title: Control ChIP-seq from whole organism (ENCLB621PHE)

description:
https://www.encodeproject.org/experiments/ENCSR742BIV/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing sdz-12-eGFP fusion proteins.
experiment encode accession: ENCSR742BIV
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB621PHE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organisms

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

value: L4 larva

value: 71 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS825FWF at ENCODE; https://www.encodeproject.org/ENCBS825FWF/


title: 45_L1

status: Public on Feb 27 2024

type: SRA

city: Nouzilly

first: Julie

last: Collet

address: Centre INRAE

country: France

institute: INRAE

description:
extraction 001 sample 02_L1 pool 06_04
DGRP45 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

library_source: transcriptomic

data_processing:
The quality of the obtained sequences was checked using FastQC [19], with particular attention given to per-base-sequence quality. We used Trimmomatic [20] to: (i) remove the first 10 bases from the start of the read; (ii) trim slide windows, using the window size of 4 and an average base quality across each window of Q=30; and (iii) to keep reads of a minimum of 35 bp at a minimum average quality of 30. To quantify gene expression, we aligned single-end RNAseq reads to the reference genome of D. melanogaster released in Aug.2014 (BDGP Release 6 + ISO 1 IT/dm6) (dm6) using STAR [21]. We applied all default parameters, except for a minimum intron size of 5 and max intron size of 200,000. We used dm6_FlyBase_Genes_assembled_chromosomes-r6.22.gtf for gene annotation. All bioinformatic analyses were done using the Galaxy portal (https://usegalaxy.org.au/).
Assembly: dm6
Supplementary files format and content: .csv raw counts

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
For each sample, we extracted RNA using phenol chloroform phase separation. We first added 500 µl of TRIzol (Thermo Fisher Scientific) to the frozen specimens and crushed them with a pestle. We then added 100 µl of chloroform to the crushed specimens, agitated the samples for 15 seconds, and incubated them at room temperature for 3 minutes. The samples were centrifuged at 12,000 RCF for 15 minutes at 4°C. We transferred the aqueous phase into fresh tubes, added an additional 250 µl of isopropanol, and inverted the tube four times to ensure mixing. After allowing the tubes to incubate at room temperature for 10 minutes, the samples were centrifuged at 12,000 RCF for 10 minutes at 4°C. We removed the supernatant, washed the pellet with 500 µl of 75% ethanol, and again centrifuged the samples at 7,500 RCF for 5 minutes at 4°C. A second wash was then carried out using 500 µl of 75% ethanol. After a final centrifugation at 7,500 RCF for 5 minutes at 4°C, the supernatant was carefully removed. The pellet was left to dry at room temperature for 30 min. RNA was resuspended in 100 µl of nuclease-free water and then the samples were heated to 55°C in a drybath for 15 minutes. We verified RNA concentration and integrity on the Bioanalyzer (Agilent) with the RNA 6000 Pico Kit according the manufacturer instructions, as well as on the NanoDrop™ 8000 Spectrophotometer (Thermo Fisher Scientific). All RNA samples were stored at -80°C.
We prepared the cDNA libraries using the Illumina® TruSeq® Stranded mRNA Sample Preparation Kit, following the manufacturer’s protocol and using a Biomek NXᴾ Automated Workstation (Biomek NXP Span-8 by Beckman). In brief, poly-A-containing mRNA molecules were purified from 1 µg total RNA using poly-T oligo-attached magnetic beads. The purified mRNA was fragmented by adding the fragmentation buffer and then heated to 94°C in a thermocycler for 8 minutes. We primed the cleaved RNA fragments with random hexamers and used reverse transcriptase to synthesize first-strand cDNA. Second-strand cDNA synthesis, end repair, A-tailing, adapter ligation, and enrich DNA fragments were carried out in accordance with the manufacturer supplied protocols. Each indexed cDNA library was verified and quantified using a dsDNA 915 Reagent Kit on a Fragment Analyzer (Agilent). We equally mixed 12 to 13 indexed cDNA libraries in each final library. The final libraries were quantified by real-time PCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms (Kapa Biosystems Ltd, SA), adjusted to 10 nM in water, and provided to the Montpellier Genomix platform (http://www.mgx.cnrs.fr/) for sequencing.
Each final mixed cDNA library was denatured with NaOH and diluted to a concentration of 18 pM using the standard library PhiX (1%) from Illumina. Flow cell was clustered using TruSeq SR Cluster Kit v3-cBot-HS, and then loaded into the Illumina HiSeq 2500 instrument following the manufacturer’s instructions. The v3 sequencing chemistry (TruSeq SBS Kit v3-HS) was used, applying a 50 cycle, single-read, indexed protocol. Image analyses and basecalling were carried out using the Hiseq Control Software (Illumina HCS) and Real-Time Analysis Software (Illumina RTA).

treatment_protocol: The flies that were collected from two vials of each biological replicate were placed together before RNA extraction. As a result of our strict age conditions, we were unable to always gather 20 flies per sample, and the total number of flies per sample ranged from 2 to 31 flies, with a median number of 20 and 17 individuals in larval and adult samples respectively.

tag: tissue

value: whole body

tag: genotype

tag: developmental stage

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB147UVC)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR272DEA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Lhr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR272DEA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR462RAG
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB147UVC
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

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

tag: antibody

value: Lhr

value: whole organism

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: note

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

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

tag: age

value: 0-14 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS086RFK at ENCODE; https://www.encodeproject.org/ENCBS086RFK/


title: TF ChIP-seq from whole organism (ENCLB715GHW)

description:
https://www.encodeproject.org/experiments/ENCSR274AAR/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8924-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR274AAR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR857ANW
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB715GHW
size range: 200-800

source_name: Drosophila melanogaster strain CG8924 mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG8924

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8924

value: 0-24 hour

value: ENCBS803CRU at ENCODE; https://www.encodeproject.org/ENCBS803CRU/


title: 486_L1

description:
extraction 097 sample 30_L1 pool 05_16
DGRP486 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB862OZM)

description:
https://www.encodeproject.org/experiments/ENCSR272DEA/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Lhr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR272DEA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR462RAG
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB862OZM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: ENCBS506EKN at ENCODE; https://www.encodeproject.org/ENCBS506EKN/


title: TF ChIP-seq from whole organism (ENCLB807IOU)

description:
https://www.encodeproject.org/experiments/ENCSR617PLK/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing drap-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR617PLK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR028XNW
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB807IOU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP700 (wgIs700(drap-1::TY1 EGFP 3xFLAG(p_wTRG5_insertion_c_0086_1E01);unc-119(+));unc-119 (tm4063)) mixed sex mixed stage (embryo) (3 hours) using egg bleaching insertion targeting C. elegans drap-1

