KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-Clock | LeSauter et al., 2012 | N/A |
| Rabbit anti-Clock | Abcam | Abcam Cat# ab3517; RRID: AB_303866 |
| Rabbit anti-Doublecortin | Abcam | Abcam Cat# ab18723; RRID: AB_732011 |
| Rat anti-CTIP2 | Abcam | Abcam Cat# ab18465; RRID: AB_10015215 |
| Rabbit anti-GluR1 | Abcam | Abcam Cat# ab31232; RRID: AB_2113447 |
| Rabbit anti-PSD95 | Abcam | Abcam Cat# ab18258; RRID: AB_444362 |
| Mouse anti-PSD95 | Abcam | Abcam Cat# ab2723; RRID: AB_303248 |
| Mouse anti-NeuN | Millipore | Millipore Cat# MAB377; RRID: AB_2298772 |
| Rabbit anti-BMAL1 | Millipore | Cat# MAB2298 |
| Goat anti-Brn-2 | Santa Cruz Biotechnology | Santa Cruz Biotechnology Cat# sc-6029; RRID: AB_2167385 |
| Mouse anti-Tubulin-β | Santa Cruz Biotechnology | Santa Cruz Biotechnology Cat# sc-51670; RRID: AB_630408 |
| Rabbit anti-CRY | Alpha Diagnostic International | Alpha Diagnostic International Cat# CRY11-A; RRID: AB_1614505 |
| Rabbit anti-PER | Alpha Diagnostic International | Alpha Diagnostic International Cat# PER11-A; RRID: AB_1620949 |
| Pig anti-Vglut1 | Synaptic Systems | Synaptic Systems Cat# 135 304; RRID: AB_887878 |
| Mouse anti-Synapsin 1 | Synaptic Systems | Synaptic Systems Cat# 106 011; RRID: AB_2619772 |
| Mouse anti-VGAT | Synaptic Systems | Synaptic Systems Cat# 131 011; RRID: AB_887872 |
| Mouse anti-Syt2 | Developmental Studies Hybridoma Bank | DSHB Cat# znp-1; RRID: AB_2315626 |
| Mouse anti-parvalbumin | Sigma-Aldrich | Sigma-Aldrich Cat# P3088; RRID: AB_477329 |
| Mouse anti-Calbindin | SWANT | Swant Cat# 300; RRID: AB_10000347 |
| Alexa 488-conjugated goat anti-rabbit IgG (H+L) | Thermo Fisher Scientific | Cat# A11036 Thermo Fisher Scientific Cat# A32731; RRID: AB_2633280 |
| Alexa 568-conjugated goat anti-rabbit IgG (H+L) | Thermo Fisher Scientific | Thermo Fisher Scientific Cat# A-11036 also A11036; RRID: AB_10563566 |
| Alexa 488-conjugated goat anti-mouse IgG (H+L) | Thermo Fisher Scientific | Thermo Fisher Scientific Cat# A32723; RRID: AB_2633275 |
| Alexa 568-conjugated goat anti-mouse IgG (H+L) | Thermo Fisher Scientific | Thermo Fisher Scientific Cat# A-11031; RRID: AB_144696 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Pentylenetetrazol (PTZ) | Sigma-Aldrich | P6500-25G |
| Lipofectamine 2000 | Thermo Fisher Scientific | Cat# 11668019 |
| Polyornithine | Sigma-Aldrich | Cat# P4957-50ML |
| B27 | Thermo Fisher Scientific | Cat# 17504044 |
| bFGF | Thermo Fisher Scientific | Cat# PHG0024 |
| Trizol Reagent | Life Technologies | Cat# 15596018 |
| Ketamine | Sigma-Aldrich | Cat# K-002 |
| Xylazine | Sigma-Aldrich | Cat# 32555 |
| Phenobarbital | MedlinePlus | Cat# a682007 |
| Isofluorane | Henry Schein | Cat# 50562-1 |
| Fluoromount-G | Southern Biotech | Cat# 0100-01 |
| TTX | Alomone Labs | Cat# T-550 |
| EZ-Link Biocytin | Thermo Fisher Scientific | Cat#28022 |
| Glutamax | Thermo Fisher Scientific | Cat# 25030081 |
| Critical Commercial Assays | ||
| Papain dissociation system | Worthington Biochemical Corporation | LK003150 |
| Illumina TotalPrep −96 RNA Amplification Kit | Ambion | IL1791 |
| Illumina HumanHT-12_v4_BeadChip | Illumina | BD-103-0604 |
| Aurum Total RNA Mini Kit | Bio-Rad | 7326820 |
| iScript Reverse Transcription Supermix | Bio-Rad | 1708840 |
| iTaq Universal SYBR Green Supermix | Bio-Rad | 1725120 |
| CFX connect Real-Time PCR Detection System | Bio-Rad | 1855200 |
| Deposited Data | ||
| Microarray Data from Human Surgical Samples | This paper | NCBI GEO under project number GEO: GSE62019 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Emx-Cre; Clockflox/flox | This paper | N/A |
| Mouse: PV-Cre; Clockflox/flox | This paper | N/A |
| Mouse: Emx1-Cre+/− | Jackson Laboratory; Gorski et al., 2002 | RRID: IMSR_JAX:005628 |
| Mouse: PV-Cre+/− | Jackson Laboratory; Hippenmeyer et al., 2005 | RRID: IMSR_JAX:017320 |
| Mouse: B6.129S4-Clocktm1Rep/J | Jackson Laboratory; Debruyne et al., 2006 | RRID: IMSR_JAX:010490 |
| Oligonucleotides | ||
| DBP forward primer: GAGCCTTCTGCAGGGAAACAG |
This paper | N/A |
| DBP reverse primer: GAGTTGCCTTGCGCTCCTTTT |
This paper | N/A |
| HLF forward primer: ACGATGGAGAAAATGTCCCG |
This paper | N/A |
| HLF reverse primer: TTTCTTTACTAAATGCGTCTTCAGG |
This paper | N/A |
| TEF forward primer: CCTTCCCTCTGGTCCTGAAGA |
This paper | N/A |
| TEF reverse primer: CCTTCCCCTTTTCCTTATCGAG |
This paper | N/A |
| GAPDH forward primer: TTGATGGCAACAATCTCCAC |
This paper | N/A |
| GAPDH reverse primer: CGTCCCGTAGACAAAATGGT |
This paper | N/A |
| Table S3 Primers used to create Clock shRNA plasmids | This paper | N/A |
| Software and Algorithms | ||
| Ingenuity Pathways Analysis (IPA) software | QIAGEN | Cat# 830003 |
| Partek Genomics Suite (version 6.5) | Partek | http://www.partek.com |
| Step-up False Discovery Rate multiple test adjustment | Benjamini and Hochberg, 1995 | N/A |
| Co-localization Threshold | ImageJ | N/A |