| Antibodies |
|
|
|
| Primary: anti-RNA Polymerase II (pSer 5) |
Active Motif |
Cat. 61085; RRID: AB_2687451 |
| Primary: anti-RNA Polymerase II (pSer 2) |
Active Motif |
Cat. 61083; RRID: AB_2687450 |
| Primary: anti-phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) |
Cell Signaling |
Cat. 9101; RRID: AB_331646 |
| Secondary: goat anti-rat 488 |
Molecular Probes |
Cat. A11006; RRID: AB_141373 |
| Secondary: donkey anti-rabbit 594 |
Invitrogen |
Cat. A21207; RRID: AB_141637 |
|
| Bacterial and virus strains |
|
|
|
|
pgl-1 RNAi |
Vidal RNAi Library |
Plate 10022: C4 |
|
cyn-7 RNAi |
Vidal RNAi Library |
Plate 11052: C11 |
|
mpk-1 RNAi (pSA001) |
Arur Lab |
|
|
spn-4 RNAi |
Vidal RNAi Library |
Plate 11069: E9 |
|
puf-3 RNAi |
Vidal RNAi Library |
Plate 10027: A4 |
|
rme-2 RNAi |
Vidal RNAi Library |
Plate 10022: B9 |
|
gfat-2 RNAi |
Vidal RNAi Library |
Plate 10028: B8 |
|
pygl-1 RNAi |
Vidal RNAi Library |
Plate 10028: G7 |
|
bet-1 RNAi |
Vidal RNAi Library |
Plate 11023: D10 |
|
pqn-80 RNAi |
Vidal RNAi Library |
Plate 11206: H7 |
|
alg-5 RNAi |
Ahringer RNAi Library |
Plate 1–5-1: B01 |
|
ule-5 RNAi |
Vidal RNAi Library |
Plate 10008: E8 |
| ZK813.1 RNAi |
Vidal RNAi Library |
Plate 11207: F7 |
| ZC373.2 RNAi |
Ahringer RNAi Library |
Plate 6–4-4: H03 |
| F17E9.4 RNAi |
Vidal RNAi Library |
Plate 11040: B11 |
| D1054.10 RNAi |
Vidal RNAi Library |
Plate 10192: H11 |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| RNase inhibitor |
Takara Bio |
Cat. 2313B |
|
| Critical commercial assays |
|
|
|
| SMART-seq v4 3’ DE Kit |
Takara Bio |
Cat. 635040 |
|
| Deposited data |
|
|
|
| Raw and analyzed RNAseq data |
This paper |
GEO: GSE209988
|
|
| Experimental models: Organisms/strains |
|
|
|
| C. elegans: Strain LW4502: rba-1(jj188 [GFP::3xFLAG::RBA-1]) |
Gift from Kelly Jun Liu |
WB Strain: LW4502 |
| C. elegans: Strain BS553: fog-2(oz40) |
CGC |
WB Strain: BS553; WormBase: WBStrain00003934 |
| C. elegans: Strain AUM1870: ZK813.1(viz166) |
This study |
|
|
| Oligonucleotides |
|
|
|
| HCR FISH Probes |
Molecular Instruments |
See Table S4
|
| CRISPR-related oligos |
This Study, Paix et al.57
|
See Table S5
|
|
| Software and algorithms |
|
|
|
| ImageJ |
Schneider et al.58
|
https://imagej.nih.gov/ij/
|
| Cutadapt v1.18 |
Martin59
|
https://cutadapt.readthedocs.io/en/v1.18/
|
| FastQC v0.11.5 |
Babraham Bioinformatics |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
| STAR aligner v2.4.0 |
Dobin et al.60
|
https://github.com/alexdobin/STAR
|
| featureCounts v1.5.3 |
Liao et al.61
|
http://subread.sourceforge.net/
|
| DESeq2 |
Love et al.26
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| Velocyto |
La Manno et al.32
|
http://velocyto.org/
|
| Imaris |
Oxford Instruments |
https://imaris.oxinst.com/
|
| Adobe Photoshop |
Adobe |
https://www.adobe.com/products/photoshop/
|
|
| Other |
|
|
|
| RNAseq analysis and figure code |
This paper |
https://doi.org/10.5281/zenodo.7847503
|