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

value: mixed stage (embryonic)

value: 3 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

value: ENCBS285YPW at ENCODE; https://www.encodeproject.org/ENCBS285YPW/


title: TF ChIP-seq from whole organism (ENCLB918WWH)

description:
https://www.encodeproject.org/experiments/ENCSR617PLK/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing drap-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR617PLK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR028XNW
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB918WWH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

value: pooled male and female

value: ENCBS987PRX at ENCODE; https://www.encodeproject.org/ENCBS987PRX/


title: 391_L2

description:
extraction 064 sample 27_L2 pool 05_15
DGRP391 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB837OXT)

description:
https://www.encodeproject.org/experiments/ENCSR617PLK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing drap-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR617PLK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR028XNW
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB837OXT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: ENCBS803FBQ at ENCODE; https://www.encodeproject.org/ENCBS803FBQ/


title: TF ChIP-seq from whole organism (ENCLB354ATR)

description:
https://www.encodeproject.org/experiments/ENCSR271ZJI/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing REPTOR-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR271ZJI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR116ZCQ
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB354ATR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG18619-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster REPTOR-BP

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS372YKB at ENCODE; https://www.encodeproject.org/ENCBS372YKB/


title: 801_L1

description:
extraction 011 sample 41_L1 pool 05_06
DGRP801 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: 787_L2

description:
extraction 076 sample 39_L2 pool 05_05
DGRP787 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB267OSH)

description:
https://www.encodeproject.org/experiments/ENCSR268FFL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing pfk-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR268FFL
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB267OSH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

value: ENCBS669QMQ at ENCODE; https://www.encodeproject.org/ENCBS669QMQ/


title: Control ChIP-seq from whole organism (ENCLB128QFX)

description:
https://www.encodeproject.org/experiments/ENCSR370OIE/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG1663-eGFP fusion proteins.
experiment encode accession: ENCSR370OIE
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB128QFX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster mixed sex pupa (24 hours) insertion targeting D. melanogaster CG1663

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG1663

value: pupa

value: 24 hour

value: ENCBS855HZR at ENCODE; https://www.encodeproject.org/ENCBS855HZR/


title: 774_L2

description:
extraction 074 sample 37_L2 pool 05_04
DGRP774 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB372DCT)

description:
https://www.encodeproject.org/experiments/ENCSR919QDM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ets-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR919QDM
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR887YEV
encode release date: 2018-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB372DCT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RAF1713 (rrrSi400[Pets-4::ets-4-GFP::ets-4 3'UTR, unc-119(+)] II; unc-119(ed3) III) mixed sex young adult (73 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ets-4

value: whole organism

value: not applicable

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

value: pooled male and female

value: young adult

value: 73 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS040LZG at ENCODE; https://www.encodeproject.org/ENCBS040LZG/


title: Control ChIP-seq from whole organism (ENCLB875ZTA)

description:
https://www.encodeproject.org/experiments/ENCSR730YCH/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing hlh-11-eGFP fusion proteins.
experiment encode accession: ENCSR730YCH
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB875ZTA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP396 (unc-119(tm4063) III; wgIs396) mixed sex L4 larva (53 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans hlh-11

value: whole organisms

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

value: L4 larva

value: 53 hour

value: ENCBS196LMX at ENCODE; https://www.encodeproject.org/ENCBS196LMX/


title: TF ChIP-seq from whole organism (ENCLB250CZE)

description:
https://www.encodeproject.org/experiments/ENCSR271ZJI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing REPTOR-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR271ZJI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR116ZCQ
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB250CZE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS015ZCE at ENCODE; https://www.encodeproject.org/ENCBS015ZCE/


title: TF ChIP-seq from whole organism (ENCLB365OTS)

description:
https://www.encodeproject.org/experiments/ENCSR266HYG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR266HYG
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR604YZN
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB365OTS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain oc embryo (2-14 hours) insertion targeting D. melanogaster oc

value: oc

value: whole organism

value: not applicable

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

value: not collected

value: ENCBS351ZFW at ENCODE; https://www.encodeproject.org/ENCBS351ZFW/


title: TF ChIP-seq from whole organism (ENCLB472YIZ)

description:
https://www.encodeproject.org/experiments/ENCSR729RHJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing gei-8-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR729RHJ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR219MAS
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB472YIZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP589 (unc-119(tm4063); wgIs589 [gei-8::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex L4 larva (48 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans gei-8

value: whole organisms

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

value: pooled male and female

value: 48 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS147ZFW at ENCODE; https://www.encodeproject.org/ENCBS147ZFW/


title: 181_L2

description:
extraction 049 sample 11_L2 pool 06_12
DGRP181 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB942HTF)

description:
https://www.encodeproject.org/experiments/ENCSR274AAR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8924-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR274AAR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR857ANW
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB942HTF
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8924

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS888FPN at ENCODE; https://www.encodeproject.org/ENCBS888FPN/


title: 356_L2

description:
extraction 057 sample 19_L2 pool 04_18
DGRP356 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB713DQP)

description:
https://www.encodeproject.org/experiments/ENCSR272DEA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Lhr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR272DEA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR462RAG
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB713DQP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Lhr

value: whole organism

value: not applicable

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

value: 0-14 hour

value: ENCBS555NUP at ENCODE; https://www.encodeproject.org/ENCBS555NUP/


title: TF ChIP-seq from whole organism (ENCLB972IJF)

description:
https://www.encodeproject.org/experiments/ENCSR729RHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing gei-8-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR729RHJ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR219MAS
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB972IJF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

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

value: pooled male and female

value: L4 larva

value: 48 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS649BOF at ENCODE; https://www.encodeproject.org/ENCBS649BOF/


title: 897_L1

description:
extraction 039 sample 49_L1 pool 04_15
DGRP897 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB340MXJ)

description:
https://www.encodeproject.org/experiments/ENCSR266HYG/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR266HYG
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR604YZN
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB340MXJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: oc

