title: Control ChIP-seq from whole organism (ENCLB419HLM)

description:
https://www.encodeproject.org/experiments/ENCSR283RSJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR283RSJ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB419HLM
fragmentation methods: sonication (generic microtip)

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

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

value: pooled male and female

value: unknown

value: Michael Snyder

value: ENCBS576EDO at ENCODE; https://www.encodeproject.org/ENCBS576EDO/


title: Control ChIP-seq from whole organism (ENCLB938KGT)

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/ENCSR101SVT/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR101SVT
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB938KGT
size range: 150-350

library_source: genomic

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

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP353 (unc-119(tm4063) III; wgIs353) mixed sex L2 larva insertion targeting C. elegans nhr-77

extract_protocol: not provided

value: whole organism

tag: geographic location

tag: encode accession

tag: Sex

tag: dev stage

value: L2 larva

tag: age

tag: lab

value: Michael Snyder, Stanford

tag: source

value: CGC

tag: link

value: ENCBS690RPC at ENCODE; https://www.encodeproject.org/ENCBS690RPC/


title: TF ChIP-seq from whole organism (ENCLB418LQY)

description:
https://www.encodeproject.org/experiments/ENCSR878RMZ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG7056-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR878RMZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR161QIN
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB418LQY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strain CG7056-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster HHEX

tag: antibody

value: HHEX

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7056

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS567HMN at ENCODE; https://www.encodeproject.org/ENCBS567HMN/


title: 783_L2

city: Nouzilly

first: Julie

last: Collet

address: Centre INRAE

country: France

institute: INRAE

description:
extraction 075 sample 38_L2 pool 18_22
DGRP783 Larvae 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: Larvae


title: 804_L1

description:
extraction 112 sample 42_L1 pool 18_20
DGRP804 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB192RGH)

description:
https://www.encodeproject.org/experiments/ENCSR200IVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing MEC-3-eGFP fusion proteins.
experiment encode accession: ENCSR200IVZ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB192RGH
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP55 (unc-119(ed3) III; wgIs55) hermaphrodite late embryo 4 hours post synchronization using egg bleaching insertion targeting C. elegans mec-3

value: whole organisms

value: not applicable

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

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS780CRX at ENCODE; https://www.encodeproject.org/ENCBS780CRX/


title: TF ChIP-seq from whole organism (ENCLB371IUF)

description:
https://www.encodeproject.org/experiments/ENCSR004JBX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-ceh-16 in L2 larva worms.
experiment encode accession: ENCSR004JBX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR445KQZ
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB371IUF
size range: 150-350

source_name: Caenorhabditis elegans strain OP82 (unc-119(tm4063) III; wgIs82) mixed sex L2 larva insertion targeting C. elegans ceh-16

value: whole organism

tag: biosample encode accession

tag: collection date

value: pooled male and female

value: L2 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS769RNK at ENCODE; https://www.encodeproject.org/ENCBS769RNK/


title: Control ChIP-seq from whole organism (ENCLB363CUE)

description:
https://www.encodeproject.org/experiments/ENCSR877IXV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Nf-Yc-eGFP fusion proteins.
experiment encode accession: ENCSR877IXV
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB363CUE
size range: 200-800

source_name: Drosophila melanogaster strain Nf-Yc mixed sex embryo (0-18 hours) insertion targeting D. melanogaster Nf-YC

value: whole organisms

tag: geographic location

tag: encode accession

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

value: embryonic

value: 0-18 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS584FBR at ENCODE; https://www.encodeproject.org/ENCBS584FBR/


title: TF ChIP-seq from whole organism (ENCLB776YNM)

description:
https://www.encodeproject.org/experiments/ENCSR878RMZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG7056-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR878RMZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR161QIN
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB776YNM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: HHEX

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7056

tag: Sex

tag: dev stage

value: 0-24 hour

value: ENCBS502BRA at ENCODE; https://www.encodeproject.org/ENCBS502BRA/


title: Control ChIP-seq from whole organism (ENCLB671ESF)

description:
https://www.encodeproject.org/experiments/ENCSR024OAH/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing LIR-3-eGFP fusion proteins.
experiment encode accession: ENCSR024OAH
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB671ESF
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP312 (unc-119(ed3) III; wgIs312) hermaphrodite L4 larva 48 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans lir-3

value: whole organism

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

value: hermaphrodite

value: L4 larva

tag: age

value: unknown

tag: lab

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS633GQO at ENCODE; https://www.encodeproject.org/ENCBS633GQO/


title: TF ChIP-seq from whole organism (ENCLB341HZQ)

description:
https://www.encodeproject.org/experiments/ENCSR878RMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG7056-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR878RMZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR161QIN
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB341HZQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS422FQD at ENCODE; https://www.encodeproject.org/ENCBS422FQD/


title: 315_L2

description:
extraction 055 sample 17_L2 pool 18_16
DGRP315 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB002AVW)

description:
https://www.encodeproject.org/experiments/ENCSR393VQP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10267-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR393VQP
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR873HOL
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB002AVW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

value: whole organism

value: not applicable

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10267

value: 0-24 hour

value: ENCBS585PUR at ENCODE; https://www.encodeproject.org/ENCBS585PUR/


title: TF ChIP-seq from whole organism (ENCLB122TEM)

description:
https://www.encodeproject.org/experiments/ENCSR393VQP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10267-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR393VQP
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR873HOL
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB122TEM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: ENCBS941FTM at ENCODE; https://www.encodeproject.org/ENCBS941FTM/


title: TF ChIP-seq from whole organism (ENCLB300JBX)

description:
https://www.encodeproject.org/experiments/ENCSR124XUB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing UNC-42-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR124XUB
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR918WXD
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB300JBX
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP173 hermaphrodite late embryo 3 hours post synchronization using egg bleaching insertion targeting C. elegans unc-42

