| Gene (Danio rerio) |
Zebrafish Genome |
UCSC |
Zv10 |
|
| Antibody |
Anti-H2Aub1(rabbit monoclonal) |
Cell Signaling Technology |
Cat# 8240; RRID:AB_10891618
|
WB (1:1000)ChIP (1:100)IF (1:500) |
| Antibody |
Anti-rnf2(rabbit monoclonal) |
Cell Signaling Technology |
Cat# 5694; RRID:AB_10705604
|
(1:100) |
| Antibody |
Anti-H2A.Z(rabbit polyclonal) |
Active Motif |
Cat# 39113; RRID: AB_2615081
|
(5 μl) |
| Antibody |
Anti-H3K4me1(rabbit polyclonal) |
Active Motif |
Cat# 39297; RRID: AB_2615075
|
(10 μl) |
| Antibody |
Anti-aebp2(rabbit monoclonal) |
Cell Signaling Technology |
Cat# 14,129 S; RRID: AB_2798398
|
ChIP (1:100)IF (1:500) |
| Antibody |
Anti-H3K27me3(rabbit polyclonal) |
Active Motif |
Cat# 39155; RRID: AB_2561020
|
ChIP (5 μl)IF (1:500) |
| Antibody |
Anti-H3(mouse monoclonal) |
Active Motif |
Cat# 39763; RRID: AB_2650522
|
(1:2000) |
| Antibody |
Anti-Jarid2rabbit polyclonal) |
Novus |
Cat# NB100-2214; RRID:AB10000529
|
(5 μl) |
| Cell line (Danio melanogaster) |
Cell line S2: S2-DRSC |
ATCC |
Cat# CRL-1963 RRID:CVCL_Z232
|
|
| Chemical compound, drug |
PRT4165 |
Tocris |
Cat# 5047 |
|
| Commercial assay or kit |
NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina |
New England Biolabs |
Cat# E6240 |
. |
| Commercial assay or kit |
Illumina TruSeq Stranded mRNA Library Prep Kit |
Illumina |
Cat# RS-122–2101, RS-122–2102 |
|
| Software, algorithm |
Novoalign |
Novocraft |
RRID:SCR_014818
|
|
| Software, algorithm |
Samtools |
Li et al., 2009
|
RRID:SCR_002105
|
|
| Software, algorithm |
deepTools |
Ramírez et al., 2016
|
RRID:SCR_016366
|
|
| Software, algorithm |
MACS2 |
Zhang et al., 2008
|
RRID:SCR_013291
|
|
| Software, algorithm |
UCSC Exe Utilities |
UCSC Genome Browser |
http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads
|
|
| Software, algorithm |
IGV |
Thorvaldsdóttir et al., 2012
|
RRID:SCR_011793
|
|
| Software, algorithm |
DAVID |
Huang et al., 2009
|
https://david.ncifcrf.gov
|
|
| Software, algorithm |
R |
R Development Core Team, 2020
|
RRID:SCR_001905
|
|
| Software, algorithm |
R Studio |
RStudio Team, 2021
|
RRID:SCR_000432
|
|
| Software, algorithm |
Chipseekr |
Yu et al., 2015
|
https://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html
|
|
| Software, algorithm |
Bio-ToolBox |
Tim Parnell of the Huntsman Cancer Institute |
Parnell, 2021b; https://github.com/tjparnell/biotoolbox
|
|
| Software, algorithm |
Multi-Replica Macs ChIPSeq Wrapper |
Tim Parnell of the Huntsman Cancer Institute |
Parnell, 2021a; https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPSeq
|
|
| Software, algorithm |
HOMER |
Heinz et al., 2010
|
RRID:SCR_010881
|
|
| Software, algorithm |
STAR |
Dobin et al., 2013
|
RRID:SCR_015899
|
|
| Software, algorithm |
featureCounts |
Liao et al., 2013
|
RRID:SCR_012919
|
|
| Software, algorithm |
DESeq |
Anders and Huber, 2010
|
RRID:SCR_000154
|
|
