| Antibodies |
| Mouse monoclonal anti-hnRNP U (SAF-A) |
Abcam |
Cat# ab10297; RRID: AB_297037 |
| Rabbit polyclonal anti-hnRNP U (SAF-A) |
Abcam |
Cat# ab20666; RRID: AB_732983 |
| Goat polyclonal anti-MATR3 |
Santa Cruz |
Cat# sc-55723; RRID: AB_2281755 |
| Goat polyclonal anti-LMNB1 |
Santa Cruz |
Cat# sc-6217; RRID: AB_648158 |
| Mouse monoclonal anti-RNA Polymerase II (H5) |
Covance |
Cat# MMS-129R-200; RRID: AB_10143905 |
| Rabbit polyclonal anti-LMNA |
Cell Signaling |
Cat# 2032; RRID: AB_2136278 |
| Rabbit polyclonal anti-Histone H3 (pan antibody) |
Millipore |
Cat# 07-690; RRID: AB_417398 |
| Bacterial and Virus Strains |
| Biological Samples |
| Chemicals, Peptides, and Recombinant Proteins |
| Actinomycin D |
Sigma |
A1410 |
| 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside |
Sigma |
D1916 |
| BAPTA-AM |
Abcam |
ab120503 |
| C0T-1 DNA (human) |
Roche |
11581074001 |
| DNase I recombinant, RNase free |
Roche |
04716728001 |
| Turbo™ DNase |
Invitrogen |
AM2238 |
| RNase A |
Thermo Scientific |
EN0531 |
| Critical Commercial Assays |
| KAPA strand-specific RNA-seq preparation with ribosome depletion |
KAPA |
KK8483 |
| NEBNext® multiplex oligos for Illumina |
NEB |
E7335S |
| KAPA Hyper DNA library preparation kits |
KAPA |
KK8501 |
| iTaq Universal SYBR Green Supermix |
BIO-RAD |
1725120 |
| Deposited Data |
| RNA-seq and SAR-seq experiments |
This paper |
GEO: GSE124979
|
| RefSeq Select protein coding transcripts |
NCBI |
https://genome-preview.soe.ucsc.edu/cgi-bin/hgTables?
|
| Ensembl reference transcripts (build 82) |
Ensembl |
https://grch37.ensembl.org/
|
| DNase I digested deproteinized genomic DNA-seq |
Lazarovici et al., 2013
|
GEO: SRA068503 |
| Human reference genome NCBI build 37, GRCh37 |
Genome Reference Consortium |
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
|
| Experimental Models: Cell Lines |
| TIG-1 untransformed female human fetal lung fibroblasts |
Coriell |
AG06173 |
| mouse-human (chr4) somatic cell hybrids |
Coriell |
GM11684 |
| Experimental Models: Organisms/Strains |
| Oligonucleotides |
| See Table S1 for oligonucleotides used in this study. |
|
|
| Recombinant DNA |
| XIST genomic DNA fragment G1A plasmid |
Addgene |
Plasmid #24690 |
|
|
|
| Software and Algorithms |
| ImageJ |
Schneider et al., 2012
|
https://imagej.nih.gov/ij/
|
| Bowtie2 |
Langmead and Salzberg, 2012
|
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| Samtools |
Li et al., 2009
|
http://samtools.sourceforge.net/
|
| Tophat2 |
Kim et al., 2103 |
https://ccb.jhu.edu/software/tophat/index.shtml
|
| Cufflinks |
Trapnell et al., 2012
|
http://cole-trapnell-lab.github.io/cufflinks/
|
| RSEM |
Li and Dewey, 2011
|
http://deweylab.biostat.wisc.edu/html
|
| IRFinder |
Middleton et al., 2017
|
https://github.com/williamritchie/IRFinder
|
| deepTools |
Ramirez et al., 2016
|
https://deeptools.readthedocs.io/en/develop/
|
| Genomic Association Tester |
Heger et al., 2013
|
https://gat.readthedocs.io/en/latest/
|
| Fastx Toolkit |
Hannon Lab |
http://hannonlab.cshl.edu/fastx_toolkit/
|
| R |
R Core Team |
https://www.r-project.org/
|
| ggplot2 |
H. Wickham, 2009
|
http://ggplot2.org
|
| Other |
|
|
|