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

value: not collected

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS828RJM at ENCODE; https://www.encodeproject.org/ENCBS828RJM/


title: TF ChIP-seq from whole organism (ENCLB804TOY)

description:
https://www.encodeproject.org/experiments/ENCSR416GJW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing mxl-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR416GJW
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR553MTY
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB804TOY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP745 (wgIs745 [mxl-3::TY1::EGFP::3xFLAG + unc-119(+)];unc-119 (tm4063)) mixed sex L4 larva (48 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans mxl-3

value: whole organism

value: whole organisms

value: not applicable

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

value: L1 larva starved after bleaching

value: ENCBS914TKP at ENCODE; https://www.encodeproject.org/ENCBS914TKP/


title: 142_L2

description:
extraction 046 sample 06_L2 pool 04_14
DGRP142 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from brain (ENCLB060FFB)

description:
https://www.encodeproject.org/experiments/ENCSR603VTC/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR603VTC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2013-07-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB060FFB

organism: Homo sapiens

source_name: Homo sapiens female embryo (120 days) brain tissue

value: brain

value: tissue

value: Brain tissue from a healthy 120 day old female human fetus. Tissue provided by Ian Glass of University of Washington, Congenital Defects Lab.

value: female

value: 120 day

value: Bradley Bernstein, Broad

value: Unknown Source

value: ENCBS604GZI at ENCODE; https://www.encodeproject.org/ENCBS604GZI/


title: TF ChIP-seq from whole organism (ENCLB396ADP)

description:
https://www.encodeproject.org/experiments/ENCSR266CSS/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG3407-eGFP fusion proteins.
experiment encode accession: ENCSR266CSS
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR572CBY
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB396ADP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG3407-GFP mixed sex embryo (0-14 hours) insertion targeting D. melanogaster CG3407

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG3407

value: pooled male and female

value: embryonic

value: 0-14 hour

value: Kevin White, UChicago

value: ENCBS815UZD at ENCODE; https://www.encodeproject.org/ENCBS815UZD/


title: 45_L2

description:
extraction 042 sample 02_L2 pool 05_14
DGRP45 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB739RAB)

description:
https://www.encodeproject.org/experiments/ENCSR271ZJI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing REPTOR-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR271ZJI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR116ZCQ
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB739RAB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

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

value: 0-24 hour

value: Kevin White

value: ENCBS456TTZ at ENCODE; https://www.encodeproject.org/ENCBS456TTZ/


title: TF ChIP-seq from whole organism (ENCLB172YIS)

description:
https://www.encodeproject.org/experiments/ENCSR416GJW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing mxl-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR416GJW
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR553MTY
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB172YIS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: L4 larva

value: 48 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS558GRP at ENCODE; https://www.encodeproject.org/ENCBS558GRP/


title: TF ChIP-seq from whole organism (ENCLB579FCB)

description:
https://www.encodeproject.org/experiments/ENCSR266CSS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG3407-eGFP fusion proteins.
experiment encode accession: ENCSR266CSS
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR572CBY
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB579FCB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG3407

value: pooled male and female

value: embryonic

value: 0-14 hour

value: Kevin White, UChicago

value: ENCBS287YBG at ENCODE; https://www.encodeproject.org/ENCBS287YBG/


title: 379_L1

description:
extraction 008 sample 25_L1 pool 04_05
DGRP379 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: 703_L2

description:
extraction 071 sample 34_L2 pool 04_04
DGRP703 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB273PWC)

description:
https://www.encodeproject.org/experiments/ENCSR919QDM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ets-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR919QDM
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR887YEV
encode release date: 2018-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB273PWC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

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

value: young adult

value: 73 hour

value: ENCBS272BWR at ENCODE; https://www.encodeproject.org/ENCBS272BWR/


title: TF ChIP-seq from whole organism (ENCLB698HAM)

description:
https://www.encodeproject.org/experiments/ENCSR914MJK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing let-607-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR914MJK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR587BKG
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB698HAM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain YL651 (let-607(tm1423); unc-119(ed3) III; vrIs121[LET-607 fosmid, unc-119 (+)]) mixed sex young adult (49.5 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans let-607

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to LET-607.

value: 49.5 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS398BNA at ENCODE; https://www.encodeproject.org/ENCBS398BNA/


title: TF ChIP-seq from whole organism (ENCLB986WSN)

description:
https://www.encodeproject.org/experiments/ENCSR367SBM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR367SBM
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR488SGR
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB986WSN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Fer3 embryo (6-24 hours) insertion targeting D. melanogaster Fer3

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Fer3

value: not collected

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS810QCN at ENCODE; https://www.encodeproject.org/ENCBS810QCN/


title: 879_L2

description:
extraction 085 sample 47_L2 pool 04_07
DGRP879 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: Control ChIP-seq from whole organism (ENCLB312QSX)

description:
https://www.encodeproject.org/experiments/ENCSR609PJK/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing cnd-1-eGFP fusion proteins.
experiment encode accession: ENCSR609PJK
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB312QSX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP349 (unc-119(ed3) III; wgIs349) mixed sex mixed stage (embryo) (3 hours) using egg bleaching insertion targeting C. elegans cnd-1

value: whole organism

value: whole organisms

value: not applicable

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

value: pooled male and female

value: mixed stage (embryonic)

value: 3 hour

value: egg bleaching

value: ENCBS002VDT at ENCODE; https://www.encodeproject.org/ENCBS002VDT/


title: 441_L2

description:
extraction 066 sample 29_L2 pool 04_02
DGRP441 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

source_name: whole body


title: Control ChIP-seq from whole organism (ENCLB826LUM)

description:
https://www.encodeproject.org/experiments/ENCSR264BNK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG9139-eGFP fusion proteins.
experiment encode accession: ENCSR264BNK
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB826LUM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

value: prepupa

value: 24 hour

value: ENCBS351DLL at ENCODE; https://www.encodeproject.org/ENCBS351DLL/


title: TF ChIP-seq from whole organism (ENCLB412DTO)

description:
https://www.encodeproject.org/experiments/ENCSR365IMJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dmrt11E-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR365IMJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR238YEP
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB412DTO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster mixed sex embryo (2-10 hours) insertion targeting D. melanogaster dmrt11E

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to dmrt11E

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS900AND at ENCODE; https://www.encodeproject.org/ENCBS900AND/


title: TF ChIP-seq from whole organism (ENCLB300EWB)

description:
https://www.encodeproject.org/experiments/ENCSR367SBM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR367SBM
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR488SGR
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB300EWB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Fer3

value: not collected

value: ENCBS844YDC at ENCODE; https://www.encodeproject.org/ENCBS844YDC/


title: TF ChIP-seq from whole organism (ENCLB700FSA)

description:
https://www.encodeproject.org/experiments/ENCSR914MJK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing let-607-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR914MJK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR587BKG
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB700FSA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to LET-607.

value: pooled male and female

value: young adult

value: 49.5 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS060BBP at ENCODE; https://www.encodeproject.org/ENCBS060BBP/


title: Control ChIP-seq from whole organism (ENCLB093SDA)

description:
https://www.encodeproject.org/experiments/ENCSR608KZR/
***************
biological replicate number: 4
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ztf-3-eGFP fusion proteins.
experiment encode accession: ENCSR608KZR
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB093SDA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP614 (unc-119(tm4063); wgIs614 [ztf-3::TY1::EGFP::3xFLAG +;unc-119(+)]) mixed sex young adult (58 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ztf-3

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

value: 58 hour

value: ENCBS239DUD at ENCODE; https://www.encodeproject.org/ENCBS239DUD/


title: 380_L1

description:
extraction 027 sample 26_L1 pool 03_13
DGRP380 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: Control ChIP-seq from whole organism (ENCLB622SKM)

description:
https://www.encodeproject.org/experiments/ENCSR721CXH/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ccch-3-eGFP fusion proteins.
experiment encode accession: ENCSR721CXH
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB622SKM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP628 (wgIs628(ccch-3::TY1 EGFP 3xFLAG(p_wTRG5_insertion_c_0161_4E04);unc-119(+));unc-119 (tm4063)) mixed sex young adult (70 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ccch-3

value: whole organism

value: whole organisms

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

value: 70 hour

value: ENCBS779COV at ENCODE; https://www.encodeproject.org/ENCBS779COV/


title: TF ChIP-seq from whole organism (ENCLB391TFU)

description:
https://www.encodeproject.org/experiments/ENCSR365IMJ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dmrt11E-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR365IMJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR238YEP
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB391TFU
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 dmrt11E

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS502DCS at ENCODE; https://www.encodeproject.org/ENCBS502DCS/


title: TF ChIP-seq from whole organism (ENCLB055ZVZ)

description:
https://www.encodeproject.org/experiments/ENCSR717JMX/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing FKH-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR717JMX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR652ZAR
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB055ZVZ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP594 (unc-119(tm4063) III; wgIs594) mixed sex young adult 63 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans fkh-3

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

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS190OXE at ENCODE; https://www.encodeproject.org/ENCBS190OXE/


title: 703_L1

description:
extraction 016 sample 34_L1 pool 03_07
DGRP703 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB964NBK)

description:
https://www.encodeproject.org/experiments/ENCSR365IMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dmrt11E-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR365IMJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR238YEP
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB964NBK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: whole organisms

value: not applicable

value: ENCBS828NBZ at ENCODE; https://www.encodeproject.org/ENCBS828NBZ/


title: 832_L1

description:
extraction 114 sample 45_L1 pool 03_02
DGRP832 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: developmental stage


title: 783_L1

description:
extraction 034 sample 38_L1 pool 02_14
DGRP783 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB269GTG)

description:
https://www.encodeproject.org/experiments/ENCSR263AYM/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG3281-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR263AYM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR858HKA
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB269GTG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG3281-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG3281

tag: biosample encode accession

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG3281

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: ENCBS111SSA at ENCODE; https://www.encodeproject.org/ENCBS111SSA/


title: Control ChIP-seq from whole organism (ENCLB329QDQ)

description:
https://www.encodeproject.org/experiments/ENCSR911LPA/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing B0261.1-eGFP fusion proteins.
experiment encode accession: ENCSR911LPA
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB329QDQ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP662 (unc-119(tm4063) III; wgIs662) mixed sex young adult 64 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans B0261.1

tag: geographic location

tag: encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to B0261.1

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: ENCBS838AEI at ENCODE; https://www.encodeproject.org/ENCBS838AEI/


title: 57_L1

description:
extraction 002 sample 03_L1 pool 02_04
DGRP57 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body


title: Control ChIP-seq from whole organism (ENCLB775SAS)

description:
https://www.encodeproject.org/experiments/ENCSR911LPA/
***************
biological replicate number: 2
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing B0261.1-eGFP fusion proteins.
experiment encode accession: ENCSR911LPA
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB775SAS
fragmentation methods: sonication (generic microtip)

tag: note

tag: Sex

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS372SDX at ENCODE; https://www.encodeproject.org/ENCBS372SDX/


title: TF ChIP-seq from whole organism (ENCLB884AIU)

description:
https://www.encodeproject.org/experiments/ENCSR717JMX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing FKH-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR717JMX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR652ZAR
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB884AIU
fragmentation methods: sonication (generic microtip)

value: whole organism

value: whole organisms

value: not applicable

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

tag: dev stage

tag: age

value: ENCBS491PRG at ENCODE; https://www.encodeproject.org/ENCBS491PRG/


title: 805_L1

description:
extraction 113 sample 43_L1 pool 01_18
DGRP805 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: Larvae


title: Control ChIP-seq from whole organism (ENCLB780DIZ)

description:
https://www.encodeproject.org/experiments/ENCSR908QFK/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing pat-9-eGFP fusion proteins.
experiment encode accession: ENCSR908QFK
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB780DIZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RW12085 (pat-9(mNG^SEC^3xFlag::pat-9]) X) mixed sex late embryo (3 hours) using egg bleaching whole organism genetically modified (insertion) using CRISPR targeting C. elegans pat-9

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

value: pooled male and female

value: late embryonic

value: 3 hour

tag: lab

tag: source

value: egg bleaching

value: ENCBS257OKX at ENCODE; https://www.encodeproject.org/ENCBS257OKX/


title: TF ChIP-seq from whole organism (ENCLB904ARM)

description:
https://www.encodeproject.org/experiments/ENCSR263AYM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG3281-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR263AYM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR858HKA
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB904ARM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG3281

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

tag: link

value: ENCBS097UXJ at ENCODE; https://www.encodeproject.org/ENCBS097UXJ/


title: TF ChIP-seq from whole organism (ENCLB935JQT)

description:
https://www.encodeproject.org/experiments/ENCSR263AYM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG3281-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR263AYM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR858HKA
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB935JQT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: ENCBS801QZJ at ENCODE; https://www.encodeproject.org/ENCBS801QZJ/


title: TF ChIP-seq from whole organism (ENCLB527KFW)

description:
https://www.encodeproject.org/experiments/ENCSR261RKJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing MTF-1-eGFP fusion proteins.
experiment encode accession: ENCSR261RKJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR657JFQ
encode release date: 2018-02-06
lab: Kevin White, UChicago
library encode accession: ENCLB527KFW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: not applicable

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

value: ENCBS961RKU at ENCODE; https://www.encodeproject.org/ENCBS961RKU/


title: 306_L2

description:
extraction 118 sample 16_L2 pool 01_13
DGRP306 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB325FWH)

description:
https://www.encodeproject.org/experiments/ENCSR261RKJ/
***************
biological replicate number: 4
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing MTF-1-eGFP fusion proteins.
experiment encode accession: ENCSR261RKJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR657JFQ
encode release date: 2018-02-06
lab: Kevin White, UChicago
library encode accession: ENCLB325FWH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: pooled male and female

value: ENCBS758WWK at ENCODE; https://www.encodeproject.org/ENCBS758WWK/


title: TF ChIP-seq from whole organism (ENCLB829OQC)

description:
https://www.encodeproject.org/experiments/ENCSR598GFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CHE-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR598GFQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR010TRT
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB829OQC
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP677 (unc-119(tm4063) III; wgIs677) mixed sex late embryo 6 hours post synchronization using egg bleaching insertion targeting C. elegans che-1

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

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

tag: post synchronization time

value: hour

value: ENCBS084OYG at ENCODE; https://www.encodeproject.org/ENCBS084OYG/


title: TF ChIP-seq from whole organism (ENCLB519FGH)

description:
https://www.encodeproject.org/experiments/ENCSR411OOP/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ATF-7-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR411OOP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR263QJN
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB519FGH
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP638 (unc-119(tm4063) III; wgIs638) mixed sex young adult at L1 larva starved after bleaching stage insertion targeting C. elegans atf-7

value: whole organism

value: whole organisms

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

value: young adult

value: L1 larva starved after bleaching

value: ENCBS241KUP at ENCODE; https://www.encodeproject.org/ENCBS241KUP/


title: 181_L1

description:
extraction 019 sample 11_L1 pool 01_07
DGRP181 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB086JVB)

description:
https://www.encodeproject.org/experiments/ENCSR411OOP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ATF-7-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR411OOP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR263QJN
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB086JVB
fragmentation methods: sonication (generic microtip)

value: not applicable

value: pooled male and female

value: ENCBS864PBB at ENCODE; https://www.encodeproject.org/ENCBS864PBB/


title: 332_L1

description:
extraction 024 sample 18_L1 pool 01_12
DGRP332 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: genotype


title: TF ChIP-seq from whole organism (ENCLB022ZOJ)

description:
https://www.encodeproject.org/experiments/ENCSR598GFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CHE-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR598GFQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR010TRT
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB022ZOJ
fragmentation methods: sonication (generic microtip)

tag: antibody

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

value: late embryonic

value: unknown

tag: post synchronization time units

value: ENCBS329SIQ at ENCODE; https://www.encodeproject.org/ENCBS329SIQ/


title: TF ChIP-seq from whole organism (ENCLB492HTH)

description:
https://www.encodeproject.org/experiments/ENCSR365BOA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR365BOA
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR884AHC
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB492HTH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain E(spl)m8-HLH mixed sex embryo (4-14 hours) insertion targeting D. melanogaster E(spl)m8-HLH

tag: biosample encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to E(spl)m8-HLH

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS248XBP at ENCODE; https://www.encodeproject.org/ENCBS248XBP/


title: Control ChIP-seq from whole organism (ENCLB660PPN)

description:
https://www.encodeproject.org/experiments/ENCSR363YDF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing sc-eGFP fusion proteins.
experiment encode accession: ENCSR363YDF
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB660PPN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

value: whole organisms

tag: collection date

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

value: 0-14 hour

value: ENCBS806AIY at ENCODE; https://www.encodeproject.org/ENCBS806AIY/


title: Control ChIP-seq from ovary (ENCLB523DAR)

description:
https://www.encodeproject.org/experiments/ENCSR818VNL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR818VNL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2023-01-31
lab: Bing Ren, UCSD
library encode accession: ENCLB523DAR

source_name: Homo sapiens female adult (30 years) ovary tissue

value: ovary

value: tissue

value: not applicable

tag: geographic location

value: Ovary tissue from a 30 year old female Caucasian human with bipolar disorder and an iron deficiency. Tissue provided by Shin Lin at Stanford University.

value: female

tag: health state

value: Bipolar disorder and iron deficiency

value: adult

value: 30 year

value: Bing Ren, UCSD

value: Shin Lin

value: ENCBS341OKA at ENCODE; https://www.encodeproject.org/ENCBS341OKA/


title: TF ChIP-seq from whole organism (ENCLB516OUM)

description:
https://www.encodeproject.org/experiments/ENCSR406NQK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ZIM-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR406NQK
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR546SLI
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB516OUM
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP581 (unc-119(tm4063) III; wgIs581) mixed sex young adult 54.5 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans zim-3

tag: encode accession

tag: note

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

value: pooled male and female

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS479EGE at ENCODE; https://www.encodeproject.org/ENCBS479EGE/


title: TF ChIP-seq from whole organism (ENCLB343PNU)

description:
https://www.encodeproject.org/experiments/ENCSR360ERR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR360ERR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR044YAD
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB343PNU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG33017 male adult insertion targeting D. melanogaster CG33017

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG33017

tag: Sex

value: male

tag: dev stage

value: Kevin White, UChicago

value: Kevin White

value: ENCBS234XFS at ENCODE; https://www.encodeproject.org/ENCBS234XFS/


title: Mint-ChIP-seq from H9 (ENCLB078EIK)

description:
https://www.encodeproject.org/experiments/ENCSR725YWL/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9.
experiment encode accession: ENCSR725YWL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR365EAV
encode release date: 2022-08-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB078EIK

source_name: Homo sapiens H9 cell line

tag: line

value: cell line

value: female

value: healthy

value: embryonic

tag: age

value: 5 day

tag: lab

value: Bradley Bernstein, Broad

value: Kevin Eggan and Ralda Nehme

value: ENCBS062ZAE at ENCODE; https://www.encodeproject.org/ENCBS062ZAE/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: TF ChIP-seq from whole organism (ENCLB391ZDH)

description:
https://www.encodeproject.org/experiments/ENCSR406NQK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing ZIM-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR406NQK
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR546SLI
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB391ZDH
fragmentation methods: sonication (generic microtip)

value: whole organism

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

value: pooled male and female

value: young adult

value: unknown

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: hour

tag: link

value: ENCBS594PBD at ENCODE; https://www.encodeproject.org/ENCBS594PBD/


title: Mint-ChIP-seq from H9 (ENCLB746WVY)

description:
https://www.encodeproject.org/experiments/ENCSR725YWL/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9.
experiment encode accession: ENCSR725YWL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR365EAV
encode release date: 2022-08-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB746WVY
fragmentation methods: none

value: cell line

value: female

value: healthy

value: ENCBS561LGY at ENCODE; https://www.encodeproject.org/ENCBS561LGY/


title: TF ChIP-seq from whole organism (ENCLB392YEX)

description:
https://www.encodeproject.org/experiments/ENCSR360ERR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR360ERR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR044YAD
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB392YEX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG33017

value: male

value: adult

value: Kevin White, UChicago

value: Kevin White

value: ENCBS572EFP at ENCODE; https://www.encodeproject.org/ENCBS572EFP/


title: Control ChIP-seq from whole organism (ENCLB299XNV)

description:
https://www.encodeproject.org/experiments/ENCSR402VXN/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing SPTF-1-eGFP fusion proteins.
experiment encode accession: ENCSR402VXN
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB299XNV
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP707 (unc-119(tm4063) III; wgIs707) mixed sex mixed stage (embryo) 2.5 hours post synchronization using egg bleaching insertion targeting C. elegans sptf-1

value: whole organism

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

value: pooled male and female

value: mixed stage (embryonic)

value: unknown

value: Valerie Reinke, Yale

value: egg bleaching

tag: post synchronization time

value: ENCBS135OVR at ENCODE; https://www.encodeproject.org/ENCBS135OVR/


title: Control ChIP-seq from whole organism (ENCLB536PSO)

description:
https://www.encodeproject.org/experiments/ENCSR357JFV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR357JFV
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB536PSO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

value: embryonic

value: ENCBS573BJG at ENCODE; https://www.encodeproject.org/ENCBS573BJG/


title: Mint-ChIP-seq from H9 (ENCLB480LQK)

description:
https://www.encodeproject.org/experiments/ENCSR725YWL/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9.
experiment encode accession: ENCSR725YWL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR365EAV
encode release date: 2022-08-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB480LQK

tag: antibody

value: cell line

value: female

value: healthy

value: 5 day

value: Bradley Bernstein, Broad

value: Kevin Eggan and Ralda Nehme

value: ENCBS062ZAE at ENCODE; https://www.encodeproject.org/ENCBS062ZAE/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: TF ChIP-seq from whole organism (ENCLB039UEN)

description:
https://www.encodeproject.org/experiments/ENCSR714ALL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing LIN-14-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR714ALL
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR557QUA
encode release date: 2018-09-19
lab: Kevin White, UChicago
library encode accession: ENCLB039UEN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP768 (unc-119(tm4063); wgls768 [lin-14::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex L1 larva (6 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans lin-14

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to LIN-14.

value: pooled male and female

value: L1 larva

value: 6 hour

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS317CLK at ENCODE; https://www.encodeproject.org/ENCBS317CLK/


title: Control ChIP-seq from whole organism (ENCLB649TDI)

description:
https://www.encodeproject.org/experiments/ENCSR257AYE/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing odd-eGFP fusion proteins.
experiment encode accession: ENCSR257AYE
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB649TDI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

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

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS014ALW at ENCODE; https://www.encodeproject.org/ENCBS014ALW/


title: 486_L2

description:
extraction 067 sample 30_L2 pool 01_02
DGRP486 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

source_name: whole body

tag: tissue

value: whole body

tag: genotype

tag: developmental stage

value: Larvae


title: Mint-ChIP-seq from H9 (ENCLB651VVB)

description:
https://www.encodeproject.org/experiments/ENCSR725YWL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9.
experiment encode accession: ENCSR725YWL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR365EAV
encode release date: 2022-08-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB651VVB
fragmentation methods: none

value: cell line

tag: biosample encode accession

value: female

value: healthy

value: 5 day

value: Bradley Bernstein, Broad

value: Kevin Eggan and Ralda Nehme

value: ENCBS161LPX at ENCODE; https://www.encodeproject.org/ENCBS161LPX/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: TF ChIP-seq from whole organism (ENCLB436XSU)

description:
https://www.encodeproject.org/experiments/ENCSR365BOA/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR365BOA
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR884AHC
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB436XSU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

tag: collection date

value: not applicable

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to E(spl)m8-HLH

value: pooled male and female

value: ENCBS448REW at ENCODE; https://www.encodeproject.org/ENCBS448REW/


title: TF ChIP-seq from whole organism (ENCLB882OIO)

description:
https://www.encodeproject.org/experiments/ENCSR714ALL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing LIN-14-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR714ALL
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR557QUA
encode release date: 2018-09-19
lab: Kevin White, UChicago
library encode accession: ENCLB882OIO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: encode accession

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to LIN-14.

