title: Control ChIP-seq from whole organism (ENCLB839JPT)

description:
https://www.encodeproject.org/experiments/ENCSR572CBY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG3407-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR572CBY
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB839JPT
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

tag: collection date

value: not applicable

tag: geographic location

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: ENCBS435CBM at ENCODE; https://www.encodeproject.org/ENCBS435CBM/


title: Control ChIP-seq from whole organism (ENCLB367UFA)

status: Public on Feb 27 2024

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR386WUO/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing zen-eGFP fusion proteins.
experiment encode accession: ENCSR386WUO
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB367UFA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

library_source: genomic

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

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster mixed sex embryo (0-4 hours) insertion targeting D. melanogaster zen

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: encode accession

tag: note

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

tag: Sex

tag: dev stage

tag: age

value: 0-4 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS169RLF at ENCODE; https://www.encodeproject.org/ENCBS169RLF/


title: Control ChIP-seq from whole organism (ENCLB087AWP)

description:
https://www.encodeproject.org/experiments/ENCSR571GMX/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Hr51-eGFP fusion proteins.
experiment encode accession: ENCSR571GMX
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB087AWP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Dhr51-GFP mixed sex embryo (14-16 hours) insertion targeting D. melanogaster Hr51

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Hr51

value: ENCBS431ZUZ at ENCODE; https://www.encodeproject.org/ENCBS431ZUZ/


title: 427_A2

city: Nouzilly

first: Julie

last: Collet

address: Centre INRAE

country: France

institute: INRAE

description:
extraction 206 sample 28_A2 pool 14_20
DGRP427 Adults Biol Rep 2
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

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: Adults


title: 217_A2

description:
extraction 215 sample 12_A2 pool 14_22
DGRP217 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB373ULU)

description:
https://www.encodeproject.org/experiments/ENCSR504SMY/
***************
biological replicate number: 4
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing bed-3-eGFP fusion proteins.
experiment encode accession: ENCSR504SMY
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB373ULU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP651 (unc-119(tm4063); wgIs651 [bed-3::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex mixed stage (embryo) (4 hours) using egg bleaching insertion targeting C. elegans bed-3

value: not applicable

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

value: mixed stage (embryonic)

value: 4 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

value: ENCBS853KIN at ENCODE; https://www.encodeproject.org/ENCBS853KIN/


title: TF ChIP-seq from whole organism (ENCLB702LAI)

description:
https://www.encodeproject.org/experiments/ENCSR823LPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing SPTF-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR823LPZ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR402VXN
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB702LAI
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

tag: antibody

value: whole organism

value: whole organisms

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

value: pooled male and female

value: unknown

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS828VGL at ENCODE; https://www.encodeproject.org/ENCBS828VGL/


title: 315_A2

description:
extraction 211 sample 17_A2 pool 14_21
DGRP315 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body


title: TF ChIP-seq from whole organism (ENCLB086WCS)

description:
https://www.encodeproject.org/experiments/ENCSR992JPS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing zip-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR992JPS
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR292LDA
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB086WCS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP590 (unc-119(tm4063); wgIs590 [zip-4::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex L1 larva (6 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans zip-4

tag: collection date

tag: geographic location

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

value: L1 larva

value: 6 hour

value: L1 larva starved after bleaching

value: ENCBS123JWG at ENCODE; https://www.encodeproject.org/ENCBS123JWG/


title: Control ChIP-seq from whole organism (ENCLB424GJU)

description:
https://www.encodeproject.org/experiments/ENCSR564FZY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing su(Hw)-eGFP fusion proteins.
experiment encode accession: ENCSR564FZY
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB424GJU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: biosample encode accession

value: not applicable

tag: encode accession

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS662XEY at ENCODE; https://www.encodeproject.org/ENCBS662XEY/


title: TF ChIP-seq from whole organism (ENCLB625PLB)

description:
https://www.encodeproject.org/experiments/ENCSR992JPS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing zip-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR992JPS
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR292LDA
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB625PLB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

tag: note

tag: Sex

value: pooled male and female

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS083QUZ at ENCODE; https://www.encodeproject.org/ENCBS083QUZ/


title: Control ChIP-seq from whole organism (ENCLB646ZSN)

description:
https://www.encodeproject.org/experiments/ENCSR504CUV/
***************
biological replicate number: 2
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing T26A5.8-eGFP fusion proteins.
experiment encode accession: ENCSR504CUV
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB646ZSN
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP598 (unc-119(tm4063) III; wgIs598) mixed sex young adult 63 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans T26A5.8

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to T26A5.8

tag: dev stage

value: young adult

tag: age

value: unknown

value: hour

value: ENCBS797KPI at ENCODE; https://www.encodeproject.org/ENCBS797KPI/


title: 356_A1

description:
extraction 162 sample 19_A1 pool 14_14
DGRP356 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: 379_A2

description:
extraction 180 sample 25_A2 pool 14_08
DGRP379 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB324YXC)

description:
https://www.encodeproject.org/experiments/ENCSR564UWC/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Vsx1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR564UWC
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR655VMI
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB324YXC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Vsx1-GFP mixed sex embryo (0-18 hours) insertion targeting D. melanogaster Vsx1

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Vsx1

value: embryonic

value: 0-18 hour

tag: lab

tag: source

value: ENCBS676CSL at ENCODE; https://www.encodeproject.org/ENCBS676CSL/


title: TF ChIP-seq from whole organism (ENCLB999STC)

description:
https://www.encodeproject.org/experiments/ENCSR564UWC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Vsx1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR564UWC
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR655VMI
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB999STC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: Kevin White, UChicago

value: Kevin White

tag: link

value: ENCBS109QFT at ENCODE; https://www.encodeproject.org/ENCBS109QFT/


title: Control ChIP-seq from whole organism (ENCLB828NTU)

description:
https://www.encodeproject.org/experiments/ENCSR504CUV/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing T26A5.8-eGFP fusion proteins.
experiment encode accession: ENCSR504CUV
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB828NTU
fragmentation methods: sonication (generic microtip)

