|
Antibodies
|
| guinea pig anti Rhino – (1:500) |
(Klattenhoff et al., 2009) |
n/a |
| mouse anti nuclear pore complex, MAb414 clone – (1:1000) |
Covance MAb414 clone |
MMS-120R |
| rat IgM anti Vasa – (1:250) |
Developmental Studies Hybridoma bank |
ID: AB_760351 |
| rabbit anti Ago3 – (1:3000) |
MAb Technologies, Inc. |
Product # Ago3–3 |
| rabbit anti Aub – (1:500) |
(Klattenhoff et al., 2009) |
n/a |
| rabbit anti Armi-CT (1:500) |
(Cook, Koppetsch, Wu, & Theurkauf, 2004) |
n/a |
| Anti Digoxigenin POD |
Roche |
Cat# 11207733910 |
|
Chemicals, Peptides, and Recombinant Proteins
|
| Superscript III |
ThermoFisher Scientific |
Cat# 18080–085 |
| RNase OUT |
ThermoFisher Scientific |
Cat# 10777–019 |
| TURBO DNase |
ThermoFisher Scientific |
Cat# AM2238 |
| RNaseH |
ThermoFisher Scientific |
Cat# 18021–071 |
| T4 RNA Ligase |
ThermoFisher Scientific |
Cat# AM2141 |
| dNTP Set (100 mM) |
ThermoFisher Scientific |
Cat# 10297018 |
| dUTP Solution (100 mM) |
ThermoFisher Scientific |
Cat# R0133 |
| dNTP mix |
NEB |
Cat# N0447L |
| DNA polymerase I |
NEB |
Cat# M0209S |
| T4 DNA polymerase |
NEB |
Cat# M0203L |
| Klenow DNA polymerase |
NEB |
Cat# M0210S |
| T4 PNK |
NEB |
Cat# M0201L |
| Klenow 3ʹ to 5ʹ exo |
NEB |
Cat# M0212L |
| UDG |
NEB |
Cat# M0280S |
| Phusion Polymerase |
NEB |
Cat# M0530S |
| T4 RNA Ligase 2, truncated |
NEB |
Cat# M0242L |
| 50% PEG8000 |
NEB |
Cat# B1004S |
| T4 DNA ligase |
Enzymatics Inc. |
Cat# L6030-HC-L |
| Hybridase™ Thermostable RNase H |
Biosearch Technologies |
Cat# H39500
|
| 16% formaldehyde |
Ted Pella Inc |
Cat# 18505 |
| 8% glutaraldehyde solution |
Millipore Sigma |
Cat# G7526–10ML |
|
Critical Commercial Assays
|
| mirVANA™ miRNA isolation kit |
ThermoFisher Scientific |
Cat# AM1560 |
| Direct-zol™ RNA MicroPrep |
Zymo Research |
Cat# R2060 |
| RiboZero™ Magnetic Kit (Human/Mouse/Rat) |
Illumina |
(Cat# MRZG12324) |
| RNA Clean & Concentrator-5 |
Zymo Research |
Cat# R1015 |
| Agencourt AMPure XP |
Beckman Coulter |
Cat# A63880 |
| TSA Cyanine 3 System |
Akoya Biosciences |
Cat# NEL704A001KT |
|
Deposited Data
|
| High Throughput sequencing |
This Study |
|
| Small RNAseq for uap56sz15/28 Rep 1 |
G. Zhang et al. (2021)
|
SRA: SRR10541139
|
| Small RNAseq for uap56sz15/28 Rep 2 |
G. Zhang et al. (2021)
|
SRA: SRR10541140
|
| Small RNAseq for w1 rep1 for cluster definition |
G. Zhang et al. (2018)
|
SRA: SRR7408119 |
| Samll RNAseq for w1 rep2 for Cluster definition |
G. Zhang et al. (2021)
|
SRA: SRR10541189
|
|
Experimental models: Organisms/strains
|
|
D. melanogaster/w1
|
William Theurkauf lab |
n/a |
|
D. melanogaster/Oregon-R |
William Theurkauf lab |
n/a |
|
D. melanogaster/mnkp6
|
(Brodsky et al., 2004) |
n/a |
|
D. melanogaster/rhi2(rhi02086)
|
(Klattenhoff et al., 2009) |
Bloomington stock center – stock # 12226 |
|
D. melanogaster/rhiKG (rhiKG00910)
|
(Klattenhoff et al., 2009) |
Bloomington stock center – stock # 13161 |
|
D. melanogaster/uap5628
|
(F. Zhang et al., 2012) |
n/a |
|
D. melanogaster/uap56sz15
|
(F. Zhang et al., 2012) |
n/a |
|
D. melanogaster/thoc7d (thoc7d05792)
|
(G. Zhang et al., 2018) |
Harvard Exelixis stock collection - stock# d05792 |
|
D. melanogaster/thoc7Df (DF(3L)BSC128)
|
(G. Zhang et al., 2018) |
Bloomington Drosophila Stock Center – Stock # 9293 |
|
D. melanogaster/vasRG53
|
(Schupbach & Wieschaus, 1991) |
n/a |
|
D. melanogaster/vasPH (vasPH165)
|
(Styhler, Nakamura, Swan, Suter, & Lasko, 1998) |
n/a |
|
D. melanogaster/vasPD (vas1) |
(Styhler et al., 1998) |
n/a |
|
D. melanogaster/aubHN
|
(Schupbach & Wieschaus, 1991) |
n/a |
|
D. melanogaster/aubQC
|
(Schupbach & Wieschaus, 1991) |
n/a |
|
D. melanogaster/ago3t2
|
(Li et al., 2009) |
Bloomington stock center – stock #28269 |
|
D. melanogaster/ago3t3
|
(Li et al., 2009) |
Bloomington stock center – stock #28270 |
|
D. melanogaster/armi1
|
(Cook et al., 2004) |
n/a |
|
D. melanogaster/armi72.1
|
(Cook et al., 2004) |
n/a |
|
D. melanogaster/piwi02
|
(Lin & Spradling, 1997) |
Bloomington stock center – stock #43319 |
|
D. melanogaster/piwiNLS
|
(Klenov et al., 2011) |
n/a |
|
Oligonucleotides
|
| Random primers |
ThermoFisher Scientific |
Cat# 48190011 |
|
Software and Algorithms
|
| RStudio |
|
https://www.rstudio.com/
|
| ImageJ |
|
https://imagej.nih.gov/ij/
|
| Inkscape |
|
https://inkscape.org
|
| Adobe Creative Suite 6 |
|
Adobe Systems Inc. |
| BEDTools |
(Langmead, Trapnell, Pop, & Salzberg, 2009) |
|
| piSet |
|
https://github.com/tianxiongbb/piSet
|