value: L1 larva

value: 6 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS016UQH at ENCODE; https://www.encodeproject.org/ENCBS016UQH/


title: Mint-ChIP-seq from H9 (ENCLB392EMA)

description:
https://www.encodeproject.org/experiments/ENCSR725YWL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9.
experiment encode accession: ENCSR725YWL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR365EAV
encode release date: 2022-08-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB392EMA
fragmentation methods: none

value: cell line

tag: Sex

value: female

tag: health state

value: healthy

tag: dev stage

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad


title: Control ChIP-seq from whole organism (ENCLB907WMZ)

description:
https://www.encodeproject.org/experiments/ENCSR900PXV/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing SOMI-1-eGFP fusion proteins.
experiment encode accession: ENCSR900PXV
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-09-19
lab: Kevin White, UChicago
library encode accession: ENCLB907WMZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP752 (unc-119(tm4063); wgIs752 [somi-1::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex young adult (65.5 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans somi-1

value: whole organism

value: whole organisms

value: not applicable

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

value: young adult

tag: age

value: 65.5 hour

tag: lab

value: ENCBS691DNK at ENCODE; https://www.encodeproject.org/ENCBS691DNK/


title: Control ChIP-seq from ovary (ENCLB522QOE)

description:
https://www.encodeproject.org/experiments/ENCSR354RHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG17801-eGFP fusion proteins.
experiment encode accession: ENCSR354RHJ
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB522QOE
size range: 200-800

source_name: Drosophila melanogaster strain CG14710 female adult ovary tissue genetically modified (insertion) using site-specific recombination targeting D. melanogaster CG14710

value: ovary

value: tissue

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG17801

value: adult

value: unknown

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS247NVK at ENCODE; https://www.encodeproject.org/ENCBS247NVK/


title: Mint-ChIP-seq from GM23338 (ENCLB679BLE)

description:
https://www.encodeproject.org/experiments/ENCSR695NNR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human GM23338.
experiment encode accession: ENCSR695NNR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB679BLE
fragmentation methods: none

source_name: Homo sapiens GM23338 cell line, preserved by cryopreservation

tag: line

value: cell line

tag: description

value: PGP1 iPSCs

value: male

value: 53 year

value: George Church

tag: link

value: ENCBS155WDP at ENCODE; https://www.encodeproject.org/ENCBS155WDP/

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


title: Control ChIP-seq from whole organism (ENCLB514OJP)

description:
https://www.encodeproject.org/experiments/ENCSR256ESG/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing ewg-eGFP fusion proteins.
experiment encode accession: ENCSR256ESG
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB514OJP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

value: whole organisms

value: not applicable

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

value: pooled male and female

value: embryonic

value: 0-14 hour

value: ENCBS554JZR at ENCODE; https://www.encodeproject.org/ENCBS554JZR/


title: TF ChIP-seq from whole organism (ENCLB417QJJ)

description:
https://www.encodeproject.org/experiments/ENCSR895KXK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing hlh-17-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR895KXK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR542XFG
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB417QJJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP643 (wgIs643 [hlh-17::TY1::EGFP::3xFLAG + unc-119(+)];unc-119 (tm4063)) mixed sex L1 larva (6 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans hlh-17

tag: antibody

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to HLH-17.

value: L1 larva

value: 6 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: ENCBS498JSH at ENCODE; https://www.encodeproject.org/ENCBS498JSH/


title: Mint-ChIP-seq from brain (ENCLB950XRC)

description:
https://www.encodeproject.org/experiments/ENCSR385SSH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR385SSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2022-08-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB950XRC
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) brain organoid, 180 days post differentiation

value: brain

value: organoid

value: female

value: healthy

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS615FKW at ENCODE; https://www.encodeproject.org/ENCBS615FKW/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: TF ChIP-seq from whole organism (ENCLB818AUP)

description:
https://www.encodeproject.org/experiments/ENCSR889PUP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing HMBX-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR889PUP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR318RVX
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB818AUP
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP656 (unc-119 (tm4063) III; wgIs656) mixed sex early embryo 45 minutes post synchronization using egg bleaching insertion targeting C. elegans hmbx-1

value: whole organism

value: whole organisms

value: not applicable

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

value: pooled male and female

value: early embryonic

value: unknown

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: minute

value: ENCBS015MDH at ENCODE; https://www.encodeproject.org/ENCBS015MDH/


title: Mint-ChIP-seq from GM23338 (ENCLB419AZY)

description:
https://www.encodeproject.org/experiments/ENCSR695NNR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human GM23338.
experiment encode accession: ENCSR695NNR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2022-07-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB419AZY
fragmentation methods: none

value: cell line

value: PGP1 iPSCs

tag: biosample encode accession

value: male

value: adult

value: 53 year

value: George Church

value: ENCBS155WDP at ENCODE; https://www.encodeproject.org/ENCBS155WDP/

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


title: TF ChIP-seq from whole organism (ENCLB071RAY)

description:
https://www.encodeproject.org/experiments/ENCSR255PHG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG6276-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR255PHG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR377KXD
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB071RAY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG6276-GFP mixed sex prepupa (72 days) insertion targeting D. melanogaster CG6276

value: whole organism

value: whole organisms

tag: collection date

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG6276

value: prepupa

value: 72 day

value: Kevin White, UChicago

value: Kevin White

value: ENCBS195BOE at ENCODE; https://www.encodeproject.org/ENCBS195BOE/


title: TF ChIP-seq from whole organism (ENCLB752JXY)

description:
https://www.encodeproject.org/experiments/ENCSR895KXK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing hlh-17-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR895KXK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR542XFG
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB752JXY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

tag: encode accession

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to HLH-17.

value: pooled male and female

value: L1 larva

value: 6 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS922VBT at ENCODE; https://www.encodeproject.org/ENCBS922VBT/


title: TF ChIP-seq from whole organism (ENCLB765RLU)

description:
https://www.encodeproject.org/experiments/ENCSR255PHG/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG6276-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR255PHG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR377KXD
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB765RLU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

tag: Sex

value: ENCBS426EOF at ENCODE; https://www.encodeproject.org/ENCBS426EOF/


title: Control ChIP-seq from whole organism (ENCLB964SVL)

description:
https://www.encodeproject.org/experiments/ENCSR887YEV/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ets-4-eGFP fusion proteins.
experiment encode accession: ENCSR887YEV
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB964SVL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain RAF1713 (rrrSi400[Pets-4::ets-4-GFP::ets-4 3'UTR, unc-119(+)] II; unc-119(ed3) III) mixed sex young adult (73 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ets-4

value: whole organisms

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

tag: dev stage

value: young adult

value: 73 hour

value: ENCBS673ONM at ENCODE; https://www.encodeproject.org/ENCBS673ONM/


title: TF ChIP-seq from whole organism (ENCLB545YKR)

description:
https://www.encodeproject.org/experiments/ENCSR889PUP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing HMBX-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR889PUP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR318RVX
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB545YKR
fragmentation methods: sonication (generic microtip)

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

value: early embryonic

tag: age

value: unknown

value: egg bleaching

value: minute

value: ENCBS188TXX at ENCODE; https://www.encodeproject.org/ENCBS188TXX/


title: Control ChIP-seq from BLaER1 (ENCLB861IRT)

description:
https://www.encodeproject.org/experiments/ENCSR399JUL/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR399JUL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB861IRT
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 3 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: cell line

value: not applicable

value: female

tag: lab

value: Roderic Guigo, CRG

value: Thomas Graf

tag: treatments

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;

value: ENCBS348QCD at ENCODE; https://www.encodeproject.org/ENCBS348QCD/


title: Control ChIP-seq from whole organism (ENCLB559BUZ)

description:
https://www.encodeproject.org/experiments/ENCSR254VFL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Hey-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR254VFL
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB559BUZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

value: whole organisms

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

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS578LIU at ENCODE; https://www.encodeproject.org/ENCBS578LIU/


title: Mint-ChIP-seq from brain (ENCLB838WPR)

description:
https://www.encodeproject.org/experiments/ENCSR385SSH/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR385SSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2022-08-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB838WPR
fragmentation methods: none

value: brain

value: organoid

tag: health state

value: healthy

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS598CLB at ENCODE; https://www.encodeproject.org/ENCBS598CLB/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Control ChIP-seq from BLaER1 (ENCLB826GVK)

description:
https://www.encodeproject.org/experiments/ENCSR399JUL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR399JUL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB826GVK
fragmentation methods: shearing (Covaris generic)

tag: line

value: cell line

value: not applicable

value: female

value: unknown

value: Roderic Guigo, CRG

value: Thomas Graf

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;

tag: link

value: ENCBS242WXP at ENCODE; https://www.encodeproject.org/ENCBS242WXP/


title: Mint-ChIP-seq from brain (ENCLB763DXJ)

description:
https://www.encodeproject.org/experiments/ENCSR385SSH/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR385SSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2022-08-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB763DXJ
fragmentation methods: none

tag: antibody

value: embryonic

value: ENCBS358VQQ at ENCODE; https://www.encodeproject.org/ENCBS358VQQ/


title: TF ChIP-seq from whole organism (ENCLB488JDP)

description:
https://www.encodeproject.org/experiments/ENCSR094HIY/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing pad-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR094HIY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR846JYS
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB488JDP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: pad

value: whole organism

value: whole organisms

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

value: adult

value: Kevin White, UChicago

value: Kevin White

value: ENCBS249KGF at ENCODE; https://www.encodeproject.org/ENCBS249KGF/


title: Control ChIP-seq from whole organism (ENCLB804GLF)

description:
https://www.encodeproject.org/experiments/ENCSR877TIV/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing F57C9.4-eGFP fusion proteins.
experiment encode accession: ENCSR877TIV
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB804GLF
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP550 (unc-119(tm4063) III; wgIs550) mixed sex young adult 66 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans F57C9.4

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F57C9.4

value: pooled male and female

value: young adult

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

value: hour

value: ENCBS889EBX at ENCODE; https://www.encodeproject.org/ENCBS889EBX/


title: Mint-ChIP-seq from H9 (ENCLB688FSM)

description:
https://www.encodeproject.org/experiments/ENCSR725YWL/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9.
experiment encode accession: ENCSR725YWL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR365EAV
encode release date: 2022-08-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB688FSM
fragmentation methods: none

source_name: Homo sapiens H9 cell line

value: cell line

tag: biosample encode accession

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Kevin Eggan and Ralda Nehme

value: ENCBS561LGY at ENCODE; https://www.encodeproject.org/ENCBS561LGY/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Mint-ChIP-seq from brain (ENCLB648WDN)

description:
https://www.encodeproject.org/experiments/ENCSR385SSH/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR385SSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2022-08-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB648WDN
fragmentation methods: none

value: brain

value: organoid

value: Paola Arlotta

value: ENCBS358VQQ at ENCODE; https://www.encodeproject.org/ENCBS358VQQ/


title: Mint-ChIP-seq from brain (ENCLB521ORC)

description:
https://www.encodeproject.org/experiments/ENCSR385SSH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR385SSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2022-08-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB521ORC
fragmentation methods: none

value: ENCBS615FKW at ENCODE; https://www.encodeproject.org/ENCBS615FKW/


title: TF ChIP-seq from whole organism (ENCLB416PVO)

description:
https://www.encodeproject.org/experiments/ENCSR094HIY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing pad-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR094HIY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR846JYS
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB416PVO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: pad

value: whole organism

value: whole organisms

tag: collection date

value: not applicable

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

value: adult

value: unknown

value: Kevin White, UChicago

value: Kevin White

value: ENCBS119MBZ at ENCODE; https://www.encodeproject.org/ENCBS119MBZ/


title: TF ChIP-seq from whole organism (ENCLB002CYW)

description:
https://www.encodeproject.org/experiments/ENCSR094HIY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing pad-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR094HIY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR846JYS
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB002CYW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: geographic location

value: female

value: ENCBS943VGK at ENCODE; https://www.encodeproject.org/ENCBS943VGK/


title: Control ChIP-seq from whole organism (ENCLB101JCL)

description:
https://www.encodeproject.org/experiments/ENCSR254VFL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Hey-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR254VFL
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB101JCL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: encode accession

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

value: pooled male and female

value: embryonic

value: ENCBS355TZU at ENCODE; https://www.encodeproject.org/ENCBS355TZU/


title: TF ChIP-seq from whole organism (ENCLB248JNJ)

description:
https://www.encodeproject.org/experiments/ENCSR092TNF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR092TNF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR512MTT
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB248JNJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain lms mixed sex embryo (6-18 hours) insertion targeting D. melanogaster lms

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG13424

value: ENCBS213TTC at ENCODE; https://www.encodeproject.org/ENCBS213TTC/


title: TF ChIP-seq from whole organism (ENCLB624WQK)

description:
https://www.encodeproject.org/experiments/ENCSR092TNF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR092TNF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR512MTT
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB624WQK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

tag: Sex

value: ENCBS499WXK at ENCODE; https://www.encodeproject.org/ENCBS499WXK/