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to T26A5.8

value: pooled male and female

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS404OYR at ENCODE; https://www.encodeproject.org/ENCBS404OYR/


title: 486_A1

description:
extraction 149 sample 30_A1 pool 14_07
DGRP486 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Adults


title: Control ChIP-seq from whole organism (ENCLB053QGB)

description:
https://www.encodeproject.org/experiments/ENCSR865FZO/
***************
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: ENCSR865FZO
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB053QGB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG1603 mixed sex embryo (0-16 hours) insertion targeting D. melanogaster CG1603

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG1603

value: 0-16 hour

value: ENCBS395IEY at ENCODE; https://www.encodeproject.org/ENCBS395IEY/


title: 787_A1

description:
extraction 132 sample 39_A1 pool 14_06
DGRP787 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: developmental stage


title: Control ChIP-seq from whole organism (ENCLB228QTE)

description:
https://www.encodeproject.org/experiments/ENCSR561OFJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG7556-eGFP fusion proteins.
experiment encode accession: ENCSR561OFJ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB228QTE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG7556-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG7556

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7556

value: embryonic

value: 0-24 hour

value: ENCBS958MDD at ENCODE; https://www.encodeproject.org/ENCBS958MDD/


title: 897_A1

description:
extraction 126 sample 49_A1 pool 14_05
DGRP897 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB522TOW)

description:
https://www.encodeproject.org/experiments/ENCSR991HIA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing HIF-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR991HIA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR799FDO
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB522TOW
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OR3349 mixed sex L4 larva 52 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans hif-1

tag: antibody

value: whole organisms

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

value: L4 larva

value: unknown

tag: worm synchronization stage

value: hour

value: ENCBS754SFL at ENCODE; https://www.encodeproject.org/ENCBS754SFL/


title: Control ChIP-seq from whole organism (ENCLB232OVE)

description:
https://www.encodeproject.org/experiments/ENCSR559OGK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing sd-eGFP fusion proteins.
experiment encode accession: ENCSR559OGK
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB232OVE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster mixed sex embryo (4-20 hours) insertion targeting D. melanogaster sd

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

value: pooled male and female

value: Kevin White, UChicago

value: Kevin White

value: ENCBS745EGY at ENCODE; https://www.encodeproject.org/ENCBS745EGY/


title: Control ChIP-seq from whole organism (ENCLB346MFP)

description:
https://www.encodeproject.org/experiments/ENCSR990RKL/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing akir-1-eGFP fusion proteins.
experiment encode accession: ENCSR990RKL
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB346MFP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain IG1654 (frSi12[pNP157(akir-1p::AKIR-1::GFP)]II) mixed sex young adult (70 hours) at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans akir-1

value: not applicable

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

value: young adult

value: 70 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS862HVB at ENCODE; https://www.encodeproject.org/ENCBS862HVB/


title: TF ChIP-seq from whole organism (ENCLB403UHV)

description:
https://www.encodeproject.org/experiments/ENCSR555TTB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Hr51-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR555TTB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR571GMX
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB403UHV
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 Hr51

value: embryonic

value: ENCBS163AEU at ENCODE; https://www.encodeproject.org/ENCBS163AEU/


title: Control ChIP-seq from whole organism (ENCLB438CNB)

description:
https://www.encodeproject.org/experiments/ENCSR504SMY/
***************
biological replicate number: 3
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing bed-3-eGFP fusion proteins.
experiment encode accession: ENCSR504SMY
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB438CNB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: pooled male and female

value: mixed stage (embryonic)

value: 4 hour

value: egg bleaching

value: ENCBS760AGH at ENCODE; https://www.encodeproject.org/ENCBS760AGH/


title: 380_A2

description:
extraction 179 sample 26_A2 pool 14_03
DGRP380 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: 158_A1

description:
extraction 122 sample 09_A1 pool 14_04
DGRP158 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB808EXW)

description:
https://www.encodeproject.org/experiments/ENCSR991HIA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing HIF-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR991HIA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR799FDO
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB808EXW
fragmentation methods: sonication (generic microtip)

value: not applicable

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

value: L4 larva

value: unknown

value: Valerie Reinke, Yale

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS990NDG at ENCODE; https://www.encodeproject.org/ENCBS990NDG/


title: TF ChIP-seq from whole organism (ENCLB397NBA)

description:
https://www.encodeproject.org/experiments/ENCSR500LPZ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing K12H6.12-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR500LPZ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR345XQL
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB397NBA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP214 (unc-119(ed3) III; wgIs214) mixed sex young adult (72 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans K12H6.12

value: whole organism

value: whole organisms

tag: collection date

tag: geographic location

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to K12H6.12.

value: young adult

value: 72 hour

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS753WZF at ENCODE; https://www.encodeproject.org/ENCBS753WZF/


title: Control ChIP-seq from whole organism (ENCLB046SYA)

description:
https://www.encodeproject.org/experiments/ENCSR990KPW/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing nhr-27-eGFP fusion proteins.
experiment encode accession: ENCSR990KPW
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB046SYA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP208 (unc-119(ed3) III; wgIs208) mixed sex young adult (78 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans nhr-27

tag: biosample encode accession

tag: encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-270.

