|
Antibodies
|
| Rat anti-Hpr1 |
(Rehwinkel et al., 2004) |
|
| Rabbit anti Piwi |
(Li et al., 2009a) |
|
| Rabbit anti Ago3 |
(Li et al., 2009a) |
|
| Rabbit anti Aub |
(Li et al., 2009a) |
|
| Rat IgM anti-Vasa |
DSHB |
|
| Mouse anti-Engrailed (4D9) |
DSHB |
|
| Rabbit anti H3K9me3 |
Abcam |
Cat# ab8898 |
| Rabbit anti H3K4me2 |
EMDMillipore |
Cat# 07–030 |
| Mouse Anti-α-Tubulin |
Sigma Aldrich |
Cat# T5168 |
| Rabbit anti-GFP |
ThermoFisher Scientific |
Cat# A11122 |
|
Chemicals, Peptides, and Recombinant Proteins
|
| 4-Thiouridine |
MilliporeSigma |
Cat# T4509 |
| Iodoacetamide |
MilliporeSigma |
Cat# I1149 |
| 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 |
| AccuPrime™ Pfx DNA Polymerase |
ThermoFisher Scientific |
Cat# 12344024 |
| TRIzol™ Reagent |
ThermoFisher Scientific |
Cat# 15596026 |
| UltraPure™ Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) |
ThermoFisher Scientific |
Cat# 15593031 |
| dNTP Set (100 mM) |
ThermoFisher Scientific |
Cat# 10297018 |
| dUTP Solution (100 mM) |
ThermoFisher Scientific |
Cat# R0133 |
| Grace's Insect Medium, unsupplemented |
ThermoFisher Scientific |
Cat# 11595030 |
| Hybridase |
Lucigen |
Cat# H39500
|
| 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 3’ to 5’ 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 |
| EDTA-free Protease Inhibitor Cocktail (Roche) |
Sigma |
Cat# 11873580001 |
| 16% formaldehyde |
Ted Pella Inc |
Cat# 18505 |
| Miracloth membrane (Calbiochem) |
EMDMillipore |
Cat# 475855 |
|
Critical Commercial Assays
|
| mirVANA™ miRNA isolation kit |
ThermoFisher Scientific |
Cat# AM1560 |
| RNeasy Mini Kit |
Qiagen |
Cat# 74104 |
| QuantiTect SYBR® Green PCR Kits |
Qiagen |
Cat# 204145 |
| Dynabeads® Protein G |
ThermoFisher Scientific |
Cat# 10004D |
| Dynabeads® Protein A |
ThermoFisher Scientific |
Cat# 10001D |
| RNA Clean & Concentrator-5 |
Zymo Research |
Cat# R1015 |
| In-Fusion® HD Cloning Plus |
Takara |
Cat# 638909 |
| Agencourt AMPure XP |
Beckman Coulter |
Cat# A63880 |
|
Deposited Data
|
| High throughput Sequencing |
This study |
PRJNA590287 |
| small RNAseq for thoc5[e00906]/thoc5[1]_rep1 |
(Zhang et al., 2018) |
SRR7686976 |
| small RNAseq for thoc5[e00906]/thoc5[1]_rep2 |
(Zhang et al., 2018) |
SRR7686977 |
| small RNAseq for w[1]_rep1 |
(Zhang et al., 2018) |
SRR7408119 |
| small RNAseq for thoc7[d05792]/Df(3L)BSC128 |
(Zhang et al., 2018) |
SRR7408136 |
| Small RNAseq of rhi mut ovary |
(Parhad et al., 2017) |
SRR5803097 |
| RNAseq for thoc5[e00906]/thoc5[1]_rep1 |
(Zhang et al., 2018) |
SRR7408102 |
| RNAseq for thoc7[d05792]/Df(3L)BSC128_rep2 |
|
SRR7408139 |
| input RNAseq from w[1]_rep1 |
(Zhang et al., 2018) |
SRR7408152 |
| input RNAseq from w[1]_rep2 |
(Zhang et al., 2018) |
SRR7408157 |
| Hpr1IP RNAseq from w[1]_rep1 |
(Zhang et al., 2018) |
SRR7408151 |
| Hpr1IPRNAseq from w[1]_rep2 |
(Zhang et al., 2018) |
SRR7408156 |
|
Experimental Models: Organisms/Strains
|
|
D. melanogaster/thoc7d05792
|
Harvard Exelixis stock collection |
Stock # d05792 |
|
D. melanogaster/Df(3L)BSC128 |
Bloomington Drosophila Stock Center |
Stock# 9293 |
|
D. melanogaster/thoc5e00906
|
Harvard Exelixis stock collection |
Stock# e00906 |
|
D. melanogaster/thoc51
|
(Moon et al., 2011) |
N.A. |
|
D. melanogaster/rhino2
|
(Klattenhoff et al., 2009) |
N.A. |
|
D. melanogaster/rhinoKG
|
(Klattenhoff et al., 2009) |
N.A. |
|
D. melanogaster/piwi2
|
Bloomington Drosophila Stock Center |
Stock# 43319 |
|
D. melanogaster/piwiNLS
|
(Klenov et al., 2011) |
N.A. |
|
D. melanogaster/panoramixM4
|
(Yu et al., 2015) |
N.A. |
|
D. melanogaster/Df(2R)BSC821 |
(Yu et al., 2015) |
Stock# 27582 |
|
D. melanogaster/ pUASp>lambdaN-HA-CG9754 [attP40]/CyO; tub>EGFP_5xBoxB_SV40 [attP2]/TM3, Ser;
|
VDRC Stock Center |
Stock# 313393 |
|
D. melanogaster/w1
|
William Theurkauf lab |
N.A. |
|
Oligonucleotides
|
| Random primers |
ThermoFisher Scientific |
Cat# 48190011 |
| Primers for qPCR, see Table S1
|
|
N.A. |
|
Software and Algorithms
|
|
| Prism 7 |
GraphPad Prism |
https://www.graphpad.com/
|
| Image Studio™ Lite |
LI-COR |
https://www.licor.com/bio/products/software/image_studio_lite/
|
| RStudio |
|
https://www.rstudio.com/
|
| ImageJ |
|
https://imagej.nih.gov/ij/
|
| UCSC Genome Browser |
(Kent et al., 2002) |
https://genome.ucsc.edu/cgi-bin/hgGateway
|