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to UNC-42

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS458ADC at ENCODE; https://www.encodeproject.org/ENCBS458ADC/


title: TF ChIP-seq from whole organism (ENCLB628HDV)

description:
https://www.encodeproject.org/experiments/ENCSR124XUB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing UNC-42-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR124XUB
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR918WXD
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB628HDV
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: hour

value: ENCBS059JMB at ENCODE; https://www.encodeproject.org/ENCBS059JMB/


title: TF ChIP-seq from whole organism (ENCLB698KLJ)

description:
https://www.encodeproject.org/experiments/ENCSR100DTS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against eGFP-mef-2 in L1 larva worms.
experiment encode accession: ENCSR100DTS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR644RXR
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB698KLJ
size range: 150-350

source_name: Caenorhabditis elegans strain OP301 (unc-119(tm4063) III; wgIs301) mixed sex L1 larva insertion targeting C. elegans mef-2

value: whole organism

value: pooled male and female

value: L1 larva

value: Michael Snyder, Stanford

value: CGC

value: ENCBS631WGO at ENCODE; https://www.encodeproject.org/ENCBS631WGO/


title: Control ChIP-seq from whole organism (ENCLB766BNM)

description:
https://www.encodeproject.org/experiments/ENCSR002EBG/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR002EBG
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB766BNM
size range: 150-350

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

value: not applicable

value: L2 larva

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


title: TF ChIP-seq from whole organism (ENCLB019VYW)

description:
https://www.encodeproject.org/experiments/ENCSR393VQP/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10267-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR393VQP
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR873HOL
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB019VYW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10267

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS129NRJ at ENCODE; https://www.encodeproject.org/ENCBS129NRJ/


title: Control ChIP-seq from whole organism (ENCLB088BIL)

description:
https://www.encodeproject.org/experiments/ENCSR291MSY/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing CEH-18-eGFP fusion proteins.
experiment encode accession: ENCSR291MSY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB088BIL
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP533 (unc-119(tm4063) III; wgIs533) hermaphrodite late embryo 3 hours post synchronization using egg bleaching insertion targeting C. elegans ceh-18

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-18

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: hour

value: ENCBS316JDA at ENCODE; https://www.encodeproject.org/ENCBS316JDA/


title: TF ChIP-seq from whole organism (ENCLB919INK)

description:
https://www.encodeproject.org/experiments/ENCSR393QBI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing BtbVII-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR393QBI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR036PHI
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB919INK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: BtbVII

value: whole organism

value: not applicable

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

value: pooled male and female

value: ENCBS641HDE at ENCODE; https://www.encodeproject.org/ENCBS641HDE/


title: 153_L1

description:
extraction 109 sample 08_L1 pool 18_11
DGRP153 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB439PRC)

description:
https://www.encodeproject.org/experiments/ENCSR013JXG/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F49E8.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR013JXG
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR533CSZ
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB439PRC
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP383 (unc-119(tm4063) III; wgIs383) hermaphrodite L4 larva 52 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans oef-1

value: whole organisms

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

value: L4 larva

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: ENCBS937PPR at ENCODE; https://www.encodeproject.org/ENCBS937PPR/


title: TF ChIP-seq from whole organism (ENCLB373TWM)

description:
https://www.encodeproject.org/experiments/ENCSR013JXG/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F49E8.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR013JXG
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR533CSZ
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB373TWM
fragmentation methods: sonication (generic microtip)

value: hermaphrodite

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: post synchronization time

value: ENCBS877BNV at ENCODE; https://www.encodeproject.org/ENCBS877BNV/


title: Control ChIP-seq from whole organism (ENCLB797CHD)

description:
https://www.encodeproject.org/experiments/ENCSR001UTJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR001UTJ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB797CHD
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP201 (unc-119(tm4063) III; wgIs201) mixed sex L4 larva insertion targeting C. elegans pqm-1

value: whole organism

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

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS219TCM at ENCODE; https://www.encodeproject.org/ENCBS219TCM/


title: 427_L2

description:
extraction 065 sample 28_L2 pool 18_19
DGRP427 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

tag: developmental stage


title: TF ChIP-seq from whole organism (ENCLB972LPJ)

description:
https://www.encodeproject.org/experiments/ENCSR004JBX/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-ceh-16 in L2 larva worms.
experiment encode accession: ENCSR004JBX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR445KQZ
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB972LPJ
size range: 150-350

tag: biosample encode accession

value: not applicable

value: pooled male and female

value: L2 larva

value: CGC

value: ENCBS222HUK at ENCODE; https://www.encodeproject.org/ENCBS222HUK/


title: Control ChIP-seq from whole organism (ENCLB198JRZ)

description:
https://www.encodeproject.org/experiments/ENCSR001UTJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input ChIP-seq in L4 larva worms.
experiment encode accession: ENCSR001UTJ
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB198JRZ
fragmentation methods: sonication (generic microtip)

value: whole organisms

tag: collection date

value: L4 larva

value: ENCBS460CPB at ENCODE; https://www.encodeproject.org/ENCBS460CPB/


title: 367_L2

description:
extraction 079 sample 23_L2 pool 17_27
DGRP367 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: Larvae


title: Control ChIP-seq from whole organism (ENCLB989BJA)

description:
https://www.encodeproject.org/experiments/ENCSR109XBO/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ZTF-16-eGFP fusion proteins.
experiment encode accession: ENCSR109XBO
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB989BJA
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP558 (unc-119(tm4063) III; wgIs558) mixed sex late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans ztf-16

tag: geographic location

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

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

tag: post synchronization time units

value: hour

value: ENCBS713MMK at ENCODE; https://www.encodeproject.org/ENCBS713MMK/


title: 380_L2

description:
extraction 063 sample 26_L2 pool 17_20
DGRP380 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body


title: TF ChIP-seq from whole organism (ENCLB481WFA)

description:
https://www.encodeproject.org/experiments/ENCSR393QBI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing BtbVII-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR393QBI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR036PHI
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB481WFA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: BtbVII

value: whole organism

value: not applicable

tag: encode accession

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

tag: Sex

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS478VVP at ENCODE; https://www.encodeproject.org/ENCBS478VVP/


title: TF ChIP-seq from whole organism (ENCLB579DNX)

description:
https://www.encodeproject.org/experiments/ENCSR100DTS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against eGFP-mef-2 in L1 larva worms.
experiment encode accession: ENCSR100DTS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR644RXR
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB579DNX
size range: 150-350

value: whole organisms

tag: dev stage

value: L1 larva

tag: age

value: unknown

value: Michael Snyder, Stanford

value: CGC

value: ENCBS921ZWG at ENCODE; https://www.encodeproject.org/ENCBS921ZWG/


title: TF ChIP-seq from whole organism (ENCLB928CBF)

description:
https://www.encodeproject.org/experiments/ENCSR875UKH/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG9705-eGFP fusion proteins.
experiment encode accession: ENCSR875UKH
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR380CVK
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB928CBF
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

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

value: wandering third instar larva

tag: lab

tag: source

value: ENCBS412EUE at ENCODE; https://www.encodeproject.org/ENCBS412EUE/


title: 57_L2

description:
extraction 043 sample 03_L2 pool 18_14
DGRP57 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: 239_L2

description:
extraction 052 sample 14_L2 pool 17_16
DGRP239 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB800OOF)

description:
https://www.encodeproject.org/experiments/ENCSR002EBG/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq in L2 larva worms.
experiment encode accession: ENCSR002EBG
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2014-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB800OOF
size range: 150-350

value: whole organism

value: not applicable

value: pooled male and female

value: L2 larva

tag: link

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


title: 153_L2

description:
extraction 047 sample 08_L2 pool 17_15
DGRP153 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB869LWO)

description:
https://www.encodeproject.org/experiments/ENCSR101QFW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing C08G9.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR101QFW
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR530XBH
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB869LWO
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP513 (unc-119(tm4063) III; wgIs513) hermaphrodite late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans C08G9.2

tag: antibody

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to C08G9.2

value: hermaphrodite

value: late embryonic

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: hour

value: ENCBS250LYB at ENCODE; https://www.encodeproject.org/ENCBS250LYB/


title: DN587, SE_2B4_KO_TumorCells

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing:
Raw paired-end reads quality control was determined using FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
read trimming was performed using Trim Galore software (https://doi.org/10.5281/zenodo.5127899) to remove residual adapters and low-quality sequences.
Trimmed reads were aligned against the human reference genome (GRCh38) using STAR with standard input parameters and only uniquely mapped reads were considered for downstream analyses.
Reads were assigned to genes with the featureCounts tool using the GENCODE primary assembly v.35 gene transfer file (GTF) as reference annotation for the genomic features.
Gene count matrices were then processed by the R/Bioconductor differential gene expression analysis packages DESeq2 (37) following standard workflows.
Assembly: GENCODE primary assembly v.35 gene transfer file (GTF)
Supplementary files format and content: Raw read counts

molecule: total RNA

organism: Homo sapiens

source_name: T lymphocyte

extract_protocol:
Total RNA was extracted with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.
RNA library preparations and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA) and Illumina Nextera XT library was used for sequencing library preparation.

tag: cell type

value: T lymphocyte

tag: genotype

tag: culture condition

value: Tumor Cells


title: 805_L2

description:
extraction 105 sample 43_L2 pool 18_12
DGRP805 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

source_name: whole body

tag: tissue

value: whole body

tag: developmental stage


title: DN587, SE_2B4_KO_Unstim

value: Unstimulated


title: TF ChIP-seq from whole organism (ENCLB071FBA)

description:
https://www.encodeproject.org/experiments/ENCSR875UKH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG9705-eGFP fusion proteins.
experiment encode accession: ENCSR875UKH
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR380CVK
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB071FBA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

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

value: wandering third instar larva

value: unknown

value: Kevin White, UChicago

value: Kevin White

value: ENCBS821ZUV at ENCODE; https://www.encodeproject.org/ENCBS821ZUV/


title: DN587, SE_Tim_3KO_Unstim


title: 360_L1

description:
extraction 025 sample 21_L1 pool 17_12
DGRP360 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB067JEV)

description:
https://www.encodeproject.org/experiments/ENCSR101QFW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing C08G9.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR101QFW
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR530XBH
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB067JEV
fragmentation methods: sonication (generic microtip)

value: not applicable

tag: geographic location

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to C08G9.2

value: hermaphrodite

value: late embryonic

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

tag: post synchronization time

tag: post synchronization time units

value: ENCBS485AYJ at ENCODE; https://www.encodeproject.org/ENCBS485AYJ/


title: DN587, SE_LAG3_KO_TumorCells

value: T lymphocyte

value: Tumor Cells


title: 379_L2

description:
extraction 062 sample 25_L2 pool 17_11
DGRP379 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body


title: TF ChIP-seq from whole organism (ENCLB743UDX)

description:
https://www.encodeproject.org/experiments/ENCSR393QBI/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing BtbVII-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR393QBI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR036PHI
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB743UDX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: BtbVII

value: whole organism

value: whole organisms

tag: encode accession

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

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

tag: age

value: 0-24 hour

value: ENCBS137PNE at ENCODE; https://www.encodeproject.org/ENCBS137PNE/


title: DN587, SE_LAG3_KO_Unstim

value: Unstimulated


title: TF ChIP-seq from whole organism (ENCLB534FSC)

description:
https://www.encodeproject.org/experiments/ENCSR581LRS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing sc-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR581LRS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR363YDF
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB534FSC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

value: sc

value: not applicable

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

value: 0-14 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS127WGT at ENCODE; https://www.encodeproject.org/ENCBS127WGT/


title: TF ChIP-seq from whole organism (ENCLB714DZF)

