Antibodies |
Rabbit monoclonal anti-Snail |
Cell Signaling Technology |
Cat#3879S; RRID: AB_2255011 |
Mouse monoclonal anti-Tubulin (clone DM1A) |
Sigma-Aldrich |
Cat#T9026; RRID: AB_477593 |
Rabbit polyclonal anti-BMAL1 |
This paper |
N/A |
Bacterial and virus strains |
pAAV-hSyn-DIO-hM3D(Gq)-mCherry |
Krashes et al.1
|
Addgene AAV5; 44361-AAV5 |
AAV5-EF1a-DIO-hChR2(H134R)-EYFP |
Hope Center Viral Vectors Core |
N/A |
Cowpox virus Brighton Red |
BEI Resources |
NR-88 |
Zika-SMGC-1, GENBANK: KX266255
|
Isolated from patient (Wang et al.2) |
N/A |
Staphylococcus aureus
|
ATCC |
ATCC 29213 |
Streptococcus pyogenes: M1 serotype strain: strain SF370; M1 GAS |
ATCC |
ATCC 700294 |
Biological samples |
Healthy adult BA9 brain tissue |
University of Maryland Brain & Tissue Bank; http://medschool.umaryland.edu/btbank/
|
Cat#UMB1455 |
Human hippocampal brain blocks |
New York Brain Bank |
http://nybb.hs.columbia.edu/
|
Patient-derived xenografts (PDX) |
Children’s Oncology Group Cell Culture and Xenograft Repository |
http://cogcell.org/
|
Chemicals, peptides, and recombinant proteins |
MK-2206 AKT inhibitor |
Selleck Chemicals |
S1078; CAS: 1032350–13-2 |
SB-505124 |
Sigma-Aldrich |
S4696; CAS: 694433–59-5 (free base) |
Picrotoxin |
Sigma-Aldrich |
P1675; CAS: 124–87-8 |
Human TGF-β |
R&D |
240-B; GenPept: P01137
|
Activated S6K1 |
Millipore |
Cat#14–486 |
GST-BMAL1 |
Novus |
Cat#H00000406-P01 |
Critical commercial assays |
EasyTag EXPRESS 35S Protein Labeling Kit |
PerkinElmer |
NEG772014MC |
CaspaseGlo 3/7 |
Promega |
G8090 |
TruSeq ChIP Sample Prep Kit |
Illumina |
IP-202–1012 |
Deposited data |
Raw and analyzed data |
This paper |
GEO: GSE63473
|
B-RAF RBD (apo) structure |
This paper |
PDB: 5J17 |
Human reference genome NCBI build 37, GRCh37 |
Genome Reference Consortium |
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
|
Nanog STILT inference |
This paper; Mendeley Data |
http://dx.doi.org/10.17632/wx6s4mj7s8.2
|
Affinity-based mass spectrometry performed with 57 genes |
This paper; Mendeley Data |
Table S8; http://dx.doi.org/10.17632/5hvpvspw82.1
|
Experimental models: Cell lines |
Hamster: CHO cells |
ATCC |
CRL-11268 |
D. melanogaster: Cell line S2: S2-DRSC |
Laboratory of Norbert Perrimon |
FlyBase: FBtc0000181 |
Human: Passage 40 H9 ES cells |
MSKCC stem cell core facility |
N/A |
Human: HUES 8 hESC line (NIH approval number NIHhESC-09–0021) |
HSCI iPS Core |
hES Cell Line: HUES-8 |
Experimental models: Organisms/strains |
C. elegans: Strain BC4011: srl-1(s2500) II; dpy-18(e364) III; unc-46(e177)rol-3(s1040) V. |
Caenorhabditis Genetics Center |
WB Strain: BC4011; WormBase: WBVar00241916 |
D. melanogaster: RNAi of Sxl: y[1] sc[*] v[1]; P{TRiP.HMS00609}attP2 |
Bloomington Drosophila Stock Center |
BDSC:34393; FlyBase: FBtp0064874 |
S. cerevisiae: Strain background: W303 |
ATCC |
ATTC: 208353 |
Mouse: R6/2: B6CBA-Tg(HDexon1)62Gpb/3J |
The Jackson Laboratory |
JAX: 006494 |
Mouse: OXTRfl/fl: B6.129(SJL)-Oxtrtm1.1Wsy/J |
The Jackson Laboratory |
RRID: IMSR_JAX:008471 |
Zebrafish: Tg(Shha:GFP)t10: t10Tg |
Neumann and Nuesslein-Volhard3
|
ZFIN: ZDB-GENO-060207–1 |
Arabidopsis: 35S::PIF4-YFP, BZR1-CFP |
Wang et al.4
|
N/A |
Arabidopsis: JYB1021.2: pS24(AT5G58010)::cS24:GFP(-G):NOS #1 |
NASC |
NASC ID: N70450
|
Oligonucleotides |
siRNA targeting sequence: PIP5K I alpha #1: ACACAGUACUCAGUUGAUA |
This paper |
N/A |
Primers for XX, see Table SX |
This paper |
N/A |
Primer: GFP/YFP/CFP Forward: GCACGACTTCTTCAAGTCCGCCATGCC |
This paper |
N/A |
Morpholino: MO-pax2a GGTCTGCTTTGCAGTGAATATCCAT |
Gene Tools |
ZFIN: ZDB-MRPHLNO-061106–5 |
ACTB (hs01060665_g1) |
Life Technologies |
Cat#4331182 |
RNA sequence: hnRNPA1_ligand: UAGGGACUUAGGGUUCUCUCUAGGGACUUAGGGUUCUCUCUAGGGA |
This paper |
N/A |
Recombinant DNA |
pLVX-Tight-Puro (TetOn) |
Clonetech |
Cat#632162 |
Plasmid: GFP-Nito |
This paper |
N/A |
cDNA GH111110
|
Drosophila Genomics Resource Center |
DGRC:5666; FlyBase:FBcl0130415 |
AAV2/1-hsyn-GCaMP6- WPRE |
Chen et al.5
|
N/A |
Mouse raptor: pLKO mouse shRNA 1 raptor |
Thoreen et al.6
|
Addgene Plasmid #21339 |
Software and algorithms |
ImageJ |
Schneider et al.7
|
https://imagej.nih.gov/ij/
|
Bowtie2 |
Langmead and Salzberg8
|
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
Samtools |
Li et al.9
|
http://samtools.sourceforge.net/
|
Weighted Maximal Information Component Analysis v0.9 |
Rau et al.10
|
https://github.com/ChristophRau/wMICA
|
ICS algorithm |
This paper; Mendeley Data |
http://dx.doi.org/10.17632/5hvpvspw82.1
|
Other |
Sequence data, analyses, and resources related to the ultra-deep sequencing of the AML31 tumor, relapse, and matched normal |
This paper |
http://aml31.genome.wustl.edu
|
Resource website for the AML31 publication |
This paper |
https://github.com/chrisamiller/aml31SuppSite
|