|
| Antibodies |
|
| Rabbit polyclonal anti-Nucleolin |
Abcam |
Cat# ab22758; RRID:AB_776878 |
|
| Chemicals, peptides, and recombinant proteins |
|
| Doxycycline |
Sigma |
D9891 |
|
| Deposited data |
|
| SPRITE data |
Quinodoz et al.28
|
GEO:GSE151515
|
| Ribo-Depleted RNA RNA-seq data in mESC |
Sigova et al.31
|
GEO:GSM903663
|
| PolyA RNA-seq data in mESC |
This Study |
GEO: GSE211287
|
| GRO-seq data in mES cells |
Jonkers et al.32
|
GEO:GSE48895
|
|
| Experimental models: Cell lines |
|
| Mouse: pSM44 ES cell line |
This Study |
pSM44 (dox-inducible Xist) |
|
| Software and algorithms |
|
| SPRITE pipeline 2.0 (v0.2) |
This Study |
https://github.com/GuttmanLab/sprite2.0-pipeline
|
| Bowtie2 (v2.3.5) |
Langmead and Salzberg51
|
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| Hisat (v2.1.0) |
Kim et al.52
|
http://www.ccb.jhu.edu/software/hisat/index.shtml
|
| Samtools (v1.4) |
Li et al.53
|
http://samtools.sourceforge.net/
|
| Bedtools (v2.30.0) |
Quinlan and Hall54
|
https://bedtools.readthedocs.io/en/latest/
|
| Trim Galore! (v0.6.2) |
Felix Krueger (The Babraham Institute) |
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
|
| Subread (v2.0.3) |
Liao et al.55,56
|
http://subread.sourceforge.net/
|
| Cooler (v0.8.5) |
Abdennur and Mirny57
|
https://github.com/open2c/cooler
|
| Cooltools (v0.4.1) |
10.5281/zenodo.5214125
|
https://github.com/open2c/cooltools
|
| Scipy (v1.7.1) |
Virtanen et al.58
|
https://scipy.org/
|
