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. Author manuscript; available in PMC: 2024 Oct 9.
Published in final edited form as: Cancer Cell. 2023 Sep 21;41(10):1803–1816.e8. doi: 10.1016/j.ccell.2023.08.013

Key resources table.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
anti-CD19 (PE-Cy7) Biolegend Cat# 302216
anti-CD5 (BV421) Biolegend Cat# 300626
anti-CD4 (FITC) Biolegend Cat# 300506
anti-CD3 (Pacific Blue) Biolegend Cat# 300330
anti-CD5 (FITC) Biolegend Cat# 364022
anti-CD19 (PE-Cy7) Biolegend Cat# 302216
anti-CD235 BD Biosciences Cat# 555570
anti-CD8 (BV785) Biolegend Cat# 344740
anti-CD4 (BV605) Biolegend Cat# 300556
anti-CD45RA (FITC) Biolegend Cat# 304106
anti-CD62L (PE-Cy7) Biolegend Cat# 304822
anti-PD-1 (BV421) Biolegend Cat# 329920
anti-KLRC1 (APC) Biolegend Cat# 375108
anti-CD226 (PE) Biolegend Cat# 338306
anti-CD38 (BV711) Biolegend Cat# 303528
7-AAD Viability Staining Solution Biolegend Cat# 420404
Zombie Violet Fixable Viability Kit Biolegend Cat# 423114
CITE-seq antibodies in Supplementary Table 9
Histone H3 antibody Cell Signaling Technology Cat# 9715S
DYKDDDDK Tag Antibody Cell Signaling Technology Cat# 2368S
HRP-linked Antibody Cell Signaling Technology Cat# 7074S
CUTANA™ ChIC/CUT&RUN Kit H3K4Me3, IgG controls EpiCypher Cat# 14–1048
anti-FLAG Fisher Cat# FG4R
CD3 MicroBeads Miltenyi Biotec Cat# 130–050-101
Bacterial and virus strains
Biological samples
Whole bone marrow and blood samples during clinical trial Clinical trial NCT 02420912 (https://clinicaltrials.gov/ct2/show/NCT02420912)
Richter syndrome extension and validation samples Clinical trial NCT03619512 (https://clinicaltrials.gov/ct2/show/NCT03619512) NCT02795182 (https://clinicaltrials.gov/ct2/show/results/NCT02795182)
Chemicals, peptides, and recombinant proteins
Doxycycline Takara Bio 631311
Puromycin Life Technologies A1113803
SuperSignal™ West Pico PLUS Chemiluminescent Substrate Thermo Scientific 34580
PrimeScript RT Master Mix Takara Bio RR036A
TaqMan Gene Expression Master Mix Life Technologies 4369514
Critical commercial assays
Chromium Next GEM Single Cell 5' Kit v2 kit 10x genomics 1000244
Chromium Next GEM Single Cell 3’ v2 kit 10x genomics PN-120237
RNeasy kit Qiagen 74106
Qiagen RNeasy Micro Kit Qiagen 74004
NEBNext single-cell/low input library Prep Kit for Illumina NEB E6420L
PrimeScript RT Master Mix for qRT-PCR Takara Bio RR036A
Pierce™ NE-PER® Nuclear and Cytoplasmic Extraction Reagent Kit Thermo Scientific 78833
Quant-iT RiboGreen RNA Assay Kit Thermo Scientific R11490
High Sensitivity DNA Kit Agilent 5067–4626
TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold Illumina 20020598
Wizard SV Gel and PCR Clean-Up System Promega A9282
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® NEB E7645S/L
MiniSeq High Output Kit (150 cycles) Illumina FC-420–1002
Deposited data
Single-cell RNA sequencing data This study dbgap (accession number phs002458.v2.p1)
Bulk RNA sequencing data This study dbgap (accession number phs002458.v2.p1)
Whole exome data This study dbgap (accession number phs002458.v2.p1)
Single-cell TCR sequencing This study dbgap (accession number phs002458.v2.p1)
Bulk TCR sequencing This study GEO GSE241091
CUT&RUN This study GEO GSE241091
Human reference genome NCBI build 37, GRCh37, hg19 Genome Reference Consortium https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
CLL Transcriptome Data dbGAP phs000435
Richter transcriptome Data EGA study EGAS00001005495 and accession number EGAD00001007922
TCGA RNA-seq Sample and Clinical Data The Cancer Genome Atlas Research Network https://portal.gdc.cancer.gov
TCGA RNA-seq Data Broad Institute GDAC Firehose https://gdac.broadinstitute.org
CHiP-seq, Davis et al. Cistrome-GO data browser ENCSR098YLE_2
ATAC-seq, Philip et al. Gene Expression Omnibus GSM2365846, GSM2365852, GSM2365855, GSM2365856, GSM2365857
Hodgkin lymphoma data, Aoki et al. EGA EGAD00001008270
Experimental models: Cell lines
Jurkat cell line, clone E6–1 ATCC TIB-152
Experimental models: Organisms/strains
Oligonucleotides
5’-AAAGGCCTCTGAGGCCACCATGAAAGAGGAATCAGC-3’ This paper FlagPCR F
5’ -AAGCTTGGCCTGACAGGCCTTTATTTGTCGTCGTCATCCTTGTAGTCTGAACCGCCATTATTTTGGTCTTGACCCA-3’ This paper FlagPCR R
5’- CTCGAAAGGCCTCTGAAAGGCCTCTGAGGCCAC-3’ This paper Gibson overlap F
5’- CATCAATGTATCTTATCATGTCTATAAGCTTGGCCTGACAGGC-3’ This paper Gibson overlap R
ZNF683 Taqman probe Life Technologies Hs00543184_m1
Beta actin Taqman probe Life Technologies 4333762T
GAPDH Taqman probe Life Technologies 4333764T
NEBNext Multiplex Oligos for Illumina, Dual Index Primers NEB E7600
Recombinant DNA
ZNF683 gene block This paper
pSB-tet-GP Addgene 60495
pCMV(CAT)T7-SB100 Addgene 34879
Software and algorithms
Cell Ranger v2.0.0, v2.1.1, v3.0.2 10x Genomics http://10xgenomics.com/
Conos v 1.3.1 Barkas et al., 2019 https://github.com/kharchenkolab/conos
DESeq2 v1.22.2 Love et al., 2014 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
fgsea v1.13.2 Korotkevich et al., 2019 https://bioconductor.org/packages/release/bioc/html/fgsea.html
scRepertoire v1.0.0 Borcherding et al., 2022 https://www.bioconductor.org/packages/release/bioc/html/scRepertoire.html
slingshot v1.8.0 Street et al., 2018 https://bioconductor.org/packages/release/bioc/html/slingshot.html
kallisto v0.46.0 Bray et al., 2016 https://pachterlab.github.io/kallisto/download.html
Cutadapt v3.5 Martin et al., 2011 https://cutadapt.readthedocs.io/en/stable/
Bowtie2 v2.4.2 Langmead et al., 2012 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
samtools v1.2 Danecek et al., 2021 http://www.htslib.org/download/
bedtools v2.30.0 Quinlan et al., 2010 https://bedtools.readthedocs.io/en/latest/index.html
SEACR v1.3 Meers et al., 2019 https://github.com/FredHutch/SEACR
deepTools v3.5.1 Ramírez et al., 2016 https://deeptools.readthedocs.io/en/develop/
DiffBind v3.4.3 Stark et al., 2011 https://bioconductor.org/packages/release/bioc/html/DiffBind.html
Cistrome-GO Li et al., 2019 http://go.cistrome.org
MEME-ChIP v5.4.1 Bailey et al., 2015 https://meme-suite.org/meme/tools/meme-chip
GSVA v1.30.0 Hänzelmann et al., 2013 https://bioconductor.org/packages/release/bioc/html/GSVA.html
CIBERSORT v1.05 Newman et al., 2015 https://cibersort.stanford.edu
RNA-SeQC v2.3.6 Graubert et al., 2021 https://github.com/getzlab/rnaseqc
Integrated Genomics Viewer (IGV) Broad Institute https://software.broadinstitute.org/software/igv/
HLAthena v1 Sarkizova et al., 2020 http://hlathena.tools/
Optitype v1 Szolek et al., 2014 https://github.com/FRED-2/OptiType
NetMHCPan version 4.1 Reynisson et al., 2020 http://www.cbs.dtu.dk/services/NetMHCpan-4.1