value: pooled male and female

value: 78 hour

value: ENCBS573TMQ at ENCODE; https://www.encodeproject.org/ENCBS573TMQ/


title: TF ChIP-seq from whole organism (ENCLB294MXR)

description:
https://www.encodeproject.org/experiments/ENCSR555TTB/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Hr51-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR555TTB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR571GMX
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB294MXR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Hr51

tag: Sex

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS900KXD at ENCODE; https://www.encodeproject.org/ENCBS900KXD/


title: Control ChIP-seq from whole organism (ENCLB800WKX)

description:
https://www.encodeproject.org/experiments/ENCSR381FHL/
***************
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: ENCSR381FHL
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB800WKX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain bsh-GFP embryo (10-12 hours) insertion targeting D. melanogaster bsh

value: whole organism

value: whole organisms

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

value: not collected

tag: dev stage

tag: age

value: ENCBS950VIR at ENCODE; https://www.encodeproject.org/ENCBS950VIR/


title: TF ChIP-seq from whole organism (ENCLB666GMC)

description:
https://www.encodeproject.org/experiments/ENCSR500LPZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing K12H6.12-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR500LPZ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR345XQL
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB666GMC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to K12H6.12.

value: young adult

value: 72 hour

tag: lab

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS015NCU at ENCODE; https://www.encodeproject.org/ENCBS015NCU/


title: Control ChIP-seq from whole organism (ENCLB477KGZ)

description:
https://www.encodeproject.org/experiments/ENCSR555KVU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG30020-eGFP fusion proteins.
experiment encode accession: ENCSR555KVU
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB477KGZ
size range: 200-800

source_name: Drosophila melanogaster strain CG30020 mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG30020

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG30020

value: pooled male and female

value: 0-24 hour

tag: link

value: ENCBS565GCA at ENCODE; https://www.encodeproject.org/ENCBS565GCA/


title: 783_A1

description:
extraction 188 sample 38_A1 pool 13_18
DGRP783 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Adults


title: 306_A1

description:
extraction 192 sample 16_A1 pool 13_19
DGRP306 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: developmental stage


title: Control ChIP-seq from whole organism (ENCLB861BGN)

description:
https://www.encodeproject.org/experiments/ENCSR553YUJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing org-1-eGFP fusion proteins.
experiment encode accession: ENCSR553YUJ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB861BGN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain org-1-GFP mixed sex embryo (2-24 hours) insertion targeting D. melanogaster org-1

value: whole organism

value: whole organisms

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

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS675EUN at ENCODE; https://www.encodeproject.org/ENCBS675EUN/


title: 796_A2

description:
extraction 145 sample 40_A2 pool 14_01
DGRP796 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

source_name: whole body


title: TF ChIP-seq from whole organism (ENCLB862KWC)

description:
https://www.encodeproject.org/experiments/ENCSR819NBT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing TBX-9-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR819NBT
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR183CDG
encode release date: 2016-10-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB862KWC
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP636 (unc-119(tm4063) III; wgIs636) mixed sex young adult 63 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans tbx-9

tag: antibody

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

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: hour

value: ENCBS469GAO at ENCODE; https://www.encodeproject.org/ENCBS469GAO/


title: 805_A1

description:
extraction 171 sample 43_A1 pool 13_16
DGRP805 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB107XGM)

description:
https://www.encodeproject.org/experiments/ENCSR552ODH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Meics-eGFP fusion proteins.
experiment encode accession: ENCSR552ODH
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB107XGM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: not applicable

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

value: pooled male and female

value: 0-24 hour

value: ENCBS190TCF at ENCODE; https://www.encodeproject.org/ENCBS190TCF/


title: TF ChIP-seq from whole organism (ENCLB128KJM)

description:
https://www.encodeproject.org/experiments/ENCSR811ZML/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing flh-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR811ZML
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR376RRP
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB128KJM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP702 (unc-119(tm4063); wgIs702 [flh-1::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex mixed stage (embryo) (2 hours) using egg bleaching insertion targeting C. elegans flh-1

value: whole organism

value: whole organisms

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

value: mixed stage (embryonic)

value: 2 hour

value: egg bleaching

value: ENCBS237RSG at ENCODE; https://www.encodeproject.org/ENCBS237RSG/


title: 235_A1

description:
extraction 167 sample 13_A1 pool 13_15
DGRP235 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: TF ChIP-seq from whole organism (ENCLB467OEF)

description:
https://www.encodeproject.org/experiments/ENCSR811ZML/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing flh-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR811ZML
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR376RRP
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB467OEF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS145WPO at ENCODE; https://www.encodeproject.org/ENCBS145WPO/


title: 332_A1

description:
extraction 163 sample 18_A1 pool 13_14
DGRP332 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB076BHL)

description:
https://www.encodeproject.org/experiments/ENCSR863DOB/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing D19A-eGFP fusion proteins.
experiment encode accession: ENCSR863DOB
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB076BHL
size range: 200-800

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

value: not applicable

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

value: embryonic

value: 0-20 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS423XJD at ENCODE; https://www.encodeproject.org/ENCBS423XJD/


title: Control ChIP-seq from whole organism (ENCLB922ZQD)

description:
https://www.encodeproject.org/experiments/ENCSR551PYQ/
***************
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: ENCSR551PYQ
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB922ZQD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG7745 embryo (0-12 hours) insertion targeting D. melanogaster CG7745

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7745

value: not collected

value: 0-12 hour

value: ENCBS089YRA at ENCODE; https://www.encodeproject.org/ENCBS089YRA/


title: Control ChIP-seq from whole organism (ENCLB036FRQ)

description:
https://www.encodeproject.org/experiments/ENCSR693BJZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG6654-eGFP fusion proteins.
experiment encode accession: ENCSR693BJZ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB036FRQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG6654-GFP mixed sex embryo (0-12 hours) insertion targeting D. melanogaster CG6654

