCLB124EFM)

description:
https://www.encodeproject.org/experiments/ENCSR589YYN/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR589YYN
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB124EFM
size range: 150-350

value: whole organism

value: not applicable

value: ENCBS610ROG at ENCODE; https://www.encodeproject.org/ENCBS610ROG/


title: Bulk RNAseq MYOD1 AroPerfect Rep 2

description: Bulk RNA-seq


title: Bulk RNAseq MYOD1 AroLite-C Rep 3

description: Bulk RNA-seq


title: Control ChIP-seq from whole organism (ENCLB949YRH)

description:
https://www.encodeproject.org/experiments/ENCSR371KOI/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing gro-eGFP fusion proteins.
experiment encode accession: ENCSR371KOI
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB949YRH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

value: embryonic

value: 0-24 hour

value: ENCBS491YQP at ENCODE; https://www.encodeproject.org/ENCBS491YQP/


title: Bulk RNAseq MYOD1 AroPerfect Rep 1

description: Bulk RNA-seq


title: TF ChIP-seq from whole organism (ENCLB851ZIG)

description:
https://www.encodeproject.org/experiments/ENCSR273JZM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing crc-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR273JZM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR479BNA
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB851ZIG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: crc

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

value: pooled male and female

value: Hugo Bellen

value: ENCBS461APE at ENCODE; https://www.encodeproject.org/ENCBS461APE/


title: Control ChIP-seq from whole organism (ENCLB465DDI)

description:
https://www.encodeproject.org/experiments/ENCSR398GAE/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR398GAE
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB465DDI
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP228 (unc-119(ed3) III; wgIs228) mixed sex L4 larva insertion targeting C. elegans nhr-237

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-237

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS877ACC at ENCODE; https://www.encodeproject.org/ENCBS877ACC/


title: Bulk RNAseq MYOD1 AroLite-C Rep 2

description: Bulk RNA-seq


title: Control ChIP-seq from whole organism (ENCLB547NYN)

description:
https://www.encodeproject.org/experiments/ENCSR370HQE/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Max-eGFP fusion proteins.
experiment encode accession: ENCSR370HQE
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB547NYN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

value: whole organisms

value: not applicable

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

value: Kevin White, UChicago

value: Kevin White

value: ENCBS426MRQ at ENCODE; https://www.encodeproject.org/ENCBS426MRQ/


title: Control ChIP-seq from whole organism (ENCLB111GAZ)

description:
https://www.encodeproject.org/experiments/ENCSR366FCQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing ADD1-eGFP fusion proteins.
experiment encode accession: ENCSR366FCQ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB111GAZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain ADD1-MiMIC-GFP mixed sex embryo (0-16 hours) insertion targeting D. melanogaster ADD1

value: D. mel line contraining an intronic eGFP exon to create a ADD1-GFP fusion gene

value: embryonic

value: 0-16 hour

value: ENCBS594SDT at ENCODE; https://www.encodeproject.org/ENCBS594SDT/


title: TF ChIP-seq from whole organism (ENCLB276KJA)

description:
https://www.encodeproject.org/experiments/ENCSR398MFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against NHR-10 in L2 larva worms.
experiment encode accession: ENCSR398MFQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR497VLF
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB276KJA
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP239 (unc-119(ed3) III; wgIs239) mixed sex L2 larva insertion targeting C. elegans nhr-10

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

value: pooled male and female

value: L2 larva

value: ENCBS045XZY at ENCODE; https://www.encodeproject.org/ENCBS045XZY/


title: Bulk RNAseq MYOD1 AroLite Rep 3

description: Bulk RNA-seq


title: Bulk RNAseq MYOD1 AroLite-C Rep 1

description: Bulk RNA-seq


title: Control ChIP-seq from whole organism (ENCLB760YUQ)

description:
https://www.encodeproject.org/experiments/ENCSR398GAE/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR398GAE
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB760YUQ
fragmentation methods: sonication (generic microtip)

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-237

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS700SML at ENCODE; https://www.encodeproject.org/ENCBS700SML/


title: Bulk RNAseq MYOD1 AroLite Rep 1

description: Bulk RNA-seq


title: Bulk RNAseq C2C12 WT Rep 3

description: Bulk RNA-seq


title: TF ChIP-seq from whole organism (ENCLB901OIP)

description:
https://www.encodeproject.org/experiments/ENCSR358XYO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Hr96-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR358XYO
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR685FEO
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB901OIP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Hr96-GFP female adult insertion targeting D. melanogaster Hr96

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Hr96

value: female

value: adult

value: Kevin White, UChicago

value: ENCBS329CID at ENCODE; https://www.encodeproject.org/ENCBS329CID/


title: TF ChIP-seq from whole organism (ENCLB285URE)

description:
https://www.encodeproject.org/experiments/ENCSR397XGG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing MED-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR397XGG
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR143TBI
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB285URE
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP391 (unc-119(ed3) III; wgIs391(med-1::TY1 EGFP FLAG C; unc-119(+))) hermaphrodite midembryo insertion targeting C. elegans med-1

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

value: hermaphrodite

value: midembryonic

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS609DZC at ENCODE; https://www.encodeproject.org/ENCBS609DZC/


title: Bulk RNAseq MYOD1  AroPerfect-C Rep 1

description: Bulk RNA-seq


title: TF ChIP-seq from whole organism (ENCLB533JQZ)

description:
https://www.encodeproject.org/experiments/ENCSR358XYO/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Hr96-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR358XYO
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR685FEO
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB533JQZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: unknown

value: Kevin White

value: ENCBS759VRC at ENCODE; https://www.encodeproject.org/ENCBS759VRC/


title: Bulk RNAseq C2C12 WT Rep 1

description: Bulk RNA-seq


title: TF ChIP-seq from whole organism (ENCLB287RVD)

description:
https://www.encodeproject.org/experiments/ENCSR398MFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against NHR-10 in L2 larva worms.
experiment encode accession: ENCSR398MFQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR497VLF
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB287RVD
fragmentation methods: sonication (generic microtip)

value: whole organism

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

value: pooled male and female

value: L2 larva

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS420MNS at ENCODE; https://www.encodeproject.org/ENCBS420MNS/


title: Control ChIP-seq from whole organism (ENCLB250DDY)

description:
https://www.encodeproject.org/experiments/ENCSR355TQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Camta-eGFP fusion proteins.
experiment encode accession: ENCSR355TQJ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB250DDY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organisms

value: not applicable

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Hugo Bellen

value: ENCBS520WMB at ENCODE; https://www.encodeproject.org/ENCBS520WMB/


title: TF ChIP-seq from whole organism (ENCLB367QPF)

description:
https://www.encodeproject.org/experiments/ENCSR397XGG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing MED-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR397XGG
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR143TBI
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB367QPF
fragmentation methods: sonication (generic microtip)

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

value: hermaphrodite

value: midembryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS841UVR at ENCODE; https://www.encodeproject.org/ENCBS841UVR/


title: NIH3T3_EZdirect_1cell_WorkflowC_22_re3

type: genomic

city: Phialdelphia

first: Wanding

last: Zhou

state: Pennsylvania

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

department: Pathology & Lab Medicine

institute: Children's Hospital of Philadelphia

description:
Testing MM285 Array on low input DNA
207363410011_R04C01
20240207_GEO_processed_matrix_GPL30650.csv
20240207_GEO_signal_intensity_matrix_GPL30650.csv

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

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

label: Cy5 and Cy3

source_name: NIH3T3 ATCC, P4

label_protocol: Standard Illumina Protocol

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

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

value: 1 cell


title: NIH3T3_EZdirect_1cell_WorkflowC_22_re2

description:
Testing MM285 Array on low input DNA
207363410011_R03C01
20240207_GEO_processed_matrix_GPL30650.csv
20240207_GEO_signal_intensity_matrix_GPL30650.csv


title: NIH3T3_EZdirect_1cell_WorkflowC_22_re

description:
Testing MM285 Array on low input DNA
207363410011_R02C01
20240207_GEO_processed_matrix_GPL30650.csv
20240207_GEO_signal_intensity_matrix_GPL30650.csv


title: Control ChIP-seq from whole organism (ENCLB665TPZ)

description:
https://www.encodeproject.org/experiments/ENCSR589NOT/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR589NOT
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2018-02-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB665TPZ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP217 (unc-119(ed3) III; ddIs172) mixed sex L4 larva insertion targeting C. elegans aly-2

value: whole organism

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

value: pooled male and female

value: L4 larva

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS062MOU at ENCODE; https://www.encodeproject.org/ENCBS062MOU/