|
Bacterial and virus strains
|
| MAX Efficiency DH5a Competent Cells |
Life Technologies |
18258012 |
|
|
|
|
Chemicals, peptides, and recombinant proteins
|
| [γ-32P]ATP |
PerkinElmer |
NEG035C001MC |
| TRI Reagent Solution |
Life Technologies |
AM9738 |
| Chloroform |
J.T. Baker Analytical |
9180-01 |
| Yeast tRNA |
Life Technologies |
15401011 |
| Superase-In |
Life Technologies |
AM2696 |
| GE Healthcare Hybond-NX Membrane |
VWR |
95038-412 |
| ULTRAhyb-Oligo hybridization buffer |
Life Technologies |
AM8663 |
| EDC (N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide) |
Thermo Scientific |
22891 |
| 1-methylimidazole |
Sigma Aldrich |
M50834 |
| Spin-X Centrifuge Tube Filters |
Corning |
CLS8162 |
| Puromycin dihydrochloride |
Life Technologies |
A1113803 |
| Halocarbon oil 700 |
Sigma Aldrich |
H8898 |
| BSA |
Research Products International |
A30075 |
| Triton X-100 |
Sigma Aldrich |
T8787 |
| DAPI |
Sigma Aldrich |
10236276001 |
| Vectashield |
Vector Laboraties |
H-1000 |
| Methanol |
Fischer chemical |
A456-4 |
| Heptane |
Sigma Aldrich |
246654 |
| Hoyer’s medium |
Stern and Sucena, 2011
|
N/A |
| Lactic Acid |
Sigma Aldrich |
252476 |
| FLAG-GST-TNRC6B |
Hauptmann et al., 2015
|
N/A |
| Quickextract |
Lucigen |
QE09050 |
| beta-Mercaptoethanol |
Sigma Aldrich |
M6250 |
| cOmplete, Mini, EDTA-free Protease Inhibitor |
Roche diagnostics |
11836170001 |
| NuPAGE LDS loading buffer |
Life Technologies |
NP0007 |
| Restore PLUS Western Blot Stripping Buffer |
Life Technologies |
46430 |
| Anti-Ago1 antibody |
Abcam |
ab5070 |
| Anti-β-Actin antibody |
Santa Cruz Biotechnology |
sc-47778 |
| Anti-HA antibody |
Cell signaling technologies |
3724 |
| ECL Anti-Rabbit IgG, HRP-linked whole antibody |
GE Healthcare |
# NA934 |
| ECL Anti-Mouse IgG, HRP-linked whole antibody |
GE Healthcare |
# NA931 |
|
|
|
|
Critical commercial assays
|
| NEXTflex stranded RNA-seq kit |
Bioo Scientific |
5138-10 |
| Effectene |
Qiagen |
301425 |
| QuikChange Lightning Multi Site-Directed Mutagenesis |
Agilent |
210515 |
| KAPA HiFi HotStart ReadyMix |
Roche |
KK2601 |
| Micro Bio-Spin P30 gell columns |
Bio-Rad |
7326250 |
| T4 PNK |
New England Biolabs |
101228-172 |
| T4 RNL2 truncated K227Q |
New England Biolabs |
MO239 |
| T4 RNL1 |
New England Biolabs |
MO204 |
| KAPA mRNA Hyperprep kit |
Roche Diagnostics |
8098115702 |
| Turbo DNase |
Thermo Fisher Scientific |
AM2238 |
| NuPAGE Bis-Tris 4–12% gel |
Life Technologies |
NP0322BOX |
| MES running buffer |
Life Technologies |
NP0002 |
| PVDF membrane |
Life Technologies |
LC2002 |
| XCell SureLock Mini-Cell |
Thermo Fisher Scientific |
EI0001 |
| Mini Gel Tank and Blot Module |
Thermo Fisher Scientific |
A25977 |
| SuperSignal West Femto Maximum Sensitivity Substrate Detection Reagent |
Thermo Fisher Scientific |
PI34095 |
|
|
|
|
Deposited data
|
| RNA-seq |
This paper |
GEO: GSE196837
|
| Small-RNA sequencing |
This paper |
GEO: GSE196837
|
| Imaging data |
This paper |
DOI: 10.17632/p6sgkky8y3.1
|
|
|
|
|
Experimental models: Cell lines
|
| Drosophila: WT clonal S2 cells |
Shi et. al, 2020
|
N/A |
| Drosophila: dora clonal S2 cells |
Shi et. al, 2020
|
N/A |
| Drosophila: ago1 clonal S2 cells |
This paper |
N/A |
| Drosophila: h clonal S2 cells |
This paper |
N/A |
| Drosophila: kah clonal S2 cells |
This paper |
N/A |
| Drosophila: mus308 clonal S2 cells |
This paper |
N/A |
| Drosophila: wgn clonal S2 cells |
This paper |
N/A |
| Drosophila: zfh1 clonal S2 cells |
This paper |
N/A |
| Drosophila: Rfx clonal S2 cells |
This paper |
N/A |
| Drosophila: CG11248 clonal S2 cells |
This paper |
N/A |
| Drosophila: Sam clonal S2 cells |
This paper |
N/A |
| Drosophila: mus81 clonal S2 cells |
This paper |
N/A |
| Drosophila: wnd clonal S2 cells |
This paper |
N/A |
|
|
|
|
Experimental models: Organisms/strains
|
| Fly: dora[A] line |
Bloomington Drosophila Stock Center (BDSC) |
52333 |
| Fly: dora[B] line |
BDSC |
52334 |
| Fly: Dp(1;3)DC353 |
BDSC |
30763 |
| Fly: FM7a |
BDSC |
35522 |
| Fly: vasa-Cas9 |
BDSC |
51323 |
| Fly: Tm3/Tm6 |
Gift from the Orr-Weaver lab |
N/A |
| Fly: OreR |
Gift from the Orr-Weaver lab |
N/A |
| Fly: CR43432 Line 1 (WT and mutant pair) |
This paper |
N/A |
| Fly: CR43432 Line 2 (WT and mutant pair) |
This paper |
N/A |
| Fly: miR-309 cluster deletion line |
BDSC |
58922 |
|
|
|
|
Oligonucleotides
|
| See Table S6 |
This paper |
N/A |
| miR-7 LNA northern probe |
Qiagen |
YD00610687-BEA |
|
|
|
|
Recombinant DNA
|
| pAc-sgRNA-Cas9 |
Addgene |
49330 |
| pU6-2-BbsI-gRNA |
Drosophila Genomics Resource Center |
1363 |
|
dora WT rescue construct |
This paper |
N/A |
|
dora[A] rescue construct |
This paper |
N/A |
|
dora[B] rescue construct |
This paper |
N/A |
| HA-dora WT rescue construct |
This paper |
N/A |
| HA-dora[A] rescue construct |
This paper |
N/A |
| HA-dora[B] rescue construct |
This paper |
N/A |
| HA-GFP rescue construct |
This paper |
N/A |
| pAc-sgRNA-Cas9.scr_1 |
Shi et al., 2020
|
N/A |
| pAc-sgRNA-Cas9.scr_2 |
Shi et al., 2020
|
N/A |
| pAc-sgRNA-Cas9.scr_3 |
Shi et al., 2020
|
N/A |
| pAc-sgRNA-Cas9.dora_1 |
Shi et al., 2020
|
N/A |
| pAc-sgRNA-Cas9.dora_2 |
Shi et al., 2020
|
N/A |
| pAc-sgRNA-Cas9.dora_3 |
Shi et al., 2020
|
N/A |
| pAc-sgRNA-Cas9.ago1_1 |
This paper |
N/A |
| pAc-sgRNA-Cas9.ago1_2 |
This paper |
N/A |
| pAc-sgRNA-Cas9.h_1 |
This paper |
N/A |
| pAc-sgRNA-Cas9.h_2 |
This paper |
N/A |
| pAc-sgRNA-Cas9.kah_1 |
This paper |
N/A |
| pAc-sgRNA-Cas9.kah_2 |
This paper |
N/A |
| pAc-sgRNA-Cas9.wgn_1 |
This paper |
N/A |
| pAc-sgRNA-Cas9.wgn_2 |
This paper |
N/A |
| pAc-sgRNA-Cas9.zfh1_1 |
This paper |
N/A |
| pAc-sgRNA-Cas9.Rfx_1 |
This paper |
N/A |
| pAc-sgRNA-Cas9.CG11248_1 |
This paper |
N/A |
| pAc-sgRNA-Cas9.CG11248_2 |
This paper |
N/A |
| pAc-sgRNA-Cas9.mus81_1 |
This paper |
N/A |
| pAc-sgRNA-Cas9.mus81_2 |
This paper |
N/A |
| pAc-sgRNA-Cas9.Sam_1 |
This paper |
N/A |
| pAc-sgRNA-Cas9.Sam_2 |
This paper |
N/A |
| pAc-sgRNA-Cas9.wnd_1 |
This paper |
N/A |
| pAc-sgRNA-Cas9.mus308_1 |
This paper |
N/A |
| pU6-2-BbsI-gRNA.CR43432 |
This paper |
N/A |
|
|
|
|
Software and algorithms
|
| ImageQuant TL |
GE Healthcare |
v8.1.0.0 |
| Fiji (v2.0.0) |
Schindelin et al., 2012
|
https://imagej.net/software/fiji/
|
| DESeq2 |
Love et al., 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| Beta-uniform mixutre modeling |
Pounds et al., 2003
|
|
| Benjamini and Hochberg correction |
Benjamini and Hochberg, 1995
|
Benjamini and Hochberg correction |
| STAR RNA-seq aligner |
Dobin et al., 2013
|
https://github.com/alexdobin/STAR
|
| Htseq-count |
Anders et al., 2015
|
https://htseq.readthedocs.io/en/release_0.9.1/
|
| TargetScanFly (Release 7.2) |
Agarwal et al., 2018
|
http://www.targetscan.org/fly_72/
|
| GSEAPreranked (v 4.1.0) |
Mootha et al., 2003 and Subramanian et al., 2005
|
https://www.gsea-msigdb.org
|
| R (v3.5.1) |
The R Foundation |
https://www.r-project.org
|
| Vienna RNA Package 2.0 |
Lorenz et al., 2011
|
https://www.tbi.univie.ac.at/RNA/
|
| Python (v3.6.9) |
Python Software Foundation |
https://www.python.org
|
| Trigger search pipeline |
This paper |
DOI: 10.5281/zenodo.6991124
|
|
|
|
|
Other
|
| Small-RNA sequencing protocol, step-by-step |
Fang and Bartel, 2015 |
http://bartellab.wi.mit.edu/protocols.html
|
| Small-RNA blot protocol, step-by-step |
Fang and Bartel, 2015 |
http://bartellab.wi.mit.edu/protocols.html
|
| CRISPR guide cloning protocol, step-by-step |
Bassett et al., 2014
|
N/A |
| Immunoprecipitation of Ago1 using FLAG-GST-Tnrc6b protocol, step-by-step |
Hauptmann et al., 2015; Kingston and Bartel 2021
|
N/A |
|
|
|