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG6654

value: pooled male and female

value: ENCBS178MQO at ENCODE; https://www.encodeproject.org/ENCBS178MQO/


title: 379_A1

description:
extraction 155 sample 25_A1 pool 13_12
DGRP379 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: TF ChIP-seq from whole organism (ENCLB232CIG)

description:
https://www.encodeproject.org/experiments/ENCSR487OER/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing nhr-111-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR487OER
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR016AZO
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB232CIG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP569 (unc-119(tm4063); wgIs569 [nhr-111::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex L4 larva (48 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans nhr-111

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-111.

value: L4 larva

value: 48 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS430DDI at ENCODE; https://www.encodeproject.org/ENCBS430DDI/


title: TF ChIP-seq from whole organism (ENCLB320WPF)

description:
https://www.encodeproject.org/experiments/ENCSR551HEY/
***************
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: ENCSR551HEY
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR139WZD
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB320WPF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG8388-GFP mixed sex embryo (0-14 hours) insertion targeting D. melanogaster CG8388

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8388

value: embryonic

value: 0-14 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS622SXU at ENCODE; https://www.encodeproject.org/ENCBS622SXU/


title: TF ChIP-seq from whole organism (ENCLB033VDR)

description:
https://www.encodeproject.org/experiments/ENCSR810BRE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing spr-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR810BRE
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR793USS
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB033VDR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP703 (unc-119(tm4063); wgIs703 [spr-3::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex L4 larva (49 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans spr-3

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

value: pooled male and female

value: 49 hour

value: ENCBS460QEX at ENCODE; https://www.encodeproject.org/ENCBS460QEX/


title: 804_A2

description:
extraction 198 sample 42_A2 pool 13_10
DGRP804 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: TF ChIP-seq from whole organism (ENCLB366NDK)

description:
https://www.encodeproject.org/experiments/ENCSR861RPB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG13775-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR861RPB
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR595LMX
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB366NDK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG13775-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG13775

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG13775

value: 0-24 hour

value: ENCBS399CEE at ENCODE; https://www.encodeproject.org/ENCBS399CEE/


title: Control ChIP-seq from whole organism (ENCLB692RME)

description:
https://www.encodeproject.org/experiments/ENCSR815ASQ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing Y22D7AL.16-eGFP fusion proteins.
experiment encode accession: ENCSR815ASQ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB692RME
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP615 (unc-119(tm4063) III; wgIs615) mixed sex late embryo 4.5 hours post synchronization using egg bleaching insertion targeting C. elegans Y22D7AL.16

value: whole organism

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to Y22D7AL.16

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS726SEY at ENCODE; https://www.encodeproject.org/ENCBS726SEY/


title: TF ChIP-seq from whole organism (ENCLB237PWH)

description:
https://www.encodeproject.org/experiments/ENCSR810BRE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing spr-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR810BRE
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR793USS
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB237PWH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: collection date

tag: geographic location

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

value: pooled male and female

value: L4 larva

value: 49 hour

value: L1 larva starved after bleaching

value: ENCBS616HUO at ENCODE; https://www.encodeproject.org/ENCBS616HUO/


title: 535_A2

description:
extraction 202 sample 33_A2 pool 13_11
DGRP535 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: 370_A2

description:
extraction 181 sample 24_A2 pool 13_08
DGRP370 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB708DDZ)

description:
https://www.encodeproject.org/experiments/ENCSR810EEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing Y55F3AM.14-eGFP fusion proteins.
experiment encode accession: ENCSR810EEJ
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB708DDZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP608 (unc-119(tm4063); wgIs608 [Y55F3AM.14::TY::EGFP::3xFLAG(p_wTRG5_insertion_c_0075_1C04) + unc-119(+)]) mixed sex L2 larva (42 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans Y55F3AM.1...

value: whole organism

value: whole organisms

tag: biosample encode accession

value: not applicable

tag: encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to Y55F3AM.14.

value: L2 larva

value: 42 hour

value: ENCBS300DQX at ENCODE; https://www.encodeproject.org/ENCBS300DQX/


title: TF ChIP-seq from whole organism (ENCLB456OPN)

description:
https://www.encodeproject.org/experiments/ENCSR809IFM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing REPO-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR809IFM
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR078ZXA
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB456OPN
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP688 (unc-119(tm4063) III; wgIs688) mixed sex young adult 53 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans repo-1

tag: note

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

tag: Sex

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: hour

value: ENCBS587OLI at ENCODE; https://www.encodeproject.org/ENCBS587OLI/


title: Control ChIP-seq from BLaER1 (ENCLB768FYU)

description:
https://www.encodeproject.org/experiments/ENCSR978XYH/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR978XYH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB768FYU
fragmentation methods: shearing (Covaris generic)

organism: Homo sapiens

source_name: Homo sapiens BLaER1 cell line 48 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

tag: line

value: cell line

value: female

tag: dev stage

tag: age

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: ENCBS766HUL at ENCODE; https://www.encodeproject.org/ENCBS766HUL/


title: TF ChIP-seq from whole organism (ENCLB530VAI)

description:
https://www.encodeproject.org/experiments/ENCSR809IFM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing REPO-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR809IFM
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR078ZXA
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB530VAI
fragmentation methods: sonication (generic microtip)

value: whole organism

value: whole organisms

value: not applicable

value: pooled male and female

tag: lab

tag: source

value: L1 larva starved after bleaching

tag: link

value: ENCBS519NPF at ENCODE; https://www.encodeproject.org/ENCBS519NPF/


title: TF ChIP-seq from whole organism (ENCLB207CGL)

description:
https://www.encodeproject.org/experiments/ENCSR861RPB/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG13775-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR861RPB
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR595LMX
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB207CGL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG13775