description:
https://www.encodeproject.org/experiments/ENCSR581LRS/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing sc-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR581LRS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR363YDF
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB714DZF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: note

value: ENCBS629SAT at ENCODE; https://www.encodeproject.org/ENCBS629SAT/


title: TF ChIP-seq from whole organism (ENCLB486TBT)

description:
https://www.encodeproject.org/experiments/ENCSR581LRS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing sc-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR581LRS
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR363YDF
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB486TBT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: ENCBS578KQB at ENCODE; https://www.encodeproject.org/ENCBS578KQB/


title: 235_L2

description:
extraction 051 sample 13_L2 pool 17_10
DGRP235 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Larvae


title: DN587, SE_TumorCells

tag: cell type

value: T lymphocyte

value: SE

tag: culture condition

value: Tumor Cells


title: Control ChIP-seq from whole organism (ENCLB838XWK)

description:
https://www.encodeproject.org/experiments/ENCSR190ONG/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing DSC-1-eGFP fusion proteins.
experiment encode accession: ENCSR190ONG
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-09-29
lab: Valerie Reinke, Yale
library encode accession: ENCLB838XWK
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP522 (unc-119(tm4063) III; wgIs522) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans dsc-1

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

tag: geographic location

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

value: hermaphrodite

value: L1 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS040VXP at ENCODE; https://www.encodeproject.org/ENCBS040VXP/


title: DN587, SE_Unstim

value: Unstimulated


title: 158_L2

description:
extraction 048 sample 09_L2 pool 17_09
DGRP158 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

tag: developmental stage


title: 441_L1

description:
extraction 015 sample 29_L1 pool 17_06
DGRP441 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: Larvae


title: DN016, SE_2B4_KO_TumorCells

value: T lymphocyte


title: TF ChIP-seq from whole organism (ENCLB887LTU)

description:
https://www.encodeproject.org/experiments/ENCSR392IEL/
***************
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: ENCSR392IEL
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR421OFW
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB887LTU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: run

value: not applicable

tag: encode accession

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

value: not collected

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS302DGQ at ENCODE; https://www.encodeproject.org/ENCBS302DGQ/


title: DN016, SE_Tim3_KO_TumorCells

value: Tumor Cells


title: 356_L1

description:
extraction 005 sample 19_L1 pool 17_01
DGRP356 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB353IEI)

description:
https://www.encodeproject.org/experiments/ENCSR873HOL/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG10267-eGFP fusion proteins.
experiment encode accession: ENCSR873HOL
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB353IEI
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 CG10267

tag: Sex

value: pooled male and female

value: 0-24 hour

value: ENCBS811VXH at ENCODE; https://www.encodeproject.org/ENCBS811VXH/


title: TF ChIP-seq from whole organism (ENCLB244DFM)

description:
https://www.encodeproject.org/experiments/ENCSR392IEL/
***************
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: ENCSR392IEL
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR421OFW
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB244DFM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: dev stage

value: ENCBS457XBU at ENCODE; https://www.encodeproject.org/ENCBS457XBU/


title: 491_L1

description:
extraction 111 sample 31_L1 pool 16_19
DGRP491 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: DN016, SE_2B4_KO_Unstim

value: T lymphocyte

value: Unstimulated


title: 357_L1

description:
extraction 006 sample 20_L1 pool 17_05
DGRP357 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: DN016, SE_LAG3_KO_TumorCells


title: DN016, SE_LAG3_KO_Unstim


title: 360_L2

description:
extraction 059 sample 21_L2 pool 16_18
DGRP360 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: 367_L1

description:
extraction 096 sample 23_L1 pool 16_16
DGRP367 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB699JHJ)

description:
https://www.encodeproject.org/experiments/ENCSR579WFC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing kni-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR579WFC
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR213QMS
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB699JHJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: kni

value: not applicable

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

value: embryonic

tag: age

value: 0-14 hour

value: ENCBS114BAR at ENCODE; https://www.encodeproject.org/ENCBS114BAR/


title: TF ChIP-seq from whole organism (ENCLB293ZWI)

description:
https://www.encodeproject.org/experiments/ENCSR579WFC/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing kni-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR579WFC
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR213QMS
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB293ZWI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: Kevin White, UChicago

value: Kevin White

value: ENCBS413RBU at ENCODE; https://www.encodeproject.org/ENCBS413RBU/


title: TF ChIP-seq from whole organism (ENCLB975ZMY)

description:
https://www.encodeproject.org/experiments/ENCSR518WKG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing pax-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR518WKG
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR443FOO
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB975ZMY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP190 (unc-119(ed3) III; wgIs190) mixed sex L1 larva (6 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans pax-3

value: whole organisms

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

value: pooled male and female

value: L1 larva

value: 6 hour

tag: lab

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: ENCBS094TOU at ENCODE; https://www.encodeproject.org/ENCBS094TOU/


title: DN016, SE_TumorCells

value: T lymphocyte

value: SE

value: Tumor Cells


title: 879_L1

description:
extraction 038 sample 47_L1 pool 16_15
DGRP879 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: DN016, SE_Unstim

value: Unstimulated


title: TF ChIP-seq from whole organism (ENCLB059VPS)

description:
https://www.encodeproject.org/experiments/ENCSR578RWH/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing pzg-eGFP fusion proteins.
experiment encode accession: ENCSR578RWH
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR071KGD
encode release date: 2018-02-06
lab: Kevin White, UChicago
library encode accession: ENCLB059VPS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: pzg

value: whole organism

value: not applicable

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS536SFA at ENCODE; https://www.encodeproject.org/ENCBS536SFA/


title: TF ChIP-seq from whole organism (ENCLB957AJD)

description:
https://www.encodeproject.org/experiments/ENCSR518WKG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing pax-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR518WKG
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR443FOO
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB957AJD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: note

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

value: pooled male and female

value: L1 larva

value: 6 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS822RGL at ENCODE; https://www.encodeproject.org/ENCBS822RGL/


title: TF ChIP-seq from whole organism (ENCLB738BRX)

description:
https://www.encodeproject.org/experiments/ENCSR518VJU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing MEL-28-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR518VJU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR143RMG
encode release date: 2016-10-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB738BRX
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP646 (unc-119(tm4063) III; wgIs646) mixed sex young adult 64 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans mel-28

value: whole organism

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to MEL-28

value: young adult

value: unknown

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS248YNT at ENCODE; https://www.encodeproject.org/ENCBS248YNT/


title: Control ChIP-seq from whole organism (ENCLB909BEK)

description:
https://www.encodeproject.org/experiments/ENCSR392OLY/
***************
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: ENCSR392OLY
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB909BEK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain fd3F-GFP embryo (8-18 hours) insertion targeting D. melanogaster fd3F

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to fd3F

value: not collected

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS548WRO at ENCODE; https://www.encodeproject.org/ENCBS548WRO/


title: DN003, SE_2B4_KO_TumorCells

tag: cell type

value: T lymphocyte

tag: genotype

tag: culture condition

value: Tumor Cells


title: TF ChIP-seq from whole organism (ENCLB833QZJ)

description:
https://www.encodeproject.org/experiments/ENCSR392IEL/
***************
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: ENCSR392IEL
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR421OFW
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB833QZJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: run

value: whole organisms

tag: biosample encode accession

tag: collection date

tag: geographic location

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

value: 0-16 hour

value: ENCBS606ZCD at ENCODE; https://www.encodeproject.org/ENCBS606ZCD/


title: TF ChIP-seq from whole organism (ENCLB040XKE)

description:
https://www.encodeproject.org/experiments/ENCSR578RWH/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing pzg-eGFP fusion proteins.
experiment encode accession: ENCSR578RWH
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR071KGD
encode release date: 2018-02-06
lab: Kevin White, UChicago
library encode accession: ENCLB040XKE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: pzg

value: whole organism

tag: encode accession

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

tag: Sex

value: pooled male and female

value: 0-24 hour

value: ENCBS218XJX at ENCODE; https://www.encodeproject.org/ENCBS218XJX/


title: Control ChIP-seq from whole organism (ENCLB075CXZ)

description:
https://www.encodeproject.org/experiments/ENCSR517WHP/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing tlf-1-eGFP fusion proteins.
experiment encode accession: ENCSR517WHP
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB075CXZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP749 (wgIs749 [tlf-1::TY1::EGFP::3xFLAG + unc-119(+)];unc-119 (tm4063)) mixed sex young adult (65.5 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans tlf-1

value: not applicable

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

tag: dev stage

value: young adult

tag: age

value: 65.5 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS952IEM at ENCODE; https://www.encodeproject.org/ENCBS952IEM/


title: 391_L1

description:
extraction 028 sample 27_L1 pool 16_13
DGRP391 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: developmental stage

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB524YFC)

description:
https://www.encodeproject.org/experiments/ENCSR518VJU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing MEL-28-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR518VJU
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR143RMG
encode release date: 2016-10-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB524YFC
fragmentation methods: sonication (generic microtip)

tag: antibody

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to MEL-28

value: unknown

tag: lab

tag: source

tag: worm synchronization stage

value: hour

value: ENCBS561UNG at ENCODE; https://www.encodeproject.org/ENCBS561UNG/


title: DN003, SE_Tim3_KO_TumorCells

value: T lymphocyte

value: Tumor Cells


title: 357_L2

description:
extraction 091 sample 20_L2 pool 16_12
DGRP357 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: 235_L1

description:
extraction 020 sample 13_L1 pool 16_07
DGRP235 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB707EJX)

description:
https://www.encodeproject.org/experiments/ENCSR577TRI/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG15710-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR577TRI
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR394EAL
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB707EJX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster mixed sex pupa (24 hours) insertion targeting D. melanogaster CG15710

value: whole organism

value: not applicable

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG15710

value: pooled male and female

value: pupa

value: 24 hour

value: Kevin White, UChicago

value: Kevin White

tag: link

value: ENCBS260ZCG at ENCODE; https://www.encodeproject.org/ENCBS260ZCG/


title: Control ChIP-seq from whole organism (ENCLB215OXD)

description:
https://www.encodeproject.org/experiments/ENCSR516NJR/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing alr-1-eGFP fusion proteins.
experiment encode accession: ENCSR516NJR
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB215OXD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP362 (unc-119(tm4063) III; wgIs362) mixed sex L1 larva (6 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans alr-1

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

value: L1 larva

value: 6 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS256YFT at ENCODE; https://www.encodeproject.org/ENCBS256YFT/


title: DN003, SE_Tim_3KO_Unstim

tag: cell type

value: T lymphocyte

tag: genotype

value: Unstimulated


title: TF ChIP-seq from whole organism (ENCLB981GPK)

description:
https://www.encodeproject.org/experiments/ENCSR579WFC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing kni-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR579WFC
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR213QMS
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB981GPK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: kni

value: whole organism

value: whole organisms

tag: biosample encode accession

value: not applicable

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

value: embryonic

value: 0-14 hour

value: ENCBS480TIP at ENCODE; https://www.encodeproject.org/ENCBS480TIP/


title: TF ChIP-seq from whole organism (ENCLB630UWQ)

description:
https://www.encodeproject.org/experiments/ENCSR577TRI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG15710-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR577TRI
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR394EAL
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB630UWQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG15710

value: pooled male and female

value: pupa

value: 24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS962PIC at ENCODE; https://www.encodeproject.org/ENCBS962PIC/


title: TF ChIP-seq from whole organism (ENCLB966UOK)

description:
https://www.encodeproject.org/experiments/ENCSR514BBN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ccch-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR514BBN
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR721CXH
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB966UOK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: geographic location

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

value: young adult

value: 70 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS286UDV at ENCODE; https://www.encodeproject.org/ENCBS286UDV/


title: DN003, SE_LAG3_KO_TumorCells

value: T lymphocyte

tag: culture condition

value: Tumor Cells


title: 535_L2

description:
extraction 070 sample 33_L2 pool 16_04
DGRP535 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB814LBC)

description:
https://www.encodeproject.org/experiments/ENCSR514BBN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ccch-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR514BBN
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR721CXH
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB814LBC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

tag: encode accession

tag: Sex

value: pooled male and female

value: ENCBS555JON at ENCODE; https://www.encodeproject.org/ENCBS555JON/


title: 774_L1

description:
extraction 033 sample 37_L1 pool 16_14
DGRP774 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB746BCX)

description:
https://www.encodeproject.org/experiments/ENCSR870KTR/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG16815-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR870KTR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR628ZUK
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB746BCX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG16815-GFP mixed sex embryo (0-10 hours) insertion targeting D. melanogaster CG16815

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG16815

tag: dev stage

value: embryonic

tag: age

value: 0-10 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS770CBV at ENCODE; https://www.encodeproject.org/ENCBS770CBV/


title: DN003, SE_LAG3_KO_Unstim

value: Unstimulated


title: 911_A2

description:
extraction 223 sample 50_A2 pool 15_25
DGRP911 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

tag: tissue

tag: developmental stage

value: Adults


title: DN003, SE_TumorCells

value: T lymphocyte

value: SE


title: TF ChIP-seq from whole organism (ENCLB588PHN)

description:
https://www.encodeproject.org/experiments/ENCSR870KTR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG16815-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR870KTR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR628ZUK
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB588PHN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

tag: lab

value: ENCBS486YJR at ENCODE; https://www.encodeproject.org/ENCBS486YJR/


title: Control ChIP-seq from whole organism (ENCLB143SBI)

description:
https://www.encodeproject.org/experiments/ENCSR830CMX/
***************
biological replicate number: 3
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing attf-5-eGFP fusion proteins.
experiment encode accession: ENCSR830CMX
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB143SBI
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: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to ATTF-5.

value: young adult

value: 66 hour

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: ENCBS540ZXB at ENCODE; https://www.encodeproject.org/ENCBS540ZXB/


title: Control ChIP-seq from whole organism (ENCLB958SSU)

description:
https://www.encodeproject.org/experiments/ENCSR830CMX/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing attf-5-eGFP fusion proteins.
experiment encode accession: ENCSR830CMX
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB958SSU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

tag: note

value: pooled male and female

tag: link

value: ENCBS543UMA at ENCODE; https://www.encodeproject.org/ENCBS543UMA/


title: TF ChIP-seq from whole organism (ENCLB288HXP)

description:
https://www.encodeproject.org/experiments/ENCSR870KTR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG16815-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR870KTR
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR628ZUK
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB288HXP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG16815

value: embryonic

value: 0-10 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS398OVQ at ENCODE; https://www.encodeproject.org/ENCBS398OVQ/


title: 882_A2

description:
extraction 218 sample 48_A2 pool 15_23
DGRP882 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

tag: genotype

value: Adults


title: 235_A2

description:
extraction 214 sample 13_A2 pool 15_22
DGRP235 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB131QFM)

description:
https://www.encodeproject.org/experiments/ENCSR578RWH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing pzg-eGFP fusion proteins.
experiment encode accession: ENCSR578RWH
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR071KGD
encode release date: 2018-02-06
lab: Kevin White, UChicago
library encode accession: ENCLB131QFM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: pzg

tag: biosample encode accession

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

value: 0-24 hour

value: ENCBS692KZF at ENCODE; https://www.encodeproject.org/ENCBS692KZF/


title: DN003, SE_2B4_KO_Unstim

tag: cell type

value: T lymphocyte

value: Unstimulated


title: Control ChIP-seq from whole organism (ENCLB837NBG)

description:
https://www.encodeproject.org/experiments/ENCSR515BKY/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing DPFF-1-eGFP fusion proteins.
experiment encode accession: ENCSR515BKY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB837NBG
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP579 (unc-119(tm4063) III; wgIs579) mixed sex young adult 48 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans dpff-1

value: whole organism

value: whole organisms

tag: collection date

value: not applicable

tag: geographic location

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

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS031FCZ at ENCODE; https://www.encodeproject.org/ENCBS031FCZ/


title: Control ChIP-seq from BLaER1 (ENCLB141SSV)

description:
https://www.encodeproject.org/experiments/ENCSR841CWN/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 72 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR841CWN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB141SSV
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 72 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

tag: encode accession

tag: Sex

value: female

tag: dev stage

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: ENCBS696TKD at ENCODE; https://www.encodeproject.org/ENCBS696TKD/


title: Control ChIP-seq from whole organism (ENCLB401ZHM)

description:
https://www.encodeproject.org/experiments/ENCSR826HHX/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing T23F11.4-eGFP fusion proteins.
experiment encode accession: ENCSR826HHX
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB401ZHM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP709 (unc-119(tm4063); wgIs709 [T23F11.4::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex late embryo (4 hours) using egg bleaching insertion targeting C. elegans T23F11.4

value: whole organism

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to T23F11.4.

value: pooled male and female

value: late embryonic

tag: age

value: 4 hour

tag: lab

value: egg bleaching

value: ENCBS561YFY at ENCODE; https://www.encodeproject.org/ENCBS561YFY/


title: TF ChIP-seq from whole organism (ENCLB858YPC)

description:
https://www.encodeproject.org/experiments/ENCSR870BBY/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing fd59A-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR870BBY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR105HNS
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB858YPC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain fd59A-GFP mixed sex prepupa (24 days) insertion targeting D. melanogaster fd59A

tag: antibody

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to fd59A

value: prepupa

value: 24 day

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS445MPF at ENCODE; https://www.encodeproject.org/ENCBS445MPF/


title: Control ChIP-seq from whole organism (ENCLB573QKB)

description:
https://www.encodeproject.org/experiments/ENCSR995PJE/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing SPTF-2-eGFP fusion proteins.
experiment encode accession: ENCSR995PJE
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-09-19
lab: Kevin White, UChicago
library encode accession: ENCLB573QKB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP769 (unc-119(tm4063); wgls769 [sptf-2::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex young adult (64.5 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans sptf-2

tag: note

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

value: young adult

value: 64.5 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: link

value: ENCBS984DAL at ENCODE; https://www.encodeproject.org/ENCBS984DAL/


title: 356_A2

description:
extraction 209 sample 19_A2 pool 15_21
DGRP356 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

source_name: whole body

tag: tissue

value: whole body

tag: genotype

tag: developmental stage

value: Adults


title: 149_L2

description:
extraction 077 sample 07_L2 pool 16_05
DGRP149 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: Larvae


title: Control ChIP-seq from BLaER1 (ENCLB600EMJ)

description:
https://www.encodeproject.org/experiments/ENCSR841CWN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 72 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR841CWN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB600EMJ
fragmentation methods: shearing (Covaris generic)

value: cell line

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

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: ENCBS912XQN at ENCODE; https://www.encodeproject.org/ENCBS912XQN/


title: 441_A2

description:
extraction 205 sample 29_A2 pool 15_20
DGRP441 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB935ORL)

description:
https://www.encodeproject.org/experiments/ENCSR994CUJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-6-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR994CUJ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR544QPD
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB935ORL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP748 (wgIs748(ceh-6::TY1 EGFP 3xFLAG(P000007_A02_9H01);unc-119(+));unc-119 (ed3); VC2010) mixed sex late embryo (3.3 hours) using egg bleaching insertion targeting C. elegans ceh-6

value: whole organism

value: whole organisms

tag: encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-6.

value: pooled male and female

value: late embryonic

value: 3.3 hour

value: egg bleaching

value: ENCBS195ZBZ at ENCODE; https://www.encodeproject.org/ENCBS195ZBZ/


title: 535_A1

description:
extraction 190 sample 33_A1 pool 15_19
DGRP535 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: Control ChIP-seq from whole organism (ENCLB430KJU)

description:
https://www.encodeproject.org/experiments/ENCSR575NOI/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing ac-eGFP fusion proteins.
experiment encode accession: ENCSR575NOI
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB430KJU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain ac-GFP mixed sex embryo (0-8 hours) insertion targeting D. melanogaster ac

value: not applicable

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

tag: Sex

value: embryonic

value: 0-8 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS556REV at ENCODE; https://www.encodeproject.org/ENCBS556REV/


title: TF ChIP-seq from whole organism (ENCLB762RIB)

description:
https://www.encodeproject.org/experiments/ENCSR870BBY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing fd59A-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR870BBY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR105HNS
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB762RIB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to fd59A

tag: dev stage

value: prepupa

value: 24 day

value: ENCBS533HSI at ENCODE; https://www.encodeproject.org/ENCBS533HSI/


title: TF ChIP-seq from whole organism (ENCLB333TFR)

description:
https://www.encodeproject.org/experiments/ENCSR994CUJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-6-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR994CUJ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR544QPD
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB333TFR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-6.

value: pooled male and female

value: late embryonic

value: 3.3 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS639UNG at ENCODE; https://www.encodeproject.org/ENCBS639UNG/


title: Control ChIP-seq from whole organism (ENCLB710NTK)

description:
https://www.encodeproject.org/experiments/ENCSR823XQM/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing sup-37-eGFP fusion proteins.
experiment encode accession: ENCSR823XQM
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB710NTK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP611 (unc-119(tm4063); wgIs611 [sup-37::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex L1 larva (6 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans sup-37

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SUP-37.

value: L1 larva

value: 6 hour

value: L1 larva starved after bleaching

value: ENCBS421WLG at ENCODE; https://www.encodeproject.org/ENCBS421WLG/


title: DN003, SE_Unstim

source_name: T lymphocyte

tag: cell type

value: T lymphocyte

value: SE

tag: culture condition

value: Unstimulated


title: 796_A1

description:
extraction 186 sample 40_A1 pool 15_18
DGRP796 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 (ENCLB656AJW)

description:
https://www.encodeproject.org/experiments/ENCSR388YUZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Jarid2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR388YUZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR089YGV
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB656AJW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Jarid2-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Jarid2

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Jarid2

value: pooled male and female

value: embryonic

tag: age

value: 0-24 hour

tag: lab

value: Kevin White, UChicago

value: Kevin White

value: ENCBS293NBL at ENCODE; https://www.encodeproject.org/ENCBS293NBL/


title: 59_L1

description:
extraction 108 sample 04_L1 pool 19_10
DGRP59 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB879QKK)

description:
https://www.encodeproject.org/experiments/ENCSR388YUZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Jarid2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR388YUZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR089YGV
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB879QKK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: not applicable

tag: source

value: ENCBS257RDB at ENCODE; https://www.encodeproject.org/ENCBS257RDB/


title: TF ChIP-seq from whole organism (ENCLB517ZZH)

description:
https://www.encodeproject.org/experiments/ENCSR388YUZ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Jarid2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR388YUZ
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR089YGV
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB517ZZH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: note

value: ENCBS409IHO at ENCODE; https://www.encodeproject.org/ENCBS409IHO/


title: TF ChIP-seq from whole organism (ENCLB567WGR)

description:
https://www.encodeproject.org/experiments/ENCSR823LPZ/
***************
biological replicate number: 2
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: ENCLB567WGR
fragmentation methods: sonication (generic microtip)

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

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

value: mixed stage (embryonic)

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

tag: link

value: ENCBS463FKU at ENCODE; https://www.encodeproject.org/ENCBS463FKU/


title: TF ChIP-seq from whole organism (ENCLB917BOU)

description:
https://www.encodeproject.org/experiments/ENCSR869ZGG/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing TFAM-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR869ZGG
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR129EXW
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB917BOU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: TFAM

value: whole organism

value: whole organisms

tag: biosample encode accession

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

value: pooled male and female

value: embryonic

value: 0-16 hour

value: ENCBS384DNZ at ENCODE; https://www.encodeproject.org/ENCBS384DNZ/


title: 832_A1

description:
extraction 170 sample 45_A1 pool 15_15
DGRP832 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

tag: developmental stage

value: Adults


title: 380_A1

description:
extraction 154 sample 26_A1 pool 15_12
DGRP380 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: 362_A1

description:
extraction 158 sample 22_A1 pool 15_13
DGRP362 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB522ALD)

description:
https://www.encodeproject.org/experiments/ENCSR388HZU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG5180-eGFP fusion proteins.
experiment encode accession: ENCSR388HZU
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB522ALD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG5180-GFP mixed sex embryo (0-16 hours) insertion targeting D. melanogaster CG5180

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG5180

tag: Sex

value: Kevin White, UChicago

value: Kevin White

value: ENCBS279ASY at ENCODE; https://www.encodeproject.org/ENCBS279ASY/


title: TF ChIP-seq from whole organism (ENCLB810KHN)

description:
https://www.encodeproject.org/experiments/ENCSR867RUX/
***************
biological replicate number: 6
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: ENCSR867RUX
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR471YLT
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB810KHN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Su(var)2-HP2 embryo (0-10 hours) insertion targeting D. melanogaster Su(var)2-HP2

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Su(var)2-HP2

value: not collected

tag: dev stage

tag: age

value: 0-10 hour

value: ENCBS566RBZ at ENCODE; https://www.encodeproject.org/ENCBS566RBZ/


title: 703_A2

description:
extraction 201 sample 34_A2 pool 15_11
DGRP703 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB487ZLS)

description:
https://www.encodeproject.org/experiments/ENCSR867RUX/
***************
biological replicate number: 4
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: ENCSR867RUX
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR471YLT
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB487ZLS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: whole organisms

tag: lab

value: ENCBS688ZUS at ENCODE; https://www.encodeproject.org/ENCBS688ZUS/


title: TF ChIP-seq from whole organism (ENCLB579KGX)

description:
https://www.encodeproject.org/experiments/ENCSR993GFS/
***************
biological replicate number: 7
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CEBP-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR993GFS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR869CPS
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB579KGX
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP563 (unc-119(tm4063) III; wgIs563) mixed sex young adult 63 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans cebp-1

tag: note

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

value: pooled male and female

value: young adult

value: unknown

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS857GRB at ENCODE; https://www.encodeproject.org/ENCBS857GRB/


title: TF ChIP-seq from whole organism (ENCLB394MHI)

description:
https://www.encodeproject.org/experiments/ENCSR572JUN/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Ets96B-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR572JUN
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR477RDG
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB394MHI
size range: 200-800

source_name: Drosophila melanogaster strain Ets96B mixed sex prepupa (24 hours) insertion targeting D. melanogaster Ets96B

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Ets96B

value: prepupa

value: 24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS235NFH at ENCODE; https://www.encodeproject.org/ENCBS235NFH/


title: TF ChIP-seq from whole organism (ENCLB831PEP)

description:
https://www.encodeproject.org/experiments/ENCSR993GFS/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CEBP-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR993GFS
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR869CPS
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB831PEP
fragmentation methods: sonication (generic microtip)

value: whole organism

value: whole organisms

tag: worm synchronization stage

tag: post synchronization time

value: ENCBS243CXV at ENCODE; https://www.encodeproject.org/ENCBS243CXV/


title: 805_A2

description:
extraction 197 sample 43_A2 pool 15_10
DGRP805 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 (ENCLB124FUC)

description:
https://www.encodeproject.org/experiments/ENCSR823IAC/
***************
biological replicate number: 5
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F57C9.4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR823IAC
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR877TIV
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB124FUC
fragmentation methods: sonication (generic microtip)

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

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

value: pooled male and female

value: young adult

value: unknown

value: Valerie Reinke, Yale

tag: post synchronization time units

tag: link

value: ENCBS362BUD at ENCODE; https://www.encodeproject.org/ENCBS362BUD/


title: 897_A2

description:
extraction 194 sample 49_A2 pool 15_09
DGRP897 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

tag: tissue


title: TF ChIP-seq from whole organism (ENCLB279TVH)

description:
https://www.encodeproject.org/experiments/ENCSR823IAC/
***************
biological replicate number: 6
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F57C9.4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR823IAC
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR877TIV
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB279TVH
fragmentation methods: sonication (generic microtip)

tag: biosample encode accession

value: not applicable

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS798IOA at ENCODE; https://www.encodeproject.org/ENCBS798IOA/


title: TF ChIP-seq from whole organism (ENCLB236BMR)

description:
https://www.encodeproject.org/experiments/ENCSR572JUN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Ets96B-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR572JUN
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR477RDG
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB236BMR
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Ets96B

value: prepupa

value: 24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS693ZKC at ENCODE; https://www.encodeproject.org/ENCBS693ZKC/


title: Control ChIP-seq from whole organism (ENCLB470CGK)

description:
https://www.encodeproject.org/experiments/ENCSR504SMY/
***************
biological replicate number: 1
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: ENCLB470CGK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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: whole organism

value: whole organisms

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: egg bleaching

value: ENCBS576STD at ENCODE; https://www.encodeproject.org/ENCBS576STD/


title: 332_A2

description:
extraction 226 sample 18_A2 pool 14_25
DGRP332 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

tag: genotype

tag: developmental stage

value: Adults


title: 774_A2

description:
extraction 220 sample 37_A2 pool 14_23
DGRP774 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv