Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Genetic reagent (Mus-musculus) | B6.129S2-Airetm1.1Doi/J | Anderson et al., 2002 | RRID:IMSR_JAX:004743 | Provided by D. Mathis and C. Benoist (Harvard Medical School) |
| Cell line (Homo-sapiens) | HEK293 cells | Martin et al., 2012 | Cell line obtained from M. Zavolan lab | |
| Cell line (Mus-musculus) | 1C6 mouse thymic epithelial cells | Mizuochi et al., 1992 | ||
| Transfected construct (mouse) | pCMV-Aire-Flag plasmid | Abramson et al., 2010 | ||
| Antibody | anti-mouse CD45-PerCPCy5.5 (Clone: 30-F11; Rat IgG2b, k) |
Biolegend | Cat# 103131 RRID:AB_893344 |
FACS (1:50) |
| Antibody | anti-mouse Ly51-PE (Clone: 6C3; Rat IgG2a, k) |
Biolegend | Cat# 108307 RRID:AB_313364 |
FACS (1:800) |
| Antibody | anti-mouse I-A/E-APC (Clone: M5/114.15.2; Rat IgG2b, k) |
eBioscience | Cat# 17–5321 RRID:AB_469455 |
FACS (1:1200) |
| Antibody | anti-Clp1 (Clone: EPR7181; Rabbit monoclonal) |
GeneTex | Cat# GTX63930 |
FACS (1:100) |
| Antibody | anti-human CLP1 (Goat polyclonal) | Santa Cruz | Cat# sc-243005 | IP and WB |
| Antibody | Flag-tag M2 (Mouse monoclonal) | Sigma | Cat# F1804 RRID:AB_262044 |
IP and WB |
| Antibody | mouse CD45 microbeads | Miltenyi Biotec | Cat# 130-052-301 |
|
| Recombinant DNA reagent | PLKO.1-Puro shRNAs (plasmids-lentiviruses) |
Broadinstitute (RNAi platform) | shRNA details: Supplementary file 1 |
|
| Recombinant DNA reagent | EF1-Tet3G (plasmid-lentivirus) |
Vectalys | ||
| Recombinant DNA reagent | pTRE3G-shClp1-GFP (plasmid-lentivirus) | Vectalys | Clp1 shRNAs: Supplementary file 1 |
|
| Sequence-based reagent | qPCR primers | this paper | primer details: Supplementary file 2 |
|
| Sequence-based reagent | oligo(dT)12–18 primers | ThermoFisher | Cat# 18418012 |
|
| Commercial assay or kit | Trans-IT-293 transfection reagent | Mirus | Cat# MIR 2700 |
|
| Commercial assay or kit | Universal Magnetic Co-IP Kit | Active Motif | Cat# 54002 |
|
| Commercial assay or kit | Superscript II Reverse Transcriptase | ThermoFisher | Cat# 18064071 |
|
| Chemical compound, drug | collagenase D | Roche | Cat# 11088866001 |
(1 mg/mL final) |
| Chemical compound, drug | DNase I | Sigma | Cat# DN25 |
(1 mg/mL final) |
| Chemical compound, drug | collagenase/dispase | Roche | Cat# 11097113001 |
(2 mg/mL final) |
| Chemical compound, drug | actinomycin D | Sigma | Cat# A9415 |
(1 µM) |
| Software, algorithm | Bowtie | Johns Hopkins University (http://bowtie-bio.sourceforge.net/index.shtml) |
RRID:SCR_005476 | |
| Software, algorithm | Samtools | Samtools (http://samtools.sourceforge.net/) | RRID:SCR_002105 | |
| Software, algorithm | Bedtools | University of Utah (https://bedtools.readthedocs.io/en/latest/) |
RRID:SCR_006646 | |
| Software, algorithm | DESeq | EMBL (http://bioconductor.org/packages/release/bioc/html/DESeq.html) |
RRID:SCR_000154 | |
| Software, algorithm | RNAseq_d3UTR_ratio_density.R | this paper | provided: Figure 1—source data 3 | |
| Software, algorithm | CEAS | CEAS (http://ceas.cbi.pku.edu.cn/index.html) | RRID:SCR_010946 | |
| Software, algorithm | aroma.affymetrix R package | UCSF (prev. UC Berkeley) (https://www.aroma-project.org) |
RRID:SCR_010919 | details: Figure 3—source data 1 |
| Software, algorithm | Microarray_d3UTR_hg19.R | this paper | provided: Figure 3—source data 2 |
|
| Software, algorithm | Microarray_d3UTR_significance.R | this paper | provided: Figure 3—source data 3 |
|
| Software, algorithm | GSEA | BroadInstitute (http://www.broadinstitute.org/gsea/) |
RRID:SCR_003199 |