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS767NCZ at ENCODE; https://www.encodeproject.org/ENCBS767NCZ/


title: TF ChIP-seq from whole organism (ENCLB156JLI)

description:
https://www.encodeproject.org/experiments/ENCSR861RPB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG13775-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR861RPB
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR595LMX
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB156JLI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: ENCBS511TEK at ENCODE; https://www.encodeproject.org/ENCBS511TEK/


title: Control ChIP-seq from whole organism (ENCLB545JSC)

description:
https://www.encodeproject.org/experiments/ENCSR688FTD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG12071-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR688FTD
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB545JSC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG12071-GFP mixed sex embryo (12-24 hours) insertion targeting D. melanogaster CG12071

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12071

value: ENCBS174LON at ENCODE; https://www.encodeproject.org/ENCBS174LON/


title: Control ChIP-seq from whole organism (ENCLB068JVJ)

description:
https://www.encodeproject.org/experiments/ENCSR481ITX/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing c02f12.10-eGFP fusion proteins.
experiment encode accession: ENCSR481ITX
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB068JVJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP742 (wgIs742 [C02F12.10::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 ceh-63

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to C02F12.10.

value: L1 larva

value: 6 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: ENCBS925HHP at ENCODE; https://www.encodeproject.org/ENCBS925HHP/


title: Control ChIP-seq from whole organism (ENCLB961KNX)

description:
https://www.encodeproject.org/experiments/ENCSR860ZFH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing fd102C-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR860ZFH
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB961KNX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain fd102C-GFP mixed sex embryo (2-6 hours) insertion targeting D. melanogaster fd102C

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to fd102C

value: pooled male and female

value: ENCBS822GEJ at ENCODE; https://www.encodeproject.org/ENCBS822GEJ/


title: TF ChIP-seq from whole organism (ENCLB007ENU)

description:
https://www.encodeproject.org/experiments/ENCSR487OER/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing nhr-111-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR487OER
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR016AZO
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB007ENU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-111.

value: L4 larva

value: 48 hour

value: L1 larva starved after bleaching

value: ENCBS834MVU at ENCODE; https://www.encodeproject.org/ENCBS834MVU/


title: 360_A1

description:
extraction 159 sample 21_A1 pool 13_13
DGRP360 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

source_name: whole body

tag: tissue

value: whole body

tag: genotype

tag: developmental stage

value: Adults


title: 703_A1

description:
extraction 136 sample 34_A1 pool 13_06
DGRP703 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB364XYN)

description:
https://www.encodeproject.org/experiments/ENCSR809DRY/
***************
biological replicate number: 2
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing Y5F2A.4-eGFP fusion proteins.
experiment encode accession: ENCSR809DRY
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB364XYN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP682 (unc-119(tm4063); wgIs682 [Y5F2A.4::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex L4 larva (48 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans Y5F2A.4

tag: collection date

tag: geographic location

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to Y5F2A.4.

value: ENCBS005YTE at ENCODE; https://www.encodeproject.org/ENCBS005YTE/


title: Control ChIP-seq from whole organism (ENCLB593AHV)

description:
https://www.encodeproject.org/experiments/ENCSR860XAM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing cic-eGFP fusion proteins.
experiment encode accession: ENCSR860XAM
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-12-14
lab: Kevin White, UChicago
library encode accession: ENCLB593AHV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: biosample encode accession

tag: encode accession

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

value: adult

value: unknown

value: Kevin White, UChicago

value: Kevin White

value: ENCBS113XEZ at ENCODE; https://www.encodeproject.org/ENCBS113XEZ/


title: Control ChIP-seq from whole organism (ENCLB116YQS)

description:
https://www.encodeproject.org/experiments/ENCSR809DRY/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing Y5F2A.4-eGFP fusion proteins.
experiment encode accession: ENCSR809DRY
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB116YQS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

tag: note

tag: Sex

value: pooled male and female

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS228HDZ at ENCODE; https://www.encodeproject.org/ENCBS228HDZ/


title: Control ChIP-seq from whole organism (ENCLB578UPQ)

description:
https://www.encodeproject.org/experiments/ENCSR860PIR/
***************
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: ENCSR860PIR
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB578UPQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG2202 embryo (0-12 hours) insertion targeting D. melanogaster CG2202

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG2202

value: not collected

tag: dev stage

value: embryonic

value: 0-12 hour

value: ENCBS263CEN at ENCODE; https://www.encodeproject.org/ENCBS263CEN/


title: 879_A2

description:
extraction 195 sample 47_A2 pool 13_09
DGRP879 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: Control ChIP-seq from BLaER1 (ENCLB169TZP)

description:
https://www.encodeproject.org/experiments/ENCSR978XYH/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR978XYH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB169TZP
fragmentation methods: shearing (Covaris generic)

tag: line

value: cell line

value: female

value: unknown

tag: age

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;

value: ENCBS777PXO at ENCODE; https://www.encodeproject.org/ENCBS777PXO/


title: TF ChIP-seq from whole organism (ENCLB407KVZ)

description:
https://www.encodeproject.org/experiments/ENCSR551HEY/
***************
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: ENCSR551HEY
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR139WZD
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB407KVZ
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 CG8388

value: pooled male and female

value: 0-14 hour

tag: lab

value: Kevin White, UChicago

value: Kevin White

value: ENCBS208GWX at ENCODE; https://www.encodeproject.org/ENCBS208GWX/


title: 306_A2

description:
extraction 212 sample 16_A2 pool 12_21
DGRP306 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: TF ChIP-seq from whole organism (ENCLB727RRZ)

description:
https://www.encodeproject.org/experiments/ENCSR479XCM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-43-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR479XCM
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR149QOO
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB727RRZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP699 (unc-119(tm4063); wgIs699 [ceh-43::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex mixed stage (embryo) (3 hours) using egg bleaching insertion targeting C. elegans ceh-43

