title: TF ChIP-seq from whole organism (ENCLB568CFM)

description:
https://www.encodeproject.org/experiments/ENCSR851UBK/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dac-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR851UBK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR303ZWP
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB568CFM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain dac-GFP mixed sex prepupa (48 days) insertion targeting D. melanogaster dac

value: dac

value: whole organism

value: whole organisms

tag: biosample encode accession

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

value: pooled male and female

value: prepupa

value: 48 day

value: Kevin White, UChicago

value: Kevin White

value: ENCBS362JKV at ENCODE; https://www.encodeproject.org/ENCBS362JKV/


title: TF ChIP-seq from whole organism (ENCLB566SFB)

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/ENCSR457RNA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing hlh-13-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR457RNA
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR058THH
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB566SFB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

library_source: genomic

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

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP744 (wgIs744 [hlh-13::TY1::EGFP::3xFLAG + unc-119(+)];unc-119 (tm4063)) mixed sex late embryo (3.5 hours) using egg bleaching insertion targeting C. elegans hlh-13

tag: antibody

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to HLH-13.

tag: Sex

tag: dev stage

value: late embryonic

tag: age

value: 3.5 hour

tag: lab

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

tag: link

value: ENCBS000CGI at ENCODE; https://www.encodeproject.org/ENCBS000CGI/


title: TF ChIP-seq from whole organism (ENCLB702DCN)

description:
https://www.encodeproject.org/experiments/ENCSR457RNA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing hlh-13-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR457RNA
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR058THH
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB702DCN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: ENCBS747QFX at ENCODE; https://www.encodeproject.org/ENCBS747QFX/


title: Control ChIP-seq from whole organism (ENCLB157ZVG)

description:
https://www.encodeproject.org/experiments/ENCSR794SVC/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing GMEB-2-eGFP fusion proteins.
experiment encode accession: ENCSR794SVC
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB157ZVG
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP622 (unc-119(tm4063) III; wgIs622) mixed sex late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans gmeb-2

value: whole organisms

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

value: unknown

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS445VZX at ENCODE; https://www.encodeproject.org/ENCBS445VZX/


title: TF ChIP-seq from whole organism (ENCLB308OVL)

description:
https://www.encodeproject.org/experiments/ENCSR547IVT/
***************
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: ENCSR547IVT
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR972CCK
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB308OVL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

organism: Drosophila melanogaster

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

value: Dek

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

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS447XSR at ENCODE; https://www.encodeproject.org/ENCBS447XSR/


title: Control ChIP-seq from whole organism (ENCLB479BOV)

description:
https://www.encodeproject.org/experiments/ENCSR662CJH/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing F57A8.1-eGFP fusion proteins.
experiment encode accession: ENCSR662CJH
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-09-19
lab: Kevin White, UChicago
library encode accession: ENCLB479BOV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP757 (unc-119(tm4063); wgls757 [F57A8.1::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex young adult (65 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans F57A8.1

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F57A8.1.

value: young adult

value: 65 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS258VEK at ENCODE; https://www.encodeproject.org/ENCBS258VEK/


title: Control ChIP-seq from whole organism (ENCLB813RPB)

description:
https://www.encodeproject.org/experiments/ENCSR793USS/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing spr-3-eGFP fusion proteins.
experiment encode accession: ENCSR793USS
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB813RPB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

value: whole organisms

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

value: L4 larva

value: 49 hour

value: ENCBS926VKT at ENCODE; https://www.encodeproject.org/ENCBS926VKT/


title: TF ChIP-seq from whole organism (ENCLB397HRO)

description:
https://www.encodeproject.org/experiments/ENCSR961TXR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing alr-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR961TXR
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR516NJR
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB397HRO
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: pooled male and female

value: L1 larva

value: 6 hour

value: ENCBS457LDK at ENCODE; https://www.encodeproject.org/ENCBS457LDK/


title: 427_A1

city: Nouzilly

first: Julie

last: Collet

address: Centre INRAE

country: France

institute: INRAE

description:
extraction 152 sample 28_A1 pool 11_07
DGRP427 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

library_source: transcriptomic

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

molecule: polyA RNA

source_name: whole body

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

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

tag: tissue

value: whole body

tag: genotype

tag: developmental stage

value: Adults


title: TF ChIP-seq from whole organism (ENCLB879JPQ)

description:
https://www.encodeproject.org/experiments/ENCSR547IVT/
***************
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: ENCSR547IVT
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR972CCK
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB879JPQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: Dek

tag: biosample encode accession

value: not applicable

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS516MQS at ENCODE; https://www.encodeproject.org/ENCBS516MQS/


title: Control ChIP-seq from whole organism (ENCLB116SLJ)

description:
https://www.encodeproject.org/experiments/ENCSR377KXD/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG6276-eGFP fusion proteins.
experiment encode accession: ENCSR377KXD
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB116SLJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

value: whole organisms

tag: collection date

tag: geographic location

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

value: prepupa

value: 72 day

value: ENCBS064GWI at ENCODE; https://www.encodeproject.org/ENCBS064GWI/


title: TF ChIP-seq from whole organism (ENCLB974BHR)

description:
https://www.encodeproject.org/experiments/ENCSR851UBK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing dac-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR851UBK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR303ZWP
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB974BHR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: dac

tag: encode accession

tag: note

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

value: pooled male and female

value: 48 day

value: ENCBS026OWX at ENCODE; https://www.encodeproject.org/ENCBS026OWX/


title: 491_A1

description:
extraction 138 sample 31_A1 pool 11_06
DGRP491 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: Control ChIP-seq from BLaER1 (ENCLB713NGK)

description:
https://www.encodeproject.org/experiments/ENCSR954ZQC/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR954ZQC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB713NGK
fragmentation methods: shearing (Covaris generic)

organism: Homo sapiens

source_name: Homo sapiens BLaER1 cell line 24 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

tag: line

value: cell line

value: not applicable

tag: Sex

value: female

tag: dev stage

value: unknown

value: Roderic Guigo, CRG

value: Thomas Graf

tag: treatments

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

value: ENCBS564GVM at ENCODE; https://www.encodeproject.org/ENCBS564GVM/


title: TF ChIP-seq from whole organism (ENCLB771DOW)

description:
https://www.encodeproject.org/experiments/ENCSR547IVT/
***************
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: ENCSR547IVT
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR972CCK
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB771DOW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Dek

value: whole organism

value: whole organisms

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

value: embryonic

tag: age

value: 0-24 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS808EKA at ENCODE; https://www.encodeproject.org/ENCBS808EKA/


title: TF ChIP-seq from whole organism (ENCLB415VJE)

description:
https://www.encodeproject.org/experiments/ENCSR961TXR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing alr-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR961TXR
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR516NJR
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB415VJE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: pooled male and female

value: L1 larva

value: 6 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: link

value: ENCBS550NSN at ENCODE; https://www.encodeproject.org/ENCBS550NSN/


title: Control ChIP-seq from BLaER1 (ENCLB282SPP)

description:
https://www.encodeproject.org/experiments/ENCSR954ZQC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR954ZQC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB282SPP
fragmentation methods: shearing (Covaris generic)

value: cell line

value: not applicable

value: female

value: unknown

value: Roderic Guigo, CRG

value: Thomas Graf

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

value: ENCBS528BRE at ENCODE; https://www.encodeproject.org/ENCBS528BRE/


title: 142_A1

description:
extraction 124 sample 06_A1 pool 11_04
DGRP142 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Adults


title: 149_A2

description:
extraction 176 sample 07_A2 pool 11_03
DGRP149 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

tag: developmental stage


title: TF ChIP-seq from whole organism (ENCLB259XSR)

description:
https://www.encodeproject.org/experiments/ENCSR656RPB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing lin-11-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR656RPB
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR743RDE
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB259XSR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP62 (unc-119(ed3) III; wgIs62) mixed sex late embryo (4.25 hours) using egg bleaching insertion targeting C. elegans lin-11

tag: antibody

value: whole organism

value: whole organisms

tag: biosample encode accession

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

value: pooled male and female

value: late embryonic

value: 4.25 hour

value: egg bleaching

value: ENCBS254APV at ENCODE; https://www.encodeproject.org/ENCBS254APV/


title: 158_A2

description:
extraction 174 sample 09_A2 pool 11_01
DGRP158 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from BLaER1 (ENCLB066ZDY)

description:
https://www.encodeproject.org/experiments/ENCSR452GUC/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-Seq on BLaER1 cell line after 120 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR452GUC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB066ZDY
fragmentation methods: shearing (Covaris generic)

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

value: cell line

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS040UGC at ENCODE; https://www.encodeproject.org/ENCBS040UGC/


title: Control ChIP-seq from whole organism (ENCLB986WUY)

description:
https://www.encodeproject.org/experiments/ENCSR784CLT/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing C34B4.2-eGFP fusion proteins.
experiment encode accession: ENCSR784CLT
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB986WUY
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP552 (unc-119(tm4063) III; wgIs552) mixed sex L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans C34B4.2

tag: encode accession

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to C34B4.2

value: L1 larva

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: ENCBS267PCU at ENCODE; https://www.encodeproject.org/ENCBS267PCU/


title: 142_A2

description:
extraction 217 sample 06_A2 pool 10_22
DGRP142 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 (ENCLB818TJP)

description:
https://www.encodeproject.org/experiments/ENCSR656RPB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing lin-11-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR656RPB
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR743RDE
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB818TJP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

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

tag: Sex

value: pooled male and female

tag: dev stage

value: late embryonic

value: ENCBS081QTG at ENCODE; https://www.encodeproject.org/ENCBS081QTG/


title: TF ChIP-seq from whole organism (ENCLB273TPE)

description:
https://www.encodeproject.org/experiments/ENCSR850IRM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG6765-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR850IRM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR130OWB
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB273TPE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG6765-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG6765

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG6765

value: embryonic

tag: age

value: 0-24 hour

tag: lab

value: Kevin White, UChicago

value: Kevin White

value: ENCBS500ECA at ENCODE; https://www.encodeproject.org/ENCBS500ECA/


title: Control ChIP-seq from whole organism (ENCLB413MQY)

description:
https://www.encodeproject.org/experiments/ENCSR544ESS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing sug-eGFP fusion proteins.
experiment encode accession: ENCSR544ESS
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB413MQY
size range: 200-800

source_name: Drosophila melanogaster strain sug mixed sex embryo (8-24 hours) insertion targeting D. melanogaster sug

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

tag: source

value: ENCBS088TMN at ENCODE; https://www.encodeproject.org/ENCBS088TMN/


title: 804_A1

description:
extraction 173 sample 42_A1 pool 10_16
DGRP804 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body


title: TF ChIP-seq from whole organism (ENCLB920STS)

description:
https://www.encodeproject.org/experiments/ENCSR956TMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing SPTF-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR956TMJ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR995PJE
encode release date: 2018-09-19
lab: Kevin White, UChicago
library encode accession: ENCLB920STS
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

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: ENCBS464XMP at ENCODE; https://www.encodeproject.org/ENCBS464XMP/


title: 181_A1

description:
extraction 169 sample 11_A1 pool 10_15
DGRP181 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

tag: genotype

value: Adults


title: 45_A1

description:
extraction 161 sample 02_A1 pool 10_13
DGRP45 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: developmental stage


title: TF ChIP-seq from whole organism (ENCLB118JHO)

description:
https://www.encodeproject.org/experiments/ENCSR956TMJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing SPTF-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR956TMJ
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR995PJE
encode release date: 2018-09-19
lab: Kevin White, UChicago
library encode accession: ENCLB118JHO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: whole organisms

tag: biosample encode accession

value: not applicable

value: pooled male and female

value: ENCBS172XOM at ENCODE; https://www.encodeproject.org/ENCBS172XOM/


title: Control ChIP-seq from whole organism (ENCLB513NRL)

description:
https://www.encodeproject.org/experiments/ENCSR684VZM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing zf30C-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR684VZM
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-06
lab: Kevin White, UChicago
library encode accession: ENCLB513NRL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain zf30C-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster zf30C

tag: collection date

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to zf30C

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS528NRR at ENCODE; https://www.encodeproject.org/ENCBS528NRR/


title: Control ChIP-seq from whole organism (ENCLB761LVA)

description:
https://www.encodeproject.org/experiments/ENCSR849IRM/
***************
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: ENCSR849IRM
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB761LVA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG13894 embryo (2-24 hours) insertion targeting D. melanogaster CG13894

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG13894

value: not collected

value: ENCBS258DNM at ENCODE; https://www.encodeproject.org/ENCBS258DNM/


title: 367_A1

description:
extraction 157 sample 23_A1 pool 10_12
DGRP367 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body


title: TF ChIP-seq from whole organism (ENCLB123KCM)

description:
https://www.encodeproject.org/experiments/ENCSR953PJS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing CEH-8-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR953PJS
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR124ARF
encode release date: 2018-09-19
lab: Kevin White, UChicago
library encode accession: ENCLB123KCM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP760 (unc-119(tm4063); wgIs760 [ceh-8::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex L1 larva (6 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ceh-8

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

value: L1 larva

value: 6 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS292ZIB at ENCODE; https://www.encodeproject.org/ENCBS292ZIB/


title: 486_A2

description:
extraction 204 sample 30_A2 pool 10_11
DGRP486 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: Adults


title: TF ChIP-seq from whole organism (ENCLB503SWZ)

description:
https://www.encodeproject.org/experiments/ENCSR951SLK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-27-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR951SLK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR925LDI
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB503SWZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP139 (wgIs139(ceh-27::TY1 EGFP 3xFLAG(P000007_F10); unc-119(+));unc-119(ed3)) mixed sex young adult (73 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ceh-27

value: whole organism

value: whole organisms

value: not applicable

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

value: pooled male and female

value: young adult

value: 73 hour

value: ENCBS491SZL at ENCODE; https://www.encodeproject.org/ENCBS491SZL/


title: TF ChIP-seq from whole organism (ENCLB540GRR)

description:
https://www.encodeproject.org/experiments/ENCSR682YQM/
***************
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: ENCSR682YQM
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR785TKF
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB540GRR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain pros-GFP mixed sex embryo (2-18 hours) insertion targeting D. melanogaster pros

value: pros

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

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS895ZHH at ENCODE; https://www.encodeproject.org/ENCBS895ZHH/


title: TF ChIP-seq from whole organism (ENCLB772SGX)

description:
https://www.encodeproject.org/experiments/ENCSR951SLK/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing ceh-27-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR951SLK
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR925LDI
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB772SGX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS119MIW at ENCODE; https://www.encodeproject.org/ENCBS119MIW/


title: 362_A2

description:
extraction 183 sample 22_A2 pool 10_08
DGRP362 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Adults


title: Control ChIP-seq from whole organism (ENCLB380UBB)

description:
https://www.encodeproject.org/experiments/ENCSR778CNK/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing CHD-7-eGFP fusion proteins.
experiment encode accession: ENCSR778CNK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB380UBB
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP609 (unc-119(tm4063) III; wgIs609) mixed sex young adult 67 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans chd-7

value: whole organism

value: whole organisms

value: not applicable

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

value: unknown

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS509UGM at ENCODE; https://www.encodeproject.org/ENCBS509UGM/


title: 153_A1

description:
extraction 123 sample 08_A1 pool 10_04
DGRP153 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB800IXA)

description:
https://www.encodeproject.org/experiments/ENCSR652ZAR/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing FKH-3-eGFP fusion proteins.
experiment encode accession: ENCSR652ZAR
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-10-27
lab: Valerie Reinke, Yale
library encode accession: ENCLB800IXA
fragmentation methods: sonication (generic microtip)

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

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

tag: Sex

value: pooled male and female

tag: dev stage

value: young adult

value: ENCBS061HMA at ENCODE; https://www.encodeproject.org/ENCBS061HMA/


title: TF ChIP-seq from whole organism (ENCLB647EYD)

description:
https://www.encodeproject.org/experiments/ENCSR846PTH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG16779-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR846PTH
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR653VKU
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB647EYD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG16779-MiMIC mixed sex prepupa insertion targeting D. melanogaster CG16779

value: D. mel line contraining an intronic eGFP exon to create a CG16779-GFP fusion gene

value: prepupa

tag: age

tag: lab

value: Kevin White, UChicago

value: Hugo Bellen

value: ENCBS827ZIP at ENCODE; https://www.encodeproject.org/ENCBS827ZIP/


title: TF ChIP-seq from whole organism (ENCLB907TFZ)

description:
https://www.encodeproject.org/experiments/ENCSR682YQM/
***************
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: ENCSR682YQM
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR785TKF
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB907TFZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: pros

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

value: embryonic

tag: source

value: Kevin White

value: ENCBS618FSS at ENCODE; https://www.encodeproject.org/ENCBS618FSS/


title: TF ChIP-seq from whole organism (ENCLB757RHC)

description:
https://www.encodeproject.org/experiments/ENCSR682YQM/
***************
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: ENCSR682YQM
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR785TKF
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB757RHC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

tag: link

value: ENCBS611STO at ENCODE; https://www.encodeproject.org/ENCBS611STO/


title: TF ChIP-seq from whole organism (ENCLB615ICC)

description:
https://www.encodeproject.org/experiments/ENCSR846PTH/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG16779-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR846PTH
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR653VKU
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB615ICC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: pooled male and female

value: unknown

value: ENCBS555HGG at ENCODE; https://www.encodeproject.org/ENCBS555HGG/


title: 57_A2

description:
extraction 177 sample 03_A2 pool 10_03
DGRP57 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

source_name: whole body

tag: tissue

value: whole body

value: Adults


title: TF ChIP-seq from whole organism (ENCLB118DQR)

description:
https://www.encodeproject.org/experiments/ENCSR846PTH/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG16779-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR846PTH
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR653VKU
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB118DQR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: D. mel line contraining an intronic eGFP exon to create a CG16779-GFP fusion gene

value: prepupa

value: Kevin White, UChicago

value: ENCBS486IKG at ENCODE; https://www.encodeproject.org/ENCBS486IKG/


title: 59_A2

description:
extraction 146 sample 04_A2 pool 10_01
DGRP59 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

tag: genotype


title: TF ChIP-seq from whole organism (ENCLB413QAL)

description:
https://www.encodeproject.org/experiments/ENCSR447OYJ/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing DPFF-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR447OYJ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR515BKY
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB413QAL
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: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to DPFF-1

value: young adult

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: hour

value: ENCBS516XMJ at ENCODE; https://www.encodeproject.org/ENCBS516XMJ/


title: TF ChIP-seq from whole organism (ENCLB563JQV)

description:
https://www.encodeproject.org/experiments/ENCSR850IRM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG6765-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR850IRM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR130OWB
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB563JQV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG6765

value: embryonic

value: 0-24 hour

value: Kevin White

value: ENCBS563FGL at ENCODE; https://www.encodeproject.org/ENCBS563FGL/


title: Control ChIP-seq from whole organism (ENCLB311YMT)

description:
https://www.encodeproject.org/experiments/ENCSR541KJI/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing bsh-eGFP fusion proteins.
experiment encode accession: ENCSR541KJI
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB311YMT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: biosample encode accession

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

value: pooled male and female

value: Kevin White, UChicago

value: ENCBS230JGZ at ENCODE; https://www.encodeproject.org/ENCBS230JGZ/


title: Control ChIP-seq from whole organism (ENCLB312PPC)

description:
https://www.encodeproject.org/experiments/ENCSR651DQT/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ztf-22-eGFP fusion proteins.
experiment encode accession: ENCSR651DQT
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB312PPC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP676 (unc-119(tm4063); wgIs676 [ztf-22::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex young adult (68 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ztf-22

tag: collection date

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to ZTF-22.

value: young adult

value: 68 hour

value: Valerie Reinke, Yale

value: ENCBS424HYD at ENCODE; https://www.encodeproject.org/ENCBS424HYD/


title: TF ChIP-seq from whole organism (ENCLB583LCB)

description:
https://www.encodeproject.org/experiments/ENCSR953PJS/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing CEH-8-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR953PJS
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR124ARF
encode release date: 2018-09-19
lab: Kevin White, UChicago
library encode accession: ENCLB583LCB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

tag: geographic location

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

value: L1 larva

value: 6 hour

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS594HQA at ENCODE; https://www.encodeproject.org/ENCBS594HQA/


title: TF ChIP-seq from whole organism (ENCLB689KYX)

description:
https://www.encodeproject.org/experiments/ENCSR850IRM/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG6765-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR850IRM
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR130OWB
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB689KYX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: not applicable

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG6765

value: embryonic

value: 0-24 hour

value: Kevin White

value: ENCBS713VNU at ENCODE; https://www.encodeproject.org/ENCBS713VNU/


title: 59_A1

description:
extraction 187 sample 04_A1 pool 09_18
DGRP59 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

tag: developmental stage

value: Adults


title: TF ChIP-seq from whole organism (ENCLB742KVP)

description:
https://www.encodeproject.org/experiments/ENCSR447OYJ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing DPFF-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR447OYJ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR515BKY
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB742KVP
fragmentation methods: sonication (generic microtip)

tag: note

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

value: pooled male and female

value: young adult

value: unknown

value: Valerie Reinke, Yale

tag: post synchronization time

value: hour

value: ENCBS461AOO at ENCODE; https://www.encodeproject.org/ENCBS461AOO/


title: 787_A2

description:
extraction 200 sample 39_A2 pool 10_10
DGRP787 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB294SRI)

description:
https://www.encodeproject.org/experiments/ENCSR443FOO/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing pax-3-eGFP fusion proteins.
experiment encode accession: ENCSR443FOO
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB294SRI
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 organism

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

tag: Sex

value: L1 larva

value: 6 hour

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS284CES at ENCODE; https://www.encodeproject.org/ENCBS284CES/


title: 801_A1

description:
extraction 172 sample 41_A1 pool 09_16
DGRP801 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB842NOU)

description:
https://www.encodeproject.org/experiments/ENCSR681RZY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG7987-eGFP fusion proteins.
experiment encode accession: ENCSR681RZY
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR641PKP
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB842NOU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG7987-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG7987

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7987

tag: dev stage

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS841JHW at ENCODE; https://www.encodeproject.org/ENCBS841JHW/


title: 360_A2

description:
extraction 184 sample 21_A2 pool 09_09
DGRP360 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 (ENCLB650VQL)

description:
https://www.encodeproject.org/experiments/ENCSR680NFF/
***************
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: ENCSR680NFF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR865FZO
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB650VQL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

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

value: pooled male and female

tag: age

value: 0-16 hour

value: ENCBS168TJR at ENCODE; https://www.encodeproject.org/ENCBS168TJR/


title: TF ChIP-seq from whole organism (ENCLB258HMZ)

description:
https://www.encodeproject.org/experiments/ENCSR766ULH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing M03D4.4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR766ULH
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR169AMM
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB258HMZ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP696 (unc-119(tm4063) III; wgIs696) mixed sex mixed stage (embryo) 2 hours post synchronization using egg bleaching insertion targeting C. elegans M03D4.4

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to M03D4.4

value: mixed stage (embryonic)

value: unknown

tag: lab

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

tag: post synchronization time units

value: hour

value: ENCBS023OFD at ENCODE; https://www.encodeproject.org/ENCBS023OFD/


title: TF ChIP-seq from whole organism (ENCLB534EVG)

description:
https://www.encodeproject.org/experiments/ENCSR680NFF/
***************
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: ENCSR680NFF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR865FZO
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB534EVG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: not applicable

value: embryonic

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS418ZFD at ENCODE; https://www.encodeproject.org/ENCBS418ZFD/


title: 149_A1

description:
extraction 135 sample 07_A1 pool 09_06
DGRP149 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Adults


title: Control ChIP-seq from whole organism (ENCLB070SXT)

description:
https://www.encodeproject.org/experiments/ENCSR846JYS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing pad-eGFP fusion proteins.
experiment encode accession: ENCSR846JYS
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB070SXT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: whole organism

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

value: female

value: adult

value: ENCBS796QEH at ENCODE; https://www.encodeproject.org/ENCBS796QEH/


title: TF ChIP-seq from whole organism (ENCLB998ERT)

description:
https://www.encodeproject.org/experiments/ENCSR643BKM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing Y22D7AL.16-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR643BKM
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR815ASQ
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB998ERT
fragmentation methods: sonication (generic microtip)

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

tag: antibody

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

value: pooled male and female

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: ENCBS356TCC at ENCODE; https://www.encodeproject.org/ENCBS356TCC/


title: TF ChIP-seq from whole organism (ENCLB188LQA)

description:
https://www.encodeproject.org/experiments/ENCSR844XMJ/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG10431-eGFP fusion proteins.
experiment encode accession: ENCSR844XMJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR470OED
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB188LQA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG10431-GFP mixed sex embryo (0-12 hours) insertion targeting D. melanogaster CG10431

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10431

value: embryonic

value: 0-12 hour

value: Kevin White, UChicago

value: ENCBS288OOM at ENCODE; https://www.encodeproject.org/ENCBS288OOM/


title: 362_L1

description:
extraction 110 sample 22_L1 pool 08_19
DGRP362 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae


title: Control ChIP-seq from whole organism (ENCLB800NAV)

description:
https://www.encodeproject.org/experiments/ENCSR843PNA/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG12391-eGFP fusion proteins.
experiment encode accession: ENCSR843PNA
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB800NAV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG12391

value: whole organism

tag: geographic location

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12391

value: 0-24 hour

value: Kevin White

value: ENCBS249GTS at ENCODE; https://www.encodeproject.org/ENCBS249GTS/


title: 367_A2

description:
extraction 182 sample 23_A2 pool 09_08
DGRP367 Adults Biol Rep 2
gene expression count table form_for GEO submission.csv

tag: developmental stage

value: Adults


title: TF ChIP-seq from whole organism (ENCLB461SKR)

description:
https://www.encodeproject.org/experiments/ENCSR766ULH/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing M03D4.4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR766ULH
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR169AMM
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB461SKR
fragmentation methods: sonication (generic microtip)

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to M03D4.4

value: pooled male and female

value: mixed stage (embryonic)

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

tag: post synchronization time

value: hour

value: ENCBS293INZ at ENCODE; https://www.encodeproject.org/ENCBS293INZ/


title: TF ChIP-seq from whole organism (ENCLB321QUZ)

description:
https://www.encodeproject.org/experiments/ENCSR643BKM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing Y22D7AL.16-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR643BKM
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR815ASQ
encode release date: 2016-10-11
lab: Valerie Reinke, Yale
library encode accession: ENCLB321QUZ
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: not applicable

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

tag: Sex

tag: dev stage

value: late embryonic

value: ENCBS207AFW at ENCODE; https://www.encodeproject.org/ENCBS207AFW/


title: 239_A1

description:
extraction 166 sample 14_A1 pool 09_14
DGRP239 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: whole body


title: TF ChIP-seq from whole organism (ENCLB497ZEB)

description:
https://www.encodeproject.org/experiments/ENCSR434ALY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing T23F11.4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR434ALY
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR826HHX
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB497ZEB
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.

tag: age

value: 4 hour

tag: lab

value: ENCBS764SOU at ENCODE; https://www.encodeproject.org/ENCBS764SOU/


title: TF ChIP-seq from whole organism (ENCLB222LWM)

description:
https://www.encodeproject.org/experiments/ENCSR844XMJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG10431-eGFP fusion proteins.
experiment encode accession: ENCSR844XMJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR470OED
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB222LWM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10431

value: pooled male and female

value: embryonic

value: 0-12 hour

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS729OLL at ENCODE; https://www.encodeproject.org/ENCBS729OLL/


title: 796_L2

description:
extraction 056 sample 40_L2 pool 08_16
DGRP796 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: Larvae


title: 57_A1

description:
extraction 150 sample 03_A1 pool 09_07
DGRP57 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

value: Adults


title: TF ChIP-seq from whole organism (ENCLB261FCU)

description:
https://www.encodeproject.org/experiments/ENCSR844XMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG10431-eGFP fusion proteins.
experiment encode accession: ENCSR844XMJ
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR470OED
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB261FCU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: not applicable

tag: link

value: ENCBS414KIL at ENCODE; https://www.encodeproject.org/ENCBS414KIL/


title: 879_A1

description:
extraction 128 sample 47_A1 pool 09_05
DGRP879 Adults Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body


title: TF ChIP-seq from whole organism (ENCLB910LMW)

description:
https://www.encodeproject.org/experiments/ENCSR641VZA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing sem-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR641VZA
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR071LAB
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB910LMW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP701 (unc-119(tm4063); wgIs701 [sem-2::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex mixed stage (embryo) (1 hour) using egg bleaching insertion targeting C. elegans sem-2

value: whole organism

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

value: mixed stage (embryonic)

value: 1 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS582GWI at ENCODE; https://www.encodeproject.org/ENCBS582GWI/


title: 882_L1

description:
extraction 101 sample 48_L1 pool 08_18
DGRP882 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: genotype


title: TF ChIP-seq from whole organism (ENCLB508XEA)

description:
https://www.encodeproject.org/experiments/ENCSR281ORM/
***************
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: ENCSR281ORM
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR707UNX
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB508XEA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Sox102F-GFP embryo (12-14 hours) insertion targeting D. melanogaster Sox102F

tag: antibody

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Sox102F

value: not collected

value: embryonic

value: Kevin White, UChicago

value: ENCBS042VJE at ENCODE; https://www.encodeproject.org/ENCBS042VJE/


title: TF ChIP-seq from whole organism (ENCLB147BIN)

description:
https://www.encodeproject.org/experiments/ENCSR281ORM/
***************
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: ENCSR281ORM
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR707UNX
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB147BIN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: Kevin White

value: ENCBS547FMD at ENCODE; https://www.encodeproject.org/ENCBS547FMD/


title: TF ChIP-seq from whole organism (ENCLB707QRL)

description:
https://www.encodeproject.org/experiments/ENCSR434ALY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing T23F11.4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR434ALY
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR826HHX
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB707QRL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

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

value: pooled male and female

value: late embryonic

value: 4 hour

tag: worm synchronization stage

value: ENCBS212WIC at ENCODE; https://www.encodeproject.org/ENCBS212WIC/


title: 491_L2

description:
extraction 068 sample 31_L2 pool 08_13
DGRP491 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 (ENCLB719WZU)

description:
https://www.encodeproject.org/experiments/ENCSR641VZA/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing sem-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR641VZA
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR071LAB
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB719WZU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

tag: biosample encode accession

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

value: mixed stage (embryonic)

value: 1 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS036EXP at ENCODE; https://www.encodeproject.org/ENCBS036EXP/


title: TF ChIP-seq from whole organism (ENCLB354CZW)

description:
https://www.encodeproject.org/experiments/ENCSR280XEB/
***************
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: ENCSR280XEB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR647WJL
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB354CZW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Hr78-GFP mixed sex embryo (8-16 hours) whole organism stably expressing C-terminal eGFP-tagged Hr78

value: whole organisms

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Hr78

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS292SST at ENCODE; https://www.encodeproject.org/ENCBS292SST/


title: TF ChIP-seq from whole organism (ENCLB923OSF)

description:
https://www.encodeproject.org/experiments/ENCSR435RXY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing FKH-8-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR435RXY
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR101ZRY
encode release date: 2016-10-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB923OSF
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP652 (unc-119(tm4063) III; wgIs652) mixed sex L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans fkh-8

value: not applicable

tag: geographic location

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

value: pooled male and female

value: L1 larva

value: unknown

value: L1 larva starved after bleaching

tag: post synchronization time units

value: hour

value: ENCBS072XKE at ENCODE; https://www.encodeproject.org/ENCBS072XKE/


title: Control ChIP-seq from whole organism (ENCLB312GRO)

description:
https://www.encodeproject.org/experiments/ENCSR282UQU/
***************
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: ENCSR282UQU
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB312GRO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG7271 embryo (0-4 hours) insertion targeting D. melanogaster CG7271

value: whole organism

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7271

value: not collected

value: 0-4 hour

value: ENCBS215JRZ at ENCODE; https://www.encodeproject.org/ENCBS215JRZ/


title: TF ChIP-seq from whole organism (ENCLB494VYY)

description:
https://www.encodeproject.org/experiments/ENCSR681RZY/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG7987-eGFP fusion proteins.
experiment encode accession: ENCSR681RZY
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR641PKP
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB494VYY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7987

value: embryonic

value: 0-24 hour

value: ENCBS629CVV at ENCODE; https://www.encodeproject.org/ENCBS629CVV/


title: 787_L1

description:
extraction 035 sample 39_L1 pool 08_14
DGRP787 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

source_name: whole body

value: whole body

tag: developmental stage

value: Larvae


title: TF ChIP-seq from whole organism (ENCLB592EPN)

description:
https://www.encodeproject.org/experiments/ENCSR435RXY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing FKH-8-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR435RXY
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR101ZRY
encode release date: 2016-10-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB592EPN
fragmentation methods: sonication (generic microtip)

value: not applicable

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

tag: Sex

value: pooled male and female

value: L1 larva

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: post synchronization time

value: ENCBS756SLF at ENCODE; https://www.encodeproject.org/ENCBS756SLF/


title: TF ChIP-seq from whole organism (ENCLB621VEH)

description:
https://www.encodeproject.org/experiments/ENCSR280XEB/
***************
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: ENCSR280XEB
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR647WJL
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB621VEH
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 Hr78

tag: dev stage

tag: age

value: Kevin White, UChicago

value: Kevin White

value: ENCBS919YBY at ENCODE; https://www.encodeproject.org/ENCBS919YBY/


title: 239_L1

description:
extraction 021 sample 14_L1 pool 08_07
DGRP239 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB256RXR)

description:
https://www.encodeproject.org/experiments/ENCSR280HPE/
***************
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: ENCSR280HPE
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB256RXR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG10147-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG10147

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10147

value: embryonic

tag: lab

tag: source

value: ENCBS728WFN at ENCODE; https://www.encodeproject.org/ENCBS728WFN/


title: TF ChIP-seq from whole organism (ENCLB350ABJ)

description:
https://www.encodeproject.org/experiments/ENCSR757OPC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing VAB-15-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR757OPC
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR569VQG
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB350ABJ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain XIL99 mixed sex L1 larva at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using CRISPR targeting C. elegans vab-15

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to VAB-15

value: unknown

value: L1 larva starved after bleaching

tag: link

value: ENCBS564SNS at ENCODE; https://www.encodeproject.org/ENCBS564SNS/


title: TF ChIP-seq from whole organism (ENCLB412NZS)

description:
https://www.encodeproject.org/experiments/ENCSR432MSI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CEH-9-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR432MSI
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR754PHW
encode release date: 2016-10-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB412NZS
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP202 (unc-119(ed3) III; wgIs202) mixed sex late embryo 4.75 hours post synchronization using egg bleaching insertion targeting C. elegans ceh-9

value: not applicable

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

value: pooled male and female

value: late embryonic

value: egg bleaching

value: hour

value: ENCBS271XQL at ENCODE; https://www.encodeproject.org/ENCBS271XQL/


title: Control ChIP-seq from whole organism (ENCLB762FLJ)

description:
https://www.encodeproject.org/experiments/ENCSR278PHU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG7045-eGFP fusion proteins.
experiment encode accession: ENCSR278PHU
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB762FLJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG7045-GFP male adult insertion targeting D. melanogaster tHMG1

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7045

value: male

value: adult

value: Kevin White, UChicago

value: Kevin White

value: ENCBS787FCA at ENCODE; https://www.encodeproject.org/ENCBS787FCA/


title: 911_L1

description:
extraction 115 sample 50_L1 pool 08_02
DGRP911 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv

tag: tissue

value: whole body

tag: genotype

value: Larvae


title: Control ChIP-seq from whole organism (ENCLB462HFH)

description:
https://www.encodeproject.org/experiments/ENCSR424EIZ/
***************
biological replicate number: 3
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing gei-17-eGFP fusion proteins.
experiment encode accession: ENCSR424EIZ
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB462HFH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP572 (unc-119(tm4063); wgIs572 [gei-17::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex young adult (64 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans gei-17

value: whole organisms

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

value: young adult

value: 64 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: ENCBS654JDO at ENCODE; https://www.encodeproject.org/ENCBS654JDO/


title: Control ChIP-seq from whole organism (ENCLB123QGP)

description:
https://www.encodeproject.org/experiments/ENCSR424EIZ/
***************
biological replicate number: 5
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing gei-17-eGFP fusion proteins.
experiment encode accession: ENCSR424EIZ
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB123QGP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

tag: biosample encode accession

value: not applicable

value: pooled male and female

value: ENCBS937WWG at ENCODE; https://www.encodeproject.org/ENCBS937WWG/


title: 306_L1

description:
extraction 004 sample 16_L1 pool 08_04
DGRP306 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB028PZX)

description:
https://www.encodeproject.org/experiments/ENCSR757OPC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing VAB-15-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR757OPC
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR569VQG
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB028PZX
fragmentation methods: sonication (generic microtip)

tag: antibody

tag: collection date

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to VAB-15

value: L1 larva

value: unknown

value: ENCBS096ZAK at ENCODE; https://www.encodeproject.org/ENCBS096ZAK/


title: TF ChIP-seq from whole organism (ENCLB360TMH)

description:
https://www.encodeproject.org/experiments/ENCSR278IBK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG6808-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR278IBK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR615VYC
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB360TMH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG6808-GFP mixed sex prepupa (24 days) insertion targeting D. melanogaster CG6808

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG6808

value: prepupa

value: 24 day

value: Kevin White, UChicago

value: Kevin White

value: ENCBS841PRW at ENCODE; https://www.encodeproject.org/ENCBS841PRW/


title: TF ChIP-seq from whole organism (ENCLB991LVK)

description:
https://www.encodeproject.org/experiments/ENCSR278IBK/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG6808-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR278IBK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR615VYC
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB991LVK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

tag: encode accession

value: ENCBS127ENQ at ENCODE; https://www.encodeproject.org/ENCBS127ENQ/


title: 370_L2

description:
extraction 061 sample 24_L2 pool 07_18
DGRP370 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 (ENCLB866UZW)

description:
https://www.encodeproject.org/experiments/ENCSR278IBK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG6808-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR278IBK
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR615VYC
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB866UZW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

tag: note

value: ENCBS881EIH at ENCODE; https://www.encodeproject.org/ENCBS881EIH/


title: 882_L2

description:
extraction 088 sample 48_L2 pool 07_07
DGRP882 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

tag: developmental stage


title: 796_L1

description:
extraction 099 sample 40_L1 pool 07_02
DGRP796 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB750DLN)

description:
https://www.encodeproject.org/experiments/ENCSR928FFW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing TRA-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR928FFW
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR086AUV
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB750DLN
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP640 (unc-119(tm4063) III; wgIs640) mixed sex early embryo using egg bleaching insertion targeting C. elegans tra-4

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

tag: Sex

value: pooled male and female

value: early embryonic

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS579VXH at ENCODE; https://www.encodeproject.org/ENCBS579VXH/


title: Control ChIP-seq from whole organism (ENCLB861CRR)

description:
https://www.encodeproject.org/experiments/ENCSR925LDI/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ceh-27-eGFP fusion proteins.
experiment encode accession: ENCSR925LDI
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB861CRR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP139 (wgIs139(ceh-27::TY1 EGFP 3xFLAG(P000007_F10); unc-119(+));unc-119(ed3)) mixed sex young adult (73 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans ceh-27

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

value: young adult

value: 73 hour

value: L1 larva starved after bleaching

value: ENCBS140GFV at ENCODE; https://www.encodeproject.org/ENCBS140GFV/


title: TF ChIP-seq from whole organism (ENCLB124TEM)

description:
https://www.encodeproject.org/experiments/ENCSR276LGX/
***************
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: ENCSR276LGX
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR013WUH
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB124TEM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

value: salm

value: whole organisms

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

value: not collected

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS172FNI at ENCODE; https://www.encodeproject.org/ENCBS172FNI/


title: TF ChIP-seq from whole organism (ENCLB409GPA)

description:
https://www.encodeproject.org/experiments/ENCSR276LGX/
***************
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: ENCSR276LGX
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR013WUH
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB409GPA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

value: ENCBS795VWD at ENCODE; https://www.encodeproject.org/ENCBS795VWD/


title: TF ChIP-seq from whole organism (ENCLB112WIH)

description:
https://www.encodeproject.org/experiments/ENCSR274AAR/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8924-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR274AAR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR857ANW
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB112WIH
size range: 200-800

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

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

value: pooled male and female

value: 0-24 hour

value: ENCBS346YVV at ENCODE; https://www.encodeproject.org/ENCBS346YVV/


title: Control ChIP-seq from whole organism (ENCLB758GWH)

description:
https://www.encodeproject.org/experiments/ENCSR633YHP/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing tbp1-eGFP fusion proteins.
experiment encode accession: ENCSR633YHP
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB758GWH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP746 (unc-119(tm4063); wgIs746 [tbp-1::TY1 EGFP 3xFLAG(GlyStock16H06_GlyStock16H06) + unc-119(+)]) mixed sex young adult (65 hours) at L1 larva starved after bleaching stage insertion targeting C. elegans tbp-1

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

value: young adult

value: 65 hour

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS739IAR at ENCODE; https://www.encodeproject.org/ENCBS739IAR/


title: 217_L2

description:
extraction 050 sample 12_L2 pool 06_19
DGRP217 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 (ENCLB781GGD)

description:
https://www.encodeproject.org/experiments/ENCSR928FFW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing TRA-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR928FFW
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR086AUV
encode release date: 2017-11-06
lab: Valerie Reinke, Yale
library encode accession: ENCLB781GGD
fragmentation methods: sonication (generic microtip)

value: whole organisms

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

value: early embryonic

value: unknown

value: egg bleaching

value: ENCBS852CUQ at ENCODE; https://www.encodeproject.org/ENCBS852CUQ/


title: TF ChIP-seq from whole organism (ENCLB889TSC)

description:
https://www.encodeproject.org/experiments/ENCSR626LGN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing C38D4.7-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR626LGN
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR100DIV
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB889TSC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP708 (unc-119(tm4063); wgIs708 [C38D4.7::TY1::EGFP::3xFLAG + unc-119(+)]) mixed sex late embryo (4 hours) using egg bleaching insertion targeting C. elegans C38D4.7

value: whole organism

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to C38D4.7.

value: pooled male and female

value: late embryonic

value: 4 hour

value: ENCBS457NBD at ENCODE; https://www.encodeproject.org/ENCBS457NBD/


title: 427_L1

description:
extraction 009 sample 28_L1 pool 07_06
DGRP427 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: TF ChIP-seq from whole organism (ENCLB536TNG)

description:
https://www.encodeproject.org/experiments/ENCSR274AAR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG8924-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR274AAR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR857ANW
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB536TNG
size range: 200-800

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS706EKA at ENCODE; https://www.encodeproject.org/ENCBS706EKA/


title: 362_L2

description:
extraction 060 sample 22_L2 pool 06_18
DGRP362 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 (ENCLB390RBM)

description:
https://www.encodeproject.org/experiments/ENCSR626LGN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic worms expressing C38D4.7-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR626LGN
assay title: TF ChIP-seq
assembly: ce11
possible controls: ENCSR100DIV
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB390RBM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organisms

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

value: ENCBS575GCI at ENCODE; https://www.encodeproject.org/ENCBS575GCI/


title: Control ChIP-seq from whole organism (ENCLB716BJP)

description:
https://www.encodeproject.org/experiments/ENCSR925LDI/
***************
biological replicate number: 2
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ceh-27-eGFP fusion proteins.
experiment encode accession: ENCSR925LDI
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB716BJP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: not applicable

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

value: pooled male and female

value: young adult

value: 73 hour

value: L1 larva starved after bleaching

value: ENCBS253FYV at ENCODE; https://www.encodeproject.org/ENCBS253FYV/


title: 804_L2

description:
extraction 081 sample 42_L2 pool 08_06
DGRP804 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv


title: 535_L1

description:
extraction 098 sample 33_L1 pool 07_16
DGRP535 Larvae Biol Rep 1
gene expression count table form_for GEO submission.csv


title: Control ChIP-seq from whole organism (ENCLB737RXT)

description:
https://www.encodeproject.org/experiments/ENCSR743RDE/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing lin-11-eGFP fusion proteins.
experiment encode accession: ENCSR743RDE
assay title: Control ChIP-seq
assembly: ce11
encode release date: 2018-03-01
lab: Kevin White, UChicago
library encode accession: ENCLB737RXT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Caenorhabditis elegans strain OP62 (unc-119(ed3) III; wgIs62) mixed sex late embryo (4.25 hours) using egg bleaching insertion targeting C. elegans lin-11

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

value: late embryonic

value: 4.25 hour

value: ENCBS429ESJ at ENCODE; https://www.encodeproject.org/ENCBS429ESJ/


title: 911_L2

description:
extraction 087 sample 50_L2 pool 06_07
DGRP911 Larvae Biol Rep 2
gene expression count table form_for GEO submission.csv

value: whole body

value: Larvae