Antibodies |
|
|
Anti- RNAPII |
Biolegend |
Cat# 664906; RRID:AB_2565554 |
Anti- Rad21 |
Schaaf et al., 2013 |
N/A |
Anti-Cap-H2 |
Li etal., 2015 |
N/A |
Anti-Slimb |
Brownlee et al., 2011 |
N/A |
Deposited Data |
|
|
CTL Hi-C |
Cubeñas-Potts et al., 2017 |
GSE80702 |
FLV Hi-C |
This study; Li et al., 2015
|
GSE63518 |
Rad21 KD Hi-C |
Li etal., 2015 |
GSE63518 |
Cap-H2 KD Hi-C |
Li etal., 2015 |
GSE63518 |
Slimb KD Hi-C |
This study |
GSE118756 |
RNAPII HiChIP |
This study |
GSE118756 |
RNAPII ChIA-PET |
Rowley et al., 2017 |
GSE89244 |
Rad21 HiChIP |
This study |
GSE118756 |
S2 Hi-C |
Wang et al., 2018 |
GSE101317 |
ATAC-seq |
Rowley et al., 2017 |
GSE89244 |
CTL Rad21 ChIP-seq |
This study; Li et al., 2015; Van Bortle et al., 2014
|
GSE54529; GSE63518
|
FLV Rad21 ChIP-seq |
This study |
GSE118756 |
CTL Cap-H2 ChIP-seq |
This study; Li et al., 2015; Van Bortle et al., 2014
|
GSE54529; GSE63518
|
FLV Cap-H2 ChIP-seq |
This study |
GSE118756 |
CTL RNAPII ChIP-seq |
This study; Li et al., 2015
|
GSE63518 |
FLV RNAPII ChIP-seq FLV |
Li etal., 2015 |
GSE63518 |
RNAPII ChIP-seq Rad21 KD |
This study |
GSE118756 |
RNAPII ChIP-seq Cap-H2 KD |
This study |
GSE118756 |
RNAPIISer2ph ChIP-seq in mouse sperm |
Yoon Hee Jung personal communication |
GSE116857 |
APBS ChIP-seq Datasets |
Cubeñas-Potts et al., 2017; Li et al., 2015; Van Bortle et al., 2014; Yang et al., 2013
|
GSE30740; |
|
GSE63518; |
|
|
GSE54529, |
|
|
GSE80702 |
Hi-C mouse sperm |
Jung et al., 2017 |
GSE79230 |
Experimental Models: Cell Lines |
|
|
D. melanogaster: Cell line Kc167 |
Drosophila Genomics Resource Center (DGRC) |
FlyBase: FBtc0000001 |
Software and Algorithms |
|
|
Juicebox |
Durand et al., 2016a |
http://aidenlab.org/juicebox/ |
Juicer |
Durand et al., 2016b |
http://aidenlab.org/juicer/ |
Chicago |
Cairns et al., 2016 |
http://regulatorygenomicsgroup.org/chicago |
ngsplot |
Shen et al., 2014 |
https://github.com/shenlab-sinai/ngsplot |
Bowtie2 |
Langmead et al., 2009 |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
MACS2 |
Zhang et al., 2008 |
https://github.com/taoliu/MACS |
MAnorm |
Shao et al., 2012 |
http://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm
|