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-43.

value: mixed stage (embryonic)

value: 3 hour

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

value: egg bleaching

value: ENCBS564BDL at ENCODE; https://www.encodeproject.org/ENCBS564BDL/


title: 357_A2

description:
extraction 207 sample 20_A2 pool 12_20
DGRP357 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB548UPE)

description:
https://www.encodeproject.org/experiments/ENCSR860PIR/
***************
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: ENCSR860PIR
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB548UPE
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 CG2202

value: not collected

value: embryonic

value: 0-12 hour

tag: link

value: ENCBS612TKE at ENCODE; https://www.encodeproject.org/ENCBS612TKE/


title: 391_A1

description:
extraction 191 sample 27_A1 pool 12_19
DGRP391 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB364ERA)

description:
https://www.encodeproject.org/experiments/ENCSR858HYS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG1832-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR858HYS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR866WVF
encode release date: 2017-12-14
lab: Kevin White, UChicago
library encode accession: ENCLB364ERA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

value: not applicable

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

value: pooled male and female

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS323AOA at ENCODE; https://www.encodeproject.org/ENCBS323AOA/


title: TF ChIP-seq from whole organism (ENCLB332PSQ)

description:
https://www.encodeproject.org/experiments/ENCSR479XCM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-43-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR479XCM
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR149QOO
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB332PSQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-43.

value: mixed stage (embryonic)

value: 3 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: ENCBS753OCP at ENCODE; https://www.encodeproject.org/ENCBS753OCP/


title: 774_A1

description:
extraction 189 sample 37_A1 pool 12_18
DGRP774 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

value: Adults


title: TF ChIP-seq from whole organism (ENCLB998WXE)

description:
https://www.encodeproject.org/experiments/ENCSR677TRQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing attf-5-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR677TRQ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR830CMX
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB998WXE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP724 (unc-119(tm4063); wgIs724 [attf-5::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex young adult (66 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans attf-5

value: whole organism

value: whole organisms

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

value: young adult

value: 66 hour

value: L1 larva starved after bleaching

value: ENCBS972CDW at ENCODE; https://www.encodeproject.org/ENCBS972CDW/


title: TF ChIP-seq from whole organism (ENCLB820KJZ)

description:
https://www.encodeproject.org/experiments/ENCSR858HYS/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG1832-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR858HYS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR866WVF
encode release date: 2017-12-14
lab: Kevin White, UChicago
library encode accession: ENCLB820KJZ
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 CG1832

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS493IZJ at ENCODE; https://www.encodeproject.org/ENCBS493IZJ/


title: 217_A1

description:
extraction 168 sample 12_A1 pool 12_15
DGRP217 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

tag: genotype


title: TF ChIP-seq from whole organism (ENCLB791XOY)

description:
https://www.encodeproject.org/experiments/ENCSR677TRQ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing attf-5-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR677TRQ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR830CMX
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB791XOY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS119LGG at ENCODE; https://www.encodeproject.org/ENCBS119LGG/


title: Control ChIP-seq from whole organism (ENCLB082NLQ)

description:
https://www.encodeproject.org/experiments/ENCSR858HKA/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG3281-eGFP fusion proteins.
experiment encode accession: ENCSR858HKA
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB082NLQ
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

value: whole organism

value: whole organisms

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

value: ENCBS576SXP at ENCODE; https://www.encodeproject.org/ENCBS576SXP/


title: TF ChIP-seq from whole organism (ENCLB712JUA)

description:
https://www.encodeproject.org/experiments/ENCSR806JUF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing B0310.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR806JUF
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR234NAI
encode release date: 2016-10-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB712JUA
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP642 (unc-119 (tm4063) III; wgIs642) mixed sex early embryo 0 hours post synchronization using egg bleaching insertion targeting C. elegans B0310.2

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to B0310.2

value: early embryonic

value: unknown

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS760ECQ at ENCODE; https://www.encodeproject.org/ENCBS760ECQ/


title: TF ChIP-seq from whole organism (ENCLB119EOG)

description:
https://www.encodeproject.org/experiments/ENCSR806JUF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing B0310.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR806JUF
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR234NAI
encode release date: 2016-10-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB119EOG
fragmentation methods: sonication (generic microtip)

tag: collection date

value: not applicable

tag: geographic location

value: pooled male and female

value: ENCBS434FBU at ENCODE; https://www.encodeproject.org/ENCBS434FBU/


title: 441_A1

description:
extraction 151 sample 29_A1 pool 13_07
DGRP441 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

tag: developmental stage

value: Adults


title: Control ChIP-seq from whole organism (ENCLB558KAP)

description:
https://www.encodeproject.org/experiments/ENCSR380CVK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG9705-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR380CVK
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB558KAP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG9705-GFP mixed sex wandering third instar larva insertion targeting D. melanogaster CG9705

tag: biosample encode accession

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG9705

value: wandering third instar larva

value: Kevin White, UChicago

value: Kevin White

value: ENCBS543QPF at ENCODE; https://www.encodeproject.org/ENCBS543QPF/


title: 491_A2

description:
extraction 203 sample 31_A2 pool 12_11
DGRP491 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB452TSW)

description:
https://www.encodeproject.org/experiments/ENCSR378UYF/
***************
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: ENCSR378UYF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR803QSF
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB452TSW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Blimp-1-GFP embryo (10-12 hours) insertion targeting D. melanogaster Blimp-1

value: whole organism

value: whole organisms

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

tag: Sex

value: not collected

tag: dev stage

value: embryonic

value: ENCBS710QYM at ENCODE; https://www.encodeproject.org/ENCBS710QYM/


title: 315_A1

description:
extraction 164 sample 17_A1 pool 12_14
DGRP315 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB223OKS)

description:
https://www.encodeproject.org/experiments/ENCSR805GAD/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ELT-2-eGFP fusion proteins.
experiment encode accession: ENCSR805GAD
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-09-29
lab: Valerie Reinke, Yale
library encode accession: ENCLB223OKS
fragmentation methods: sonication (generic microtip)
instrument models: Illumina HiSeq 4000,Illumina HiSeq 2500

source_name: Caenorhabditis elegans strain OP56 (unc-119(ed3) III; wgIs56) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans elt-2

