title: TF ChIP-seq from whole organism (ENCLB974SHP)

description:
https://www.encodeproject.org/experiments/ENCSR797YWF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing HLHm7-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR797YWF
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR564PVU
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB974SHP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: note

value: pooled male and female

tag: dev stage

value: embryonic

value: Kevin White, UChicago

value: ENCBS320WRZ at ENCODE; https://www.encodeproject.org/ENCBS320WRZ/


title: C03 vineyard block spot 14 time point 8

status: Public on Feb 27 2024

type: RNA

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

country: Italy

institute: University of Verona

description: gene expression in C03 vineyard block spot 14 time point 8

hyb_protocol: The cDNA synthesis, labeling, hybridization and washing reactions were performed according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

scan_protocol: Scanning and Feature Extraction was performed by using an Agilent Scanner following the settings and parameters indicated in the instruction manual.

data_processing: A data-matrix was prepared selecting from each single sub-array outcome file the gProcessedSignalvalues, which are the raw fluorescence intensities of each probe. The data were normalized on the 75th percentile and a correlation analysis was then conducted to assess the consistency of the biological triplicates. Correlation matrixes were prepared using R software and Pearson's Correlation Coefficient (PCC) as the statistical metric.

molecule: total RNA

organism: Vitis vinifera

source_name: C03 vineyard block spot 14 time point 8

growth_protocol: The experiment was conducted in 2017 growing season in a commercial vineyard of approximately 12 hectares of Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock). The vineyard was planted in 1992 and located in the Alexander Valley American Viticultural Area of California (38°42'50N, 122°55'4W). The vines were trained as a bilateral cordon, established at 1.5 m above the ground, in a split canopy configuration, with the two cordons installed on two separate wires and pointing in opposite directions. Vine and row spacings were 1.8 and 3.35 m respectively.

extract_protocol: Total RNA was extracted from ~200 mg frozen powder berry pericarp (pulp plus skin without seeds) using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, Missouri, USA) as previously described (Fasoli et al., 2012).

treatment_protocol: The vineyard was dissected in 14 homogenously distributed spots across the block to account for any vine vigor and fruit quality spatial variability. Each spot comprised a square of nine vines (3 adjacent vines x 3 rows).

tag: cultivar

tag: spot

tag: time point

tag: phenology

value: harvest ~ 24 .5 Brix

tag: sampling date


title: TF ChIP-seq from whole organism (ENCLB235SEZ)

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR972RZE/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing sens-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR972RZE
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR599UYD
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB235SEZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

library_source: genomic

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

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strain sens-GFP mixed sex embryo (4-14 hours) insertion targeting D. melanogaster sens

tag: antibody

value: sens

value: whole organism

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

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

tag: Sex

tag: age

tag: lab

tag: source

value: Kevin White

tag: link

value: ENCBS157RLD at ENCODE; https://www.encodeproject.org/ENCBS157RLD/


title: TF ChIP-seq from whole organism (ENCLB612REI)

description:
https://www.encodeproject.org/experiments/ENCSR471YQA/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Eip78C-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR471YQA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR242RQJ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB612REI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Eip78C-GFP mixed sex prepupa at white prepupa stage insertion targeting D. melanogaster Eip78C

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Eip78C

value: prepupa

value: unknown

tag: fly synchronization stage

value: white prepupa

value: ENCBS773JSK at ENCODE; https://www.encodeproject.org/ENCBS773JSK/


title: Control ChIP-seq from whole organism (ENCLB120VBV)

description:
https://www.encodeproject.org/experiments/ENCSR640BRI/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in D4 worms.
experiment encode accession: ENCSR640BRI
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB120VBV
fragmentation methods: sonication (generic microtip)

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP600 (unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119)) mixed sex dauer insertion targeting C. elegans unc-62

extract_protocol: not provided

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to UNC-62

tag: dev stage

value: dauer

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS310PQM at ENCODE; https://www.encodeproject.org/ENCBS310PQM/


title: Control ChIP-seq from whole organism (ENCLB393HTR)

description:
https://www.encodeproject.org/experiments/ENCSR758JFY/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in 4 day young adult worms.
experiment encode accession: ENCSR758JFY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB393HTR
size range: 150-350

source_name: Caenorhabditis elegans strain OP600 (unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119)) mixed sex young adult (4 days) insertion targeting C. elegans unc-62

value: pooled male and female

value: young adult

value: 4 day

value: CGC

value: ENCBS878HNM at ENCODE; https://www.encodeproject.org/ENCBS878HNM/


title: C03 vineyard block spot 13 time point 8

description: gene expression in C03 vineyard block spot 13 time point 8

source_name: C03 vineyard block spot 13 time point 8

label_protocol: The cDNA synthesis, labeling, hybridization and washing reactions were performed according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

tag: cultivar

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

tag: spot

value: harvest ~ 24 .5 Brix


title: TF ChIP-seq from whole organism (ENCLB667WNX)

description:
https://www.encodeproject.org/experiments/ENCSR471YQA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Eip78C-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR471YQA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR242RQJ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB667WNX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Eip78C

value: prepupa

value: Kevin White, UChicago

value: Kevin White

value: ENCBS742FLB at ENCODE; https://www.encodeproject.org/ENCBS742FLB/


title: Control ChIP-seq from whole organism (ENCLB670MAP)

description:
https://www.encodeproject.org/experiments/ENCSR756JUX/
***************
biological replicate number: 4
technical replicate number: 1
description: Input ChIP-seq in L4 worms.
experiment encode accession: ENCSR756JUX
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB670MAP
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP177 (unc-119(ed3) III; wgIs177) mixed sex L4 larva insertion targeting C. elegans egl-27

value: whole organisms

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

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: ENCBS676QAV at ENCODE; https://www.encodeproject.org/ENCBS676QAV/


title: TF ChIP-seq from whole organism (ENCLB849BCV)

description:
https://www.encodeproject.org/experiments/ENCSR471YQA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Eip78C-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR471YQA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR242RQJ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB849BCV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: pooled male and female

value: white prepupa

value: ENCBS789DVA at ENCODE; https://www.encodeproject.org/ENCBS789DVA/


title: TF ChIP-seq from whole organism (ENCLB388UCQ)

description:
https://www.encodeproject.org/experiments/ENCSR640NTR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-fkh-2 in L3 larva worms.
experiment encode accession: ENCSR640NTR
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR606NPE
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB388UCQ
size range: 150-350

source_name: Caenorhabditis elegans strain OP185 (unc-119(ed3) III; wgIs185) mixed sex L3 larva insertion targeting C. elegans fkh-2

value: L3 larva

value: CGC

value: ENCBS049EST at ENCODE; https://www.encodeproject.org/ENCBS049EST/


title: Control ChIP-seq from whole organism (ENCLB103AKH)

description:
https://www.encodeproject.org/experiments/ENCSR756JUX/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L4 worms.
experiment encode accession: ENCSR756JUX
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB103AKH
fragmentation methods: sonication (generic microtip)

value: whole organism

value: not applicable

value: Michael Snyder

value: ENCBS737KNQ at ENCODE; https://www.encodeproject.org/ENCBS737KNQ/


title: Control ChIP-seq from whole organism (ENCLB190BBY)

description:
https://www.encodeproject.org/experiments/ENCSR756JUX/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 worms.
experiment encode accession: ENCSR756JUX
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB190BBY
fragmentation methods: sonication (generic microtip)

value: ENCBS276CAU at ENCODE; https://www.encodeproject.org/ENCBS276CAU/


title: Control ChIP-seq from whole organism (ENCLB599HSN)

description:
https://www.encodeproject.org/experiments/ENCSR758JFY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in 4 day young adult worms.
experiment encode accession: ENCSR758JFY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB599HSN
size range: 150-350

value: whole organisms

value: young adult

value: 4 day

value: ENCBS232YNZ at ENCODE; https://www.encodeproject.org/ENCBS232YNZ/


title: TF ChIP-seq from whole organism (ENCLB824ABJ)

description:
https://www.encodeproject.org/experiments/ENCSR969SUB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Eip93F-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR969SUB
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR899CDG
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB824ABJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Eip93F-MiMIC-GFP mixed sex prepupa insertion targeting D. melanogaster Eip93F

value: D. mel line contraining an intronic eGFP exon to create a Eip93F-GFP fusion gene

value: prepupa

value: unknown

value: Kevin White, UChicago

value: Hugo Bellen

value: ENCBS610NMW at ENCODE; https://www.encodeproject.org/ENCBS610NMW/


title: TF ChIP-seq from whole organism (ENCLB643XOS)

description:
https://www.encodeproject.org/experiments/ENCSR471YQA/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Eip78C-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR471YQA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR242RQJ
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB643XOS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Eip78C

value: pooled male and female

value: Kevin White

value: white prepupa

value: ENCBS717FSF at ENCODE; https://www.encodeproject.org/ENCBS717FSF/


title: C03 vineyard block spot 12 time point 8

description: gene expression in C03 vineyard block spot 12 time point 8

source_name: C03 vineyard block spot 12 time point 8

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

tag: time point

tag: phenology

value: harvest ~ 24 .5 Brix


title: C03 vineyard block spot 10 time point 8

description: gene expression in C03 vineyard block spot 10 time point 8

source_name: C03 vineyard block spot 10 time point 8

tag: sampling date


title: C03 vineyard block spot 6 time point 8

description: gene expression in C03 vineyard block spot 6 time point 8

source_name: C03 vineyard block spot 6 time point 8


title: C03 vineyard block spot 4 time point 8

description: gene expression in C03 vineyard block spot 4 time point 8

source_name: C03 vineyard block spot 4 time point 8


title: C03 vineyard block spot 9 time point 8

description: gene expression in C03 vineyard block spot 9 time point 8

source_name: C03 vineyard block spot 9 time point 8


title: C03 vineyard block spot 1 time point 8

description: gene expression in C03 vineyard block spot 1 time point 8

source_name: C03 vineyard block spot 1 time point 8


title: C03 vineyard block spot 5 time point 8

description: gene expression in C03 vineyard block spot 5 time point 8

source_name: C03 vineyard block spot 5 time point 8


title: C03 vineyard block spot 3 time point 8

description: gene expression in C03 vineyard block spot 3 time point 8

source_name: C03 vineyard block spot 3 time point 8


title: C03 vineyard block spot 7 time point 8

description: gene expression in C03 vineyard block spot 7 time point 8

source_name: C03 vineyard block spot 7 time point 8


title: TF ChIP-seq from whole organism (ENCLB513OCH)

description:
https://www.encodeproject.org/experiments/ENCSR969SUB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Eip93F-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR969SUB
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR899CDG
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB513OCH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: whole organisms

tag: biosample encode accession

value: not applicable

value: ENCBS118TZO at ENCODE; https://www.encodeproject.org/ENCBS118TZO/


title: C03 vineyard block spot 11 time point 8

description: gene expression in C03 vineyard block spot 11 time point 8

source_name: C03 vineyard block spot 11 time point 8


title: lung_ adenocarcinoma_brain_metastasis_4

city: Rotterdam

first: Shiva

last: Najjary

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

description: BM-LUAD 4

hyb_protocol: For each sample, 300 ng of good quality RNA, with a maximum of 7 μL was used for hybridization with the PanCancer IO 360™  probes for 17 hours at 67⁰C, following the manufacturing procedure (NanoString Technologies Inc., Seattle, WA, USA).

scan_protocol: The nCounter FLEX platform was used and genes were counted by scanning 490 Fields-of-view (FOV).

data_processing: Data analysis was performed using the advanced analysis module (version 2.0) of nSolver software (version 4.0, NanoString Technology).

organism: Homo sapiens

source_name: lung_brain metastasis

extract_protocol: Tissue sections of 5 μm were stained with hematoxylin and eosin (H&E), and examined by a pathologist. Total RNA was extracted from 10-12 sections of 10 μm thickness. RNA was stored in RNase/DNase-free water at -80°C. The nCounter® PanCancer IO 360™ Panel was used for NanoString targeted gene expression analysis. The total RNA was isolated from tumor tissue using the RNeasy® FFPE isolation kit (Qiagen, Hilden, Germany). The RNA quantity and quality were measured using the Agilent 2100 BioAnalyzer (Santa Clara, CA, USA), RNA degradation was calculated using percentages of fragments of 300-4000 nucleotides. The 300 ng of good quality RNA, with a maximum of 7 μL was used for hybridization with the panel probes for 17 hours at 65°C using a SimpliAmp Thermal Cycler (Applied Biosystems, Foster City, CA, USA).

tag: tissue

value: lung adenocarcinoma

tag: metastatic site

value: brain

tag: age at diagnosis

value: female

tag: histology

value: adenocaricnoma

tag: smoking status

value: smoker

tag: treatment after surgery of bm

value: Radiotherapy


title: TF ChIP-seq from whole organism (ENCLB408DCW)

description:
https://www.encodeproject.org/experiments/ENCSR431IBS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-pha-4 in L4 larva worms.
experiment encode accession: ENCSR431IBS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR494DGU
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB408DCW
size range: 150-350

source_name: Caenorhabditis elegans strain OP37 (unc-119(ed3) III; wgIs37) mixed sex L4 larva insertion targeting C. elegans pha-4

tag: collection date

tag: geographic location

tag: encode accession

tag: Sex

value: L4 larva

tag: age

value: unknown

tag: lab

value: Michael Snyder, Stanford

tag: source

value: CGC

tag: link

value: ENCBS747GTQ at ENCODE; https://www.encodeproject.org/ENCBS747GTQ/


title: TF ChIP-seq from whole organism (ENCLB837KFK)

description:
https://www.encodeproject.org/experiments/ENCSR431IBS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-pha-4 in L4 larva worms.
experiment encode accession: ENCSR431IBS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR494DGU
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB837KFK
size range: 150-350

value: pooled male and female

tag: dev stage

value: ENCBS297HGH at ENCODE; https://www.encodeproject.org/ENCBS297HGH/


title: TF ChIP-seq from whole organism (ENCLB925MQZ)

description:
https://www.encodeproject.org/experiments/ENCSR755UCK/
***************
biological replicate number: 3
technical replicate number: 1
description: Input ChIP-seq in L3 worms.
experiment encode accession: ENCSR755UCK
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR134PTC
encode release date: 2018-01-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB925MQZ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP202 (unc-119(ed3) III; wgIs202) mixed sex L3 larva insertion targeting C. elegans ceh-9

tag: antibody

value: whole organism

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-9

value: L3 larva

value: Michael Snyder

value: ENCBS871OHF at ENCODE; https://www.encodeproject.org/ENCBS871OHF/


title: C03 vineyard block spot 12 time point 6

description: gene expression in C03 vineyard block spot 12 time point 6

source_name: C03 vineyard block spot 12 time point 6

tag: cultivar

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

tag: spot

tag: time point

tag: phenology

value: pea size + 51 days

tag: sampling date


title: TF ChIP-seq from whole organism (ENCLB300OXA)

description:
https://www.encodeproject.org/experiments/ENCSR461AXL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing h-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR461AXL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR904QAP
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB300OXA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain 15T-GFP mixed sex wandering third instar larva insertion targeting D. melanogaster h

value: h

value: whole organisms

tag: biosample encode accession

value: not applicable

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

value: wandering third instar larva

value: Kevin White, UChicago

value: Kevin White

value: ENCBS222MKD at ENCODE; https://www.encodeproject.org/ENCBS222MKD/


title: C03 vineyard block spot 8 time point 8

description: gene expression in C03 vineyard block spot 8 time point 8

source_name: C03 vineyard block spot 8 time point 8

value: harvest ~ 24 .5 Brix


title: C03 vineyard block spot 13 time point 6

description: gene expression in C03 vineyard block spot 13 time point 6

source_name: C03 vineyard block spot 13 time point 6


title: C03 vineyard block spot 2 time point 8

description: gene expression in C03 vineyard block spot 2 time point 8

source_name: C03 vineyard block spot 2 time point 8


title: TF ChIP-seq from whole organism (ENCLB532WIF)

description:
https://www.encodeproject.org/experiments/ENCSR460LRT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG13624-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR460LRT
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR296KEA
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB532WIF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG13624-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster REPTOR

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG13624

value: pooled male and female

value: embryonic

value: 0-24 hour

value: ENCBS733MUH at ENCODE; https://www.encodeproject.org/ENCBS733MUH/


title: C03 vineyard block spot 11 time point 6

description: gene expression in C03 vineyard block spot 11 time point 6

source_name: C03 vineyard block spot 11 time point 6


title: C03 vineyard block spot 9 time point 6

description: gene expression in C03 vineyard block spot 9 time point 6

source_name: C03 vineyard block spot 9 time point 6


title: Control ChIP-seq from whole organism (ENCLB840ZCS)

description:
https://www.encodeproject.org/experiments/ENCSR938FCA/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR938FCA
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB840ZCS
size range: 150-350

source_name: Caenorhabditis elegans strain OP218 (unc-119(ed3) III; wgIs218) mixed sex L4 larva insertion targeting C. elegans R02D3.7

value: whole organism

tag: geographic location

value: L4 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS521DON at ENCODE; https://www.encodeproject.org/ENCBS521DON/


title: C03 vineyard block spot 7 time point 6

description: gene expression in C03 vineyard block spot 7 time point 6

source_name: C03 vineyard block spot 7 time point 6

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

value: pea size + 51 days


title: C03 vineyard block spot 14 time point 6

description: gene expression in C03 vineyard block spot 14 time point 6

source_name: C03 vineyard block spot 14 time point 6


title: C03 vineyard block spot 6 time point 6

description: gene expression in C03 vineyard block spot 6 time point 6

source_name: C03 vineyard block spot 6 time point 6


title: C03 vineyard block spot 8 time point 6

description: gene expression in C03 vineyard block spot 8 time point 6

source_name: C03 vineyard block spot 8 time point 6


title: TF ChIP-seq from whole organism (ENCLB642DVC)

description:
https://www.encodeproject.org/experiments/ENCSR755UCK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L3 worms.
experiment encode accession: ENCSR755UCK
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR134PTC
encode release date: 2018-01-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB642DVC
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: not applicable

tag: encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-9

value: L3 larva

value: Michael Snyder

value: ENCBS936LMC at ENCODE; https://www.encodeproject.org/ENCBS936LMC/


title: TF ChIP-seq from whole organism (ENCLB102HKC)

description:
https://www.encodeproject.org/experiments/ENCSR963YPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Atf-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR963YPQ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR950VOB
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB102HKC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Atf-2-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Atf-2

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Atf-2

tag: Sex

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS390SGO at ENCODE; https://www.encodeproject.org/ENCBS390SGO/


title: Control ChIP-seq from whole organism (ENCLB874POZ)

description:
https://www.encodeproject.org/experiments/ENCSR938FCA/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR938FCA
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB874POZ
size range: 150-350

value: whole organism

value: L4 larva

tag: age

value: unknown

value: Michael Snyder, Stanford

value: ENCBS147MZT at ENCODE; https://www.encodeproject.org/ENCBS147MZT/


title: TF ChIP-seq from whole organism (ENCLB732ORU)

description:
https://www.encodeproject.org/experiments/ENCSR963YPQ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Atf-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR963YPQ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR950VOB
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB732ORU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: 0-24 hour

tag: lab

value: ENCBS377GSX at ENCODE; https://www.encodeproject.org/ENCBS377GSX/


title: Control ChIP-seq from whole organism (ENCLB723ORG)

description:
https://www.encodeproject.org/experiments/ENCSR938FCA/
***************
biological replicate number: 3
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR938FCA
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB723ORG
fragmentation methods: sonication (generic microtip)

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to R02D3.7

tag: source

value: ENCBS905QII at ENCODE; https://www.encodeproject.org/ENCBS905QII/


title: C03 vineyard block spot 5 time point 6

description: gene expression in C03 vineyard block spot 5 time point 6

source_name: C03 vineyard block spot 5 time point 6

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

value: pea size + 51 days


title: TF ChIP-seq from whole organism (ENCLB543DCX)

description:
https://www.encodeproject.org/experiments/ENCSR461AXL/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing h-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR461AXL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR904QAP
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB543DCX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: h

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

value: pooled male and female

value: wandering third instar larva

tag: link

value: ENCBS517FBD at ENCODE; https://www.encodeproject.org/ENCBS517FBD/


title: TF ChIP-seq from whole organism (ENCLB054VNT)

description:
https://www.encodeproject.org/experiments/ENCSR456UZW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG2116-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR456UZW
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR325OBK
encode release date: 2018-02-01
lab: Kevin White, UChicago
library encode accession: ENCLB054VNT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG2116-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG2116

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG2116

tag: dev stage

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS697QUQ at ENCODE; https://www.encodeproject.org/ENCBS697QUQ/


title: C03 vineyard block spot 3 time point 6

description: gene expression in C03 vineyard block spot 3 time point 6

source_name: C03 vineyard block spot 3 time point 6


title: TF ChIP-seq from whole organism (ENCLB598ZFL)

description:
https://www.encodeproject.org/experiments/ENCSR937QZT/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against NHR-237 in L4 larva worms.
experiment encode accession: ENCSR937QZT
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR398GAE
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB598ZFL
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

tag: antibody

value: whole organisms

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: ENCBS225GAT at ENCODE; https://www.encodeproject.org/ENCBS225GAT/


title: TF ChIP-seq from whole organism (ENCLB988VDX)

description:
https://www.encodeproject.org/experiments/ENCSR456UZW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG2116-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR456UZW
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR325OBK
encode release date: 2018-02-01
lab: Kevin White, UChicago
library encode accession: ENCLB988VDX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

tag: note

value: 0-24 hour

value: ENCBS266YXM at ENCODE; https://www.encodeproject.org/ENCBS266YXM/


title: C03 vineyard block spot 4 time point 6

description: gene expression in C03 vineyard block spot 4 time point 6

source_name: C03 vineyard block spot 4 time point 6

tag: cultivar

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

value: pea size + 51 days


title: C03 vineyard block spot 10 time point 6

description: gene expression in C03 vineyard block spot 10 time point 6

source_name: C03 vineyard block spot 10 time point 6

tag: spot


title: C03 vineyard block spot 14 time point 5

description: gene expression in C03 vineyard block spot 14 time point 5

source_name: C03 vineyard block spot 14 time point 5

tag: time point

value: pea size + 39 days


title: C03 vineyard block spot 13 time point 5

description: gene expression in C03 vineyard block spot 13 time point 5

source_name: C03 vineyard block spot 13 time point 5

tag: phenology


title: C03 vineyard block spot 2 time point 6

description: gene expression in C03 vineyard block spot 2 time point 6

source_name: C03 vineyard block spot 2 time point 6

tag: sampling date


title: C03 vineyard block spot 11 time point 5

description: gene expression in C03 vineyard block spot 11 time point 5

source_name: C03 vineyard block spot 11 time point 5


title: C03 vineyard block spot 1 time point 6

description: gene expression in C03 vineyard block spot 1 time point 6

source_name: C03 vineyard block spot 1 time point 6


title: TF ChIP-seq from whole organism (ENCLB659YBT)

description:
https://www.encodeproject.org/experiments/ENCSR456UZW/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG2116-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR456UZW
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR325OBK
encode release date: 2018-02-01
lab: Kevin White, UChicago
library encode accession: ENCLB659YBT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

tag: biosample encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG2116

value: pooled male and female

value: embryonic

value: ENCBS650WOR at ENCODE; https://www.encodeproject.org/ENCBS650WOR/


title: TF ChIP-seq from whole organism (ENCLB146EIT)

description:
https://www.encodeproject.org/experiments/ENCSR957XDI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG18764-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR957XDI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR897QOF
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB146EIT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG18764-GFP mixed sex embryo (0-16 hours) insertion targeting D. melanogaster CG18764

value: whole organisms

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG18764

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS541OZQ at ENCODE; https://www.encodeproject.org/ENCBS541OZQ/


title: TF ChIP-seq from whole organism (ENCLB529YZD)

description:
https://www.encodeproject.org/experiments/ENCSR426MPH/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ODD-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR426MPH
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR284TTZ
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB529YZD
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP405 (unc-119(tm4063) III; wgIs405) hermaphrodite late embryo insertion targeting C. elegans odd-2

value: not applicable

tag: geographic location

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

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS770KSY at ENCODE; https://www.encodeproject.org/ENCBS770KSY/


title: TF ChIP-seq from whole organism (ENCLB102SEE)

description:
https://www.encodeproject.org/experiments/ENCSR426MPH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ODD-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR426MPH
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR284TTZ
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB102SEE
fragmentation methods: sonication (generic microtip)

value: whole organism

tag: encode accession

value: ENCBS735PQO at ENCODE; https://www.encodeproject.org/ENCBS735PQO/


title: TF ChIP-seq from whole organism (ENCLB768ODU)

description:
https://www.encodeproject.org/experiments/ENCSR957XDI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG18764-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR957XDI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR897QOF
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB768ODU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: Sex

value: pooled male and female

value: embryonic

value: ENCBS441VAW at ENCODE; https://www.encodeproject.org/ENCBS441VAW/


title: TF ChIP-seq from whole organism (ENCLB807SWJ)

description:
https://www.encodeproject.org/experiments/ENCSR424CLY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against ama-1 in late embryonic worms.
experiment encode accession: ENCSR424CLY
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR917EGR
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB807SWJ
size range: 150-350

source_name: Caenorhabditis elegans strain N2 (C. elegans wild isolate) mixed sex late embryo whole organism

value: whole organisms

tag: age

value: Michael Snyder, Stanford

value: CGC

value: ENCBS727IZA at ENCODE; https://www.encodeproject.org/ENCBS727IZA/


title: TF ChIP-seq from whole organism (ENCLB010SVJ)

description:
https://www.encodeproject.org/experiments/ENCSR957XDI/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG18764-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR957XDI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR897QOF
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB010SVJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG18764

value: 0-16 hour

tag: lab

value: Kevin White, UChicago

value: Kevin White

value: ENCBS604GKT at ENCODE; https://www.encodeproject.org/ENCBS604GKT/


title: TF ChIP-seq from whole organism (ENCLB885IJN)

description:
https://www.encodeproject.org/experiments/ENCSR937QZT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against NHR-237 in L4 larva worms.
experiment encode accession: ENCSR937QZT
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR398GAE
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB885IJN
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

tag: source

value: Michael Snyder

value: ENCBS791VRI at ENCODE; https://www.encodeproject.org/ENCBS791VRI/


title: TF ChIP-seq from whole organism (ENCLB314KVD)

description:
https://www.encodeproject.org/experiments/ENCSR957HDY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ADD1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR957HDY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR366FCQ
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB314KVD
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: whole organism

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

value: pooled male and female

value: embryonic

value: Hugo Bellen

tag: link

value: ENCBS408NUK at ENCODE; https://www.encodeproject.org/ENCBS408NUK/


title: TF ChIP-seq from whole organism (ENCLB436KHM)

description:
https://www.encodeproject.org/experiments/ENCSR424CLY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against ama-1 in late embryonic worms.
experiment encode accession: ENCSR424CLY
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR917EGR
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB436KHM
size range: 150-350

value: whole organisms

value: not applicable

tag: dev stage

value: late embryonic

value: Michael Snyder, Stanford

value: CGC

value: ENCBS275OTR at ENCODE; https://www.encodeproject.org/ENCBS275OTR/


title: TF ChIP-seq from whole organism (ENCLB601TPE)

description:
https://www.encodeproject.org/experiments/ENCSR934OMU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing B0336.3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR934OMU
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR528TJN
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB601TPE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP801 (wgIs801(B0336.3::TY1 EGFP 3xFLAG(p_wTRG5_insertion_c_0040_1B04);unc-119(+));unc-119 (tm4063)) young adult (66 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans rbm-26

tag: antibody

value: not collected

value: young adult

value: 66 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: ENCBS913YIN at ENCODE; https://www.encodeproject.org/ENCBS913YIN/


title: C03 vineyard block spot 9 time point 5

description: gene expression in C03 vineyard block spot 9 time point 5

source_name: C03 vineyard block spot 9 time point 5

tag: cultivar

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

value: pea size + 39 days


title: C03 vineyard block spot 3 time point 5

description: gene expression in C03 vineyard block spot 3 time point 5

source_name: C03 vineyard block spot 3 time point 5

tag: spot


title: C03 vineyard block spot 2 time point 5

description: gene expression in C03 vineyard block spot 2 time point 5

source_name: C03 vineyard block spot 2 time point 5

tag: time point


title: TF ChIP-seq from whole organism (ENCLB309NYX)

description:
https://www.encodeproject.org/experiments/ENCSR934OMU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing B0336.3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR934OMU
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR528TJN
encode release date: 2022-11-01
lab: Valerie Reinke, Yale
library encode accession: ENCLB309NYX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: ENCBS408MQE at ENCODE; https://www.encodeproject.org/ENCBS408MQE/


title: C03 vineyard block spot 7 time point 5

description: gene expression in C03 vineyard block spot 7 time point 5

source_name: C03 vineyard block spot 7 time point 5

tag: phenology


title: TF ChIP-seq from whole organism (ENCLB257EYZ)

description:
https://www.encodeproject.org/experiments/ENCSR957HDY/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ADD1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR957HDY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR366FCQ
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB257EYZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: note

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

value: pooled male and female

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Hugo Bellen

value: ENCBS045TPH at ENCODE; https://www.encodeproject.org/ENCBS045TPH/


title: C03 vineyard block spot 8 time point 5

description: gene expression in C03 vineyard block spot 8 time point 5

source_name: C03 vineyard block spot 8 time point 5

tag: sampling date


title: C03 vineyard block spot 5 time point 5

description: gene expression in C03 vineyard block spot 5 time point 5

source_name: C03 vineyard block spot 5 time point 5


title: C03 vineyard block spot 12 time point 5

description: gene expression in C03 vineyard block spot 12 time point 5

source_name: C03 vineyard block spot 12 time point 5


title: C03 vineyard block spot 6 time point 5

description: gene expression in C03 vineyard block spot 6 time point 5

source_name: C03 vineyard block spot 6 time point 5


title: Control ChIP-seq from whole organism (ENCLB151WTM)

description:
https://www.encodeproject.org/experiments/ENCSR782YFF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing E(spl)m3-eGFP fusion proteins.
experiment encode accession: ENCSR782YFF
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB151WTM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain E(spl)m3-HLH-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster E(spl)m3-HLH

tag: biosample encode accession

tag: collection date

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to E(spl)m3

value: 0-24 hour

value: Kevin White

value: ENCBS587FFI at ENCODE; https://www.encodeproject.org/ENCBS587FFI/


title: C03 vineyard block spot 10 time point 5

description: gene expression in C03 vineyard block spot 10 time point 5

source_name: C03 vineyard block spot 10 time point 5

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)


title: C03 vineyard block spot 14 time point 4

description: gene expression in C03 vineyard block spot 14 time point 4

source_name: C03 vineyard block spot 14 time point 4

value: pea size + 30 days


title: C03 vineyard block spot 4 time point 5

description: gene expression in C03 vineyard block spot 4 time point 5

source_name: C03 vineyard block spot 4 time point 5

value: pea size + 39 days


title: TF ChIP-seq from whole organism (ENCLB263JLM)

description:
https://www.encodeproject.org/experiments/ENCSR934KZU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against ama-1 in early embryonic worms.
experiment encode accession: ENCSR934KZU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR780YWP
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB263JLM
size range: 150-350

source_name: Caenorhabditis elegans strain N2 (C. elegans wild isolate) mixed sex early embryo whole organism

value: whole organism

tag: geographic location

tag: encode accession

value: early embryonic

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS515ILF at ENCODE; https://www.encodeproject.org/ENCBS515ILF/


title: C03 vineyard block spot 11 time point 4

description: gene expression in C03 vineyard block spot 11 time point 4

source_name: C03 vineyard block spot 11 time point 4


title: C03 vineyard block spot 12 time point 4

description: gene expression in C03 vineyard block spot 12 time point 4

source_name: C03 vineyard block spot 12 time point 4


title: C03 vineyard block spot 1 time point 5

description: gene expression in C03 vineyard block spot 1 time point 5

source_name: C03 vineyard block spot 1 time point 5


title: C03 vineyard block spot 13 time point 4

description: gene expression in C03 vineyard block spot 13 time point 4

source_name: C03 vineyard block spot 13 time point 4


title: C03 vineyard block spot 9 time point 4

description: gene expression in C03 vineyard block spot 9 time point 4

source_name: C03 vineyard block spot 9 time point 4


title: C03 vineyard block spot 10 time point 4

description: gene expression in C03 vineyard block spot 10 time point 4

source_name: C03 vineyard block spot 10 time point 4


title: TF ChIP-seq from whole organism (ENCLB814OJB)

description:
https://www.encodeproject.org/experiments/ENCSR655FTR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG4820-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR655FTR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR000WON
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB814OJB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG4820-GFP mixed sex embryo (0-16 hours) insertion targeting D. melanogaster CG4820

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG4820

tag: Sex

value: pooled male and female

value: embryonic

tag: age

value: 0-16 hour

value: Kevin White, UChicago

value: ENCBS557RJS at ENCODE; https://www.encodeproject.org/ENCBS557RJS/


title: C03 vineyard block spot 6 time point 4

description: gene expression in C03 vineyard block spot 6 time point 4

source_name: C03 vineyard block spot 6 time point 4


title: TF ChIP-seq from whole organism (ENCLB760OLT)

description:
https://www.encodeproject.org/experiments/ENCSR934KZU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against ama-1 in early embryonic worms.
experiment encode accession: ENCSR934KZU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR780YWP
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB760OLT
size range: 150-350

value: not applicable

tag: lab

tag: source

value: ENCBS627JVV at ENCODE; https://www.encodeproject.org/ENCBS627JVV/


title: TF ChIP-seq from whole organism (ENCLB542ANV)

description:
https://www.encodeproject.org/experiments/ENCSR751MCL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against ZTF-11 in L2 worms.
experiment encode accession: ENCSR751MCL
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR812NDR
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB542ANV
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP236 (unc-119(ed3) III; wgIs236) mixed sex L2 larva insertion targeting C. elegans ztf-11

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

tag: dev stage

value: L2 larva

value: Michael Snyder

tag: link

value: ENCBS824DEX at ENCODE; https://www.encodeproject.org/ENCBS824DEX/


title: TF ChIP-seq from whole organism (ENCLB692TUA)

description:
https://www.encodeproject.org/experiments/ENCSR655FTR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG4820-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR655FTR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR000WON
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB692TUA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: Kevin White

value: ENCBS248NDB at ENCODE; https://www.encodeproject.org/ENCBS248NDB/


title: TF ChIP-seq from whole organism (ENCLB222GZR)

description:
https://www.encodeproject.org/experiments/ENCSR655FTR/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG4820-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR655FTR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR000WON
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB222GZR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: ENCBS402YCS at ENCODE; https://www.encodeproject.org/ENCBS402YCS/


title: Control ChIP-seq from whole organism (ENCLB229TOY)

description:
https://www.encodeproject.org/experiments/ENCSR633VXV/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR633VXV
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB229TOY
size range: 150-350

source_name: Caenorhabditis elegans strain OP200 (unc-119(ed3) III; wgIs200) mixed sex L2 larva insertion targeting C. elegans alr-1

value: whole organisms

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS403UXF at ENCODE; https://www.encodeproject.org/ENCBS403UXF/


title: TF ChIP-seq from whole organism (ENCLB180BOV)

description:
https://www.encodeproject.org/experiments/ENCSR951FDL/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing rgr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR951FDL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR565WHH
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB180BOV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: rgr

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: Kevin White, UChicago

value: ENCBS893ZAL at ENCODE; https://www.encodeproject.org/ENCBS893ZAL/


title: TF ChIP-seq from whole organism (ENCLB601MNN)

description:
https://www.encodeproject.org/experiments/ENCSR751MCL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against ZTF-11 in L2 worms.
experiment encode accession: ENCSR751MCL
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR812NDR
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB601MNN
fragmentation methods: sonication (generic microtip)

value: not applicable

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

value: L2 larva

value: Michael Snyder

value: ENCBS875UHD at ENCODE; https://www.encodeproject.org/ENCBS875UHD/


title: Control ChIP-seq from whole organism (ENCLB347JDF)

description:
https://www.encodeproject.org/experiments/ENCSR633VXV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR633VXV
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB347JDF
size range: 150-350

value: whole organism

value: ENCBS953ZYB at ENCODE; https://www.encodeproject.org/ENCBS953ZYB/


title: TF ChIP-seq from whole organism (ENCLB499DEL)

description:
https://www.encodeproject.org/experiments/ENCSR951FDL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing rgr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR951FDL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR565WHH
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB499DEL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: unknown

value: Kevin White

value: ENCBS803NXL at ENCODE; https://www.encodeproject.org/ENCBS803NXL/


title: TF ChIP-seq from whole organism (ENCLB829PEP)

description:
https://www.encodeproject.org/experiments/ENCSR951FDL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing rgr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR951FDL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR565WHH
encode release date: 2016-09-29
lab: Kevin White, UChicago
library encode accession: ENCLB829PEP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: rgr

value: ENCBS838NMP at ENCODE; https://www.encodeproject.org/ENCBS838NMP/


title: C03 vineyard block spot 5 time point 4

description: gene expression in C03 vineyard block spot 5 time point 4

source_name: C03 vineyard block spot 5 time point 4

tag: cultivar

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

value: pea size + 30 days


title: C03 vineyard block spot 7 time point 4

description: gene expression in C03 vineyard block spot 7 time point 4

source_name: C03 vineyard block spot 7 time point 4

tag: spot


title: C03 vineyard block spot 3 time point 4

description: gene expression in C03 vineyard block spot 3 time point 4

source_name: C03 vineyard block spot 3 time point 4

tag: time point


title: C03 vineyard block spot 14 time point 2

description: gene expression in C03 vineyard block spot 14 time point 2

source_name: C03 vineyard block spot 14 time point 2

tag: phenology

value: pea size + 10 days


title: C03 vineyard block spot 13 time point 2

description: gene expression in C03 vineyard block spot 13 time point 2

source_name: C03 vineyard block spot 13 time point 2


title: C03 vineyard block spot 8 time point 4

description: gene expression in C03 vineyard block spot 8 time point 4

source_name: C03 vineyard block spot 8 time point 4


title: C03 vineyard block spot 2 time point 4

description: gene expression in C03 vineyard block spot 2 time point 4

source_name: C03 vineyard block spot 2 time point 4


title: Control ChIP-seq from whole organism (ENCLB179DBJ)

description:
https://www.encodeproject.org/experiments/ENCSR748QRA/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR748QRA
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB179DBJ
size range: 150-350

source_name: Caenorhabditis elegans strain OP178 (unc-119(ed3) III; wgIs178) mixed sex L1 larva insertion targeting C. elegans skn-1

value: pooled male and female

value: L1 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS394RYI at ENCODE; https://www.encodeproject.org/ENCBS394RYI/


title: Control ChIP-seq from whole organism (ENCLB978QXZ)

description:
https://www.encodeproject.org/experiments/ENCSR748QRA/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR748QRA
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB978QXZ
size range: 150-350

value: not applicable

value: ENCBS221QBO at ENCODE; https://www.encodeproject.org/ENCBS221QBO/


title: C03 vineyard block spot 4 time point 4

description: gene expression in C03 vineyard block spot 4 time point 4

source_name: C03 vineyard block spot 4 time point 4


title: C03 vineyard block spot 9 time point 2

description: gene expression in C03 vineyard block spot 9 time point 2

source_name: C03 vineyard block spot 9 time point 2


title: C03 vineyard block spot 1 time point 4

description: gene expression in C03 vineyard block spot 1 time point 4

source_name: C03 vineyard block spot 1 time point 4


title: Control ChIP-seq from whole organism (ENCLB214BSF)

description:
https://www.encodeproject.org/experiments/ENCSR950VOB/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Atf-2-eGFP fusion proteins.
experiment encode accession: ENCSR950VOB
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB214BSF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Atf-2-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Atf-2

value: whole organism

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Atf-2

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: ENCBS639FDS at ENCODE; https://www.encodeproject.org/ENCBS639FDS/


title: C03 vineyard block spot 8 time point 2

description: gene expression in C03 vineyard block spot 8 time point 2

source_name: C03 vineyard block spot 8 time point 2

tag: sampling date


title: TF ChIP-seq from whole organism (ENCLB541KQS)

description:
https://www.encodeproject.org/experiments/ENCSR950LBC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG12744-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR950LBC
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR075LYH
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB541KQS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG12744-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG12744

value: whole organisms

tag: biosample encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12744

value: Kevin White

value: ENCBS524DNO at ENCODE; https://www.encodeproject.org/ENCBS524DNO/


title: TF ChIP-seq from whole organism (ENCLB668EOL)

description:
https://www.encodeproject.org/experiments/ENCSR927RAW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-unc-62 in mixed stage (embryonic) worms.
experiment encode accession: ENCSR927RAW
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR837ZAW
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB668EOL
size range: 150-350

source_name: Caenorhabditis elegans strain OP600 (unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119)) mixed sex mixed stage (embryo) insertion targeting C. elegans unc-62

tag: collection date

value: pooled male and female

value: mixed stage (embryonic)

value: unknown

value: ENCBS866INU at ENCODE; https://www.encodeproject.org/ENCBS866INU/


title: TF ChIP-seq from whole organism (ENCLB149RWD)

description:
https://www.encodeproject.org/experiments/ENCSR948RHA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing mam-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR948RHA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR404KWM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB149RWD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: mam

tag: geographic location

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

value: Hugo Bellen

value: ENCBS284ZJM at ENCODE; https://www.encodeproject.org/ENCBS284ZJM/


title: TF ChIP-seq from whole organism (ENCLB626EPT)

description:
https://www.encodeproject.org/experiments/ENCSR927RAW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-unc-62 in mixed stage (embryonic) worms.
experiment encode accession: ENCSR927RAW
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR837ZAW
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB626EPT
size range: 150-350

value: whole organism

value: not applicable

tag: encode accession

value: Michael Snyder, Stanford

value: CGC

value: ENCBS048XGP at ENCODE; https://www.encodeproject.org/ENCBS048XGP/


title: Control ChIP-seq from whole organism (ENCLB215FIV)

description:
https://www.encodeproject.org/experiments/ENCSR778ELF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG10462-eGFP fusion proteins.
experiment encode accession: ENCSR778ELF
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB215FIV
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: whole organisms

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

tag: Sex

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: ENCBS060UFM at ENCODE; https://www.encodeproject.org/ENCBS060UFM/


title: TF ChIP-seq from whole organism (ENCLB965YVQ)

description:
https://www.encodeproject.org/experiments/ENCSR461AXL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing h-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR461AXL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR904QAP
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB965YVQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain 15T-GFP mixed sex wandering third instar larva insertion targeting D. melanogaster h

value: h

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

value: pooled male and female

value: wandering third instar larva

tag: age

value: unknown

value: Kevin White

value: ENCBS689FAH at ENCODE; https://www.encodeproject.org/ENCBS689FAH/


title: TF ChIP-seq from whole organism (ENCLB511EMB)

description:
https://www.encodeproject.org/experiments/ENCSR925OOO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-76 in L4 larva worms.
experiment encode accession: ENCSR925OOO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR482PKO
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB511EMB
size range: 150-350

source_name: Caenorhabditis elegans strain OP203 (unc-119(ed3) III; wgIs203) mixed sex L4 larva insertion targeting C. elegans nhr-76

value: whole organism

value: not applicable

value: L4 larva

tag: lab

value: ENCBS589KRW at ENCODE; https://www.encodeproject.org/ENCBS589KRW/


title: TF ChIP-seq from whole organism (ENCLB852YAR)

description:
https://www.encodeproject.org/experiments/ENCSR948RHA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing mam-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR948RHA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR404KWM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB852YAR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: mam

value: whole organisms

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

tag: source

value: Hugo Bellen

value: ENCBS581MNM at ENCODE; https://www.encodeproject.org/ENCBS581MNM/


title: Control ChIP-seq from whole organism (ENCLB203YHZ)

description:
https://www.encodeproject.org/experiments/ENCSR927LZU/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L1 larva worms.
experiment encode accession: ENCSR927LZU
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB203YHZ
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

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

tag: dev stage

value: L1 larva

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS028VMY at ENCODE; https://www.encodeproject.org/ENCBS028VMY/


title: C03 vineyard block spot 11 time point 2

description: gene expression in C03 vineyard block spot 11 time point 2

source_name: C03 vineyard block spot 11 time point 2

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

value: pea size + 10 days


title: C03 vineyard block spot 12 time point 2

description: gene expression in C03 vineyard block spot 12 time point 2

source_name: C03 vineyard block spot 12 time point 2


title: C03 vineyard block spot 6 time point 2

description: gene expression in C03 vineyard block spot 6 time point 2

source_name: C03 vineyard block spot 6 time point 2


title: TF ChIP-seq from whole organism (ENCLB379RAI)

description:
https://www.encodeproject.org/experiments/ENCSR948RHA/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing mam-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR948RHA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR404KWM
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB379RAI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

tag: link

value: ENCBS493BXZ at ENCODE; https://www.encodeproject.org/ENCBS493BXZ/


title: C03 vineyard block spot 7 time point 2

description: gene expression in C03 vineyard block spot 7 time point 2

source_name: C03 vineyard block spot 7 time point 2


title: C03 vineyard block spot 3 time point 2

description: gene expression in C03 vineyard block spot 3 time point 2

source_name: C03 vineyard block spot 3 time point 2


title: C03 vineyard block spot 10 time point 2

description: gene expression in C03 vineyard block spot 10 time point 2

source_name: C03 vineyard block spot 10 time point 2


title: C03 vineyard block spot 5 time point 2

description: gene expression in C03 vineyard block spot 5 time point 2

source_name: C03 vineyard block spot 5 time point 2


title: Control ChIP-seq from whole organism (ENCLB325QXZ)

description:
https://www.encodeproject.org/experiments/ENCSR772QGN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG1602-eGFP fusion proteins.
experiment encode accession: ENCSR772QGN
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB325QXZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG1602-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG1602

value: whole organism

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG1602

value: Kevin White

value: ENCBS779ZPZ at ENCODE; https://www.encodeproject.org/ENCBS779ZPZ/


title: TF ChIP-seq from whole organism (ENCLB918PPM)

description:
https://www.encodeproject.org/experiments/ENCSR925OOO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-nhr-76 in L4 larva worms.
experiment encode accession: ENCSR925OOO
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR482PKO
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB918PPM
size range: 150-350

tag: antibody

value: whole organisms

value: L4 larva

value: unknown

value: CGC

value: ENCBS546DPR at ENCODE; https://www.encodeproject.org/ENCBS546DPR/


title: KO 2C Female

city: Tama Ward

first: Jiuxiang

last: Cao

state: Kanagawa

address: 1 Chome-1-1 Higashimita

department: School of Agriculture

country: Japan

institute: Meiji University

library_source: transcriptomic

data_processing:
The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted from the tissues using TriPure Isolation Reagent (Roche Applied Science)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

tag: tissue

value: Liver

tag: genotype

value: Vldlr KO

tag: treatment

value: 2% casein


title: KO 2C Male


title: WT 2C Female


title: C03 vineyard block spot 4 time point 2

description: gene expression in C03 vineyard block spot 4 time point 2

source_name: C03 vineyard block spot 4 time point 2

tag: cultivar

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

tag: spot

tag: time point

tag: phenology

value: pea size + 10 days


title: TF ChIP-seq from whole organism (ENCLB009KUY)

description:
https://www.encodeproject.org/experiments/ENCSR771CMI/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ems-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR771CMI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR680BUH
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB009KUY
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: ems

tag: biosample encode accession

tag: collection date

tag: note

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

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: ENCBS633CZQ at ENCODE; https://www.encodeproject.org/ENCBS633CZQ/


title: Control ChIP-seq from whole organism (ENCLB138EQW)

description:
https://www.encodeproject.org/experiments/ENCSR626WON/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR626WON
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB138EQW
size range: 150-350
instrument models: Illumina Genome Analyzer IIx,Illumina Genome Analyzer

source_name: Caenorhabditis elegans strain N2 (C. elegans wild isolate) mixed sex L4 larva whole organism

value: whole organism

value: whole organisms

value: not applicable

tag: geographic location

tag: encode accession

tag: Sex

value: Michael Snyder, Stanford

value: ENCBS003NAQ at ENCODE; https://www.encodeproject.org/ENCBS003NAQ/


title: WT 20C Female

value: Liver

value: 20% casein


title: KO 20C Female

value: Vldlr KO


title: KO 20C Male


title: C03 vineyard block spot 1 time point 2

description: gene expression in C03 vineyard block spot 1 time point 2

source_name: C03 vineyard block spot 1 time point 2

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

tag: sampling date


title: TF ChIP-seq from whole organism (ENCLB317LPL)

description:
https://www.encodeproject.org/experiments/ENCSR771CMI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ems-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR771CMI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR680BUH
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB317LPL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: dev stage

tag: age

tag: lab

tag: source

value: Kevin White

value: ENCBS808YPZ at ENCODE; https://www.encodeproject.org/ENCBS808YPZ/


title: Control ChIP-seq from whole organism (ENCLB121QYX)

description:
https://www.encodeproject.org/experiments/ENCSR626WOI/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR626WOI
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB121QYX
size range: 150-350

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

value: L3 larva

value: unknown

value: CGC

tag: link

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


title: WT 20C Male

tag: tissue

tag: genotype

tag: treatment


title: Control ChIP-seq from whole organism (ENCLB783DYK)

description:
https://www.encodeproject.org/experiments/ENCSR626THZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in mixed stage (embryonic) worms.
experiment encode accession: ENCSR626THZ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB783DYK
size range: 150-350

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

value: pooled male and female

value: mixed stage (embryonic)

value: ENCBS208ZOC at ENCODE; https://www.encodeproject.org/ENCBS208ZOC/


title: TF ChIP-seq from whole organism (ENCLB814EGK)

description:
https://www.encodeproject.org/experiments/ENCSR771CMI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ems-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR771CMI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR680BUH
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB814EGK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: ems

value: whole organism

value: whole organisms

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: ENCBS059XSB at ENCODE; https://www.encodeproject.org/ENCBS059XSB/


title: C03 vineyard block spot 2 time point 2

description: gene expression in C03 vineyard block spot 2 time point 2

source_name: C03 vineyard block spot 2 time point 2

tag: cultivar

value: Vitis vinifera cv. Cabernet Sauvignon (FPS clone 8 grafted onto 110R rootstock)

tag: spot

tag: time point

tag: phenology

value: pea size + 10 days


title: Control ChIP-seq from whole organism (ENCLB311XVW)

description:
https://www.encodeproject.org/experiments/ENCSR626THZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in mixed stage (embryonic) worms.
experiment encode accession: ENCSR626THZ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB311XVW
size range: 150-350

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

value: Michael Snyder, Stanford

value: ENCBS013TOT at ENCODE; https://www.encodeproject.org/ENCBS013TOT/


title: Control ChIP-seq from whole organism (ENCLB203GHR)

description:
https://www.encodeproject.org/experiments/ENCSR626WOI/
***************
biological replicate number: 3
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR626WOI
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB203GHR
fragmentation methods: sonication (generic microtip)

tag: encode accession

tag: note

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

tag: Sex

value: L3 larva

value: unknown

value: Michael Snyder

value: ENCBS492UAH at ENCODE; https://www.encodeproject.org/ENCBS492UAH/


title: TF ChIP-seq from whole organism (ENCLB194ASP)

description:
https://www.encodeproject.org/experiments/ENCSR770AUN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing luna-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR770AUN
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR118DLX
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB194ASP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: luna

value: whole organism

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

value: pooled male and female

tag: dev stage

tag: age

tag: lab

value: Hugo Bellen

value: ENCBS835FYR at ENCODE; https://www.encodeproject.org/ENCBS835FYR/


title: TF ChIP-seq from whole organism (ENCLB382DUX)

description:
https://www.encodeproject.org/experiments/ENCSR770AUN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing luna-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR770AUN
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR118DLX
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB382DUX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

tag: source

tag: link

value: ENCBS562WTT at ENCODE; https://www.encodeproject.org/ENCBS562WTT/


title: Control ChIP-seq from whole organism (ENCLB057BQT)

description:
https://www.encodeproject.org/experiments/ENCSR441OGV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing pum-eGFP fusion proteins.
experiment encode accession: ENCSR441OGV
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB057BQT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: not applicable

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

value: ENCBS927IJX at ENCODE; https://www.encodeproject.org/ENCBS927IJX/


title: MII,high-fat diet,rep5

city: Zhengzhou

first: Lin-Li

last: Yang

state: Henan

address: No. 1, Jianshe East Road, Erqi District

department: department of obstetrics and gynecology

country: China

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Illumina high-throughput sequencing results are converted into original sequencing sequences by bcl2fastq software and stored in FASTQ file format.
Clean Reads of high quality were obtained after the original sequences were filtered. The filtered sequencing sequences of each sample were compared with the reference genome Mus_musculus.GRCm38.90.chr to locate the genome.
FPKM (Fragments per Kilobase per Million Mapped Fragments) method was used to obtain differentially expressed genes that could be directly used to compare different samples.
Assembly: ftp://ftp.ensembl.org/pub/release-90/gtf/mus_musculus/Mus_musculus.GRCm38.90.gtf.gz
Supplementary files format and content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: oocytes

growth_protocol: The embryos were cultured in KSOM in vitro.

extract_protocol:
The single-cell samples were collected in tubes with lysis component and ribonuclease inhibitor. Then we carried out the amplification by the Smart-Seq2 method. An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production. Then the cDNA production was checked by Qubit® 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2kbp. Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation. After library preparation, PerkinElmer LabChip® GX Touch and Step OnePlus™ Real-Time PCR System were introduced for library quality inspection.Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.
RNA libraries were prepared foe sequencing using standard Illumina protocols.

treatment_protocol: The transcript of siAcox1 group  were deleted by small-interfering-RNA(siRNA) microinjection into mouse zygotes.

tag: tissue

value: oocytes

tag: cell type

tag: treatment

value: oocyte maturation

value: high-fat diet


title: MII,high-fat diet,rep6


title: MII,high-fat diet,rep4


title: WT 2C Male

value: Liver

tag: genotype

value: 2% casein


title: MII,high-fat diet,rep3


title: MII,high-fat diet,rep2


title: Control ChIP-seq from whole organism (ENCLB587ZKG)

description:
https://www.encodeproject.org/experiments/ENCSR923VWK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in starved L1 larva worms.
experiment encode accession: ENCSR923VWK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB587ZKG
size range: 150-350

source_name: Caenorhabditis elegans strain OP367 (unc-119(tm4063) III; wgIs367) mixed sex L1 larva at L1 larva starved after bleaching stage insertion targeting C. elegans lsy-2

value: whole organism

value: L1 larva

value: unknown

value: Michael Snyder, Stanford

value: CGC

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: ENCBS391XJT at ENCODE; https://www.encodeproject.org/ENCBS391XJT/


title: MII,high-fat diet,rep1


title: Control ChIP-seq from whole organism (ENCLB482KBX)

description:
https://www.encodeproject.org/experiments/ENCSR923VWK/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in starved L1 larva worms.
experiment encode accession: ENCSR923VWK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB482KBX
size range: 150-350

value: whole organisms

value: pooled male and female

value: ENCBS821MVC at ENCODE; https://www.encodeproject.org/ENCBS821MVC/


title: Control ChIP-seq from whole organism (ENCLB915CLC)

description:
https://www.encodeproject.org/experiments/ENCSR626WOI/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR626WOI
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB915CLC
size range: 150-350

value: not applicable

value: L3 larva

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


title: Rela-KO mouse Tconv CD8+ T cells, rep. 2

city: Lyon

first: Yenkel

last: Grinberg-Bleyer

address: 28 rue Laennec

department: Immunity, viruses and inflammation

country: France

institute: Cancer Research Center of Lyon

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

molecule: polyA RNA

source_name: Spleen+lymph nodes

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

value: Spleen+lymph nodes

value: CD8+ T cells

value: Rela-cKO


title: Ctrl mouse Tconv CD8+ T cells, rep. 4

value: WT


title: Rela-KO mouse Tconv CD8+ T cells, rep. 3


title: Rela-KO mouse Tconv CD8+ T cells, rep. 4


title: Rela-KO mouse Tconv CD8+ T cells, rep. 1


title: Control ChIP-seq from whole organism (ENCLB296WTZ)

description:
https://www.encodeproject.org/experiments/ENCSR921YEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L3 larva worms.
experiment encode accession: ENCSR921YEJ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB296WTZ
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: whole organism

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

value: Michael Snyder

value: ENCBS369CUA at ENCODE; https://www.encodeproject.org/ENCBS369CUA/


title: TF ChIP-seq from whole organism (ENCLB928RDL)

description:
https://www.encodeproject.org/experiments/ENCSR648YVN/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG3163-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR648YVN
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR340PDD
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB928RDL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS802AWU at ENCODE; https://www.encodeproject.org/ENCBS802AWU/


title: Ctrl mouse Tconv CD8+ T cells, rep. 1


title: TF ChIP-seq from whole organism (ENCLB228ABP)

description:
https://www.encodeproject.org/experiments/ENCSR648YVN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG3163-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR648YVN
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR340PDD
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB228ABP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: biosample encode accession

value: not applicable

value: pooled male and female

value: ENCBS413VGR at ENCODE; https://www.encodeproject.org/ENCBS413VGR/


title: Ctrl mouse Tconv CD8+ T cells, rep. 2

value: Spleen+lymph nodes

value: CD8+ T cells