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

value: hermaphrodite

value: L1 larva

tag: age

value: unknown

tag: lab

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS885YPC at ENCODE; https://www.encodeproject.org/ENCBS885YPC/


title: TF ChIP-seq from whole organism (ENCLB165JLQ)

description:
https://www.encodeproject.org/experiments/ENCSR378UYF/
***************
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: ENCSR378UYF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR803QSF
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB165JLQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS422HUK at ENCODE; https://www.encodeproject.org/ENCBS422HUK/


title: 181_A2

description:
extraction 216 sample 11_A2 pool 12_22
DGRP181 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: Control ChIP-seq from BLaER1 (ENCLB137QLD)

description:
https://www.encodeproject.org/experiments/ENCSR455AFK/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR455AFK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB137QLD
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line

tag: line

value: cell line

value: female

value: Roderic Guigo, CRG

value: Thomas Graf

value: ENCBS017NGB at ENCODE; https://www.encodeproject.org/ENCBS017NGB/


title: 801_A2

description:
extraction 199 sample 41_A2 pool 12_10
DGRP801 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

tag: tissue


title: 882_A1

description:
extraction 127 sample 48_A1 pool 12_05
DGRP882 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: genotype


title: TF ChIP-seq from whole organism (ENCLB478OSH)

description:
https://www.encodeproject.org/experiments/ENCSR668BTV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing MLS-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR668BTV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR225LWH
encode release date: 2016-10-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB478OSH
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP645 (unc-119(tm4063) III; wgIs645) mixed sex mixed stage (embryo) 2 hours post synchronization using egg bleaching insertion targeting C. elegans mls-2

tag: antibody

value: whole organism

value: whole organisms

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

value: pooled male and female

value: mixed stage (embryonic)

value: unknown

tag: worm synchronization stage

value: egg bleaching

tag: post synchronization time

value: ENCBS797YYO at ENCODE; https://www.encodeproject.org/ENCBS797YYO/


title: TF ChIP-seq from whole organism (ENCLB699QUS)

description:
https://www.encodeproject.org/experiments/ENCSR378UYF/
***************
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: ENCSR378UYF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR803QSF
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB699QUS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: collection date

value: not applicable

tag: geographic location

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

value: not collected

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS109QIY at ENCODE; https://www.encodeproject.org/ENCBS109QIY/


title: TF ChIP-seq from whole organism (ENCLB976NIS)

description:
https://www.encodeproject.org/experiments/ENCSR668BTV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing MLS-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR668BTV
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR225LWH
encode release date: 2016-10-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB976NIS
fragmentation methods: sonication (generic microtip)

tag: biosample encode accession

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: post synchronization time units

value: hour

value: ENCBS372QTG at ENCODE; https://www.encodeproject.org/ENCBS372QTG/


title: Control ChIP-seq from whole organism (ENCLB258LKM)

description:
https://www.encodeproject.org/experiments/ENCSR857ANW/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG8924-eGFP fusion proteins.
experiment encode accession: ENCSR857ANW
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB258LKM
size range: 200-800

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

value: whole organism

value: whole organisms

tag: encode accession

tag: note

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

value: 0-24 hour

value: ENCBS849WDJ at ENCODE; https://www.encodeproject.org/ENCBS849WDJ/


title: Control ChIP-seq from whole organism (ENCLB492MOA)

description:
https://www.encodeproject.org/experiments/ENCSR667YZB/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing K02D7.2-eGFP fusion proteins.
experiment encode accession: ENCSR667YZB
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB492MOA
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP698 (unc-119(tm4063) III; wgIs698) mixed sex late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans snai-1

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to K02D7.2

tag: Sex

value: pooled male and female

tag: dev stage

value: late embryonic

value: unknown

value: egg bleaching

value: ENCBS666TAA at ENCODE; https://www.encodeproject.org/ENCBS666TAA/


title: Control ChIP-seq from BLaER1 (ENCLB780WVU)

description:
https://www.encodeproject.org/experiments/ENCSR455AFK/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR455AFK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB780WVU
fragmentation methods: shearing (Covaris generic)

value: cell line

value: not applicable

value: female

tag: age

tag: lab

value: Roderic Guigo, CRG

value: Thomas Graf

value: ENCBS137KWE at ENCODE; https://www.encodeproject.org/ENCBS137KWE/


title: 911_A1

description:
extraction 125 sample 50_A1 pool 12_04
DGRP911 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

tag: developmental stage

value: Adults


title: TF ChIP-seq from whole organism (ENCLB466YHQ)

description:
https://www.encodeproject.org/experiments/ENCSR856SZD/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG8290-eGFP fusion proteins.
experiment encode accession: ENCSR856SZD
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR235ERJ
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB466YHQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG8290 mixed sex embryo (0-14 hours) insertion targeting D. melanogaster ADD1

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8290

value: embryonic

value: 0-14 hour

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS849CSJ at ENCODE; https://www.encodeproject.org/ENCBS849CSJ/


title: 153_A2

description:
extraction 175 sample 08_A2 pool 12_03
DGRP153 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

source_name: whole body

tag: tissue

tag: genotype


title: 783_A2

description:
extraction 147 sample 38_A2 pool 12_01
DGRP783 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB548FJU)

description:
https://www.encodeproject.org/experiments/ENCSR856SZD/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG8290-eGFP fusion proteins.
experiment encode accession: ENCSR856SZD
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR235ERJ
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB548FJU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: pooled male and female

value: ENCBS382FSW at ENCODE; https://www.encodeproject.org/ENCBS382FSW/


title: Control ChIP-seq from whole organism (ENCLB470IVE)

description:
https://www.encodeproject.org/experiments/ENCSR799FDO/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing HIF-1-eGFP fusion proteins.
experiment encode accession: ENCSR799FDO
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB470IVE
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OR3349 mixed sex L4 larva 52 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans hif-1

value: not applicable

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

value: L4 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

value: hour

value: ENCBS585IFK at ENCODE; https://www.encodeproject.org/ENCBS585IFK/


title: 391_A2

description:
extraction 222 sample 27_A2 pool 11_23
DGRP391 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: Control ChIP-seq from whole organism (ENCLB515XDQ)

description:
https://www.encodeproject.org/experiments/ENCSR378LQR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing E(spl)m-delta-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR378LQR
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB515XDQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain E(spl)m-delta-GFP mixed sex embryo (2-12 hours) insertion targeting D. melanogaster E(spl)mdelta-HLH

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 E(spl)m-delta

value: embryonic

value: ENCBS190XRB at ENCODE; https://www.encodeproject.org/ENCBS190XRB/


title: Control ChIP-seq from whole organism (ENCLB067HBE)

description:
https://www.encodeproject.org/experiments/ENCSR661GOR/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing LSY-12-eGFP fusion proteins.
experiment encode accession: ENCSR661GOR
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB067HBE
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP568 (unc-119(tm4063) III; wgIs568) mixed sex L3 larva 43 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans lsy-12

tag: biosample encode accession

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

value: pooled male and female

value: L3 larva

tag: post synchronization time units

value: ENCBS829JKV at ENCODE; https://www.encodeproject.org/ENCBS829JKV/


title: 239_A2

description:
extraction 213 sample 14_A2 pool 11_21
DGRP239 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from BLaER1 (ENCLB245UJG)

description:
https://www.encodeproject.org/experiments/ENCSR958BKG/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 9 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR958BKG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB245UJG
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 9 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

tag: line

value: cell line

value: not applicable

tag: encode accession

value: female

value: unknown

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: ENCBS214PGM at ENCODE; https://www.encodeproject.org/ENCBS214PGM/


title: TF ChIP-seq from whole organism (ENCLB200ESK)

description:
https://www.encodeproject.org/experiments/ENCSR969MNX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing lsl-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR969MNX
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR127CDI
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB200ESK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP720 (unc-119(tm4063); wgIs720 [lsl-1::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex young adult (69 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans lsl-1

value: whole organism

tag: note

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

tag: Sex

tag: dev stage

value: young adult

tag: age

value: 69 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS106TAZ at ENCODE; https://www.encodeproject.org/ENCBS106TAZ/


title: 357_A1

description:
extraction 160 sample 20_A1 pool 11_13
DGRP357 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

tag: developmental stage

value: Adults


title: TF ChIP-seq from whole organism (ENCLB169FJU)

description:
https://www.encodeproject.org/experiments/ENCSR855JSV/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG8301-eGFP fusion proteins.
experiment encode accession: ENCSR855JSV
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR637IJM
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB169FJU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG8301 mixed sex pupa (48 hours) insertion targeting D. melanogaster CG8301

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8301

value: pooled male and female

value: pupa

value: 48 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS861RWM at ENCODE; https://www.encodeproject.org/ENCBS861RWM/


title: TF ChIP-seq from whole organism (ENCLB002EUS)

description:
https://www.encodeproject.org/experiments/ENCSR855JSV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG8301-eGFP fusion proteins.
experiment encode accession: ENCSR855JSV
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR637IJM
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB002EUS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: ENCBS404CEB at ENCODE; https://www.encodeproject.org/ENCBS404CEB/


title: TF ChIP-seq from whole organism (ENCLB464JLY)

description:
https://www.encodeproject.org/experiments/ENCSR969MNX/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing lsl-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR969MNX
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR127CDI
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB464JLY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: young adult

value: 69 hour

value: Valerie Reinke, Yale

tag: worm synchronization stage

value: ENCBS551YSA at ENCODE; https://www.encodeproject.org/ENCBS551YSA/


title: Control ChIP-seq from BLaER1 (ENCLB156ECT)

description:
https://www.encodeproject.org/experiments/ENCSR452GUC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 120 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR452GUC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB156ECT
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 120 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: cell line

tag: collection date

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;

value: ENCBS019UMZ at ENCODE; https://www.encodeproject.org/ENCBS019UMZ/


title: Control ChIP-seq from BLaER1 (ENCLB280PWI)

description:
https://www.encodeproject.org/experiments/ENCSR958BKG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 9 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR958BKG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB280PWI
fragmentation methods: shearing (Covaris generic)

value: not applicable

tag: geographic location

value: ENCBS902TME at ENCODE; https://www.encodeproject.org/ENCBS902TME/


title: 45_A2

description:
extraction 208 sample 02_A2 pool 11_20
DGRP45 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Adults


title: 370_A1

description:
extraction 156 sample 24_A1 pool 11_12
DGRP370 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: 832_A2

description:
extraction 196 sample 45_A2 pool 11_09
DGRP832 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv