Betain

Steam pretreated poplar wood was kindly obtained from Forest Products Biotechnology/Bioenergy Group, Department of Wood Science (University of British Columbia, Vancouver, BC, Canada). Diphenyl-1-picrylhydrazyl (DPPH), 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (Trolox), dimethyl sulfoxide (DMSO), cyclohexanol, anhydrous pyridine, deuterated chloroform, chromium(III) acetylacetonate, 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP, Product No. 447536), betain, sodium salicylate, anthraquinone, commercial Kraft lignin (Product No. 370959) and microcrystalline cellulose (Avicel^® PH-101) were purchased from Sigma-Aldrich. Other common chemicals and organic solvents with analytical grade were purchased from Kelong Chemical Regent Co., Ltd. (Chengdu, China).

The LAMP reactions starting from a dumbbell are called IDEA. Every reaction was carried out within 20 µL working volume composed of 18 µL of LAMP mix solution and 2 µL of the dumbbell solution at a fixed concentration. The LAMP mix solution was composed of several reagents with final concentrations as follows except otherwise specified: FIP and BIP at 2.4 µM, 1X Isothermal amplification Buffer (NEB, France), 1 mM MgSO ${}_4$ (NEB, France), 0.8 M Betain (Sigma Aldrich, France), 1.4 mM of deoxyribonucleotide tri-phosphates (dNTPs) solution (Sigma Aldrich, France), 0.4 U/mL of Bst 2.0 DNA polymerase (NEB, France), and 1X of Eva Green Fluorescent DNA intercalating dye (Jena Bioscience, Germany). Finally, the solutions were placed in the QuantStudio 3 Real-Time PCR System (ThermoFisher) and heated at 65 ${}^{\circ }$ C for one hour. The fluorescence F of the solution was recorded every 30 s. Furthermore, for each sample, duplicate amplifications were systematically performed. The normalized fluorescence was defined as $\Delta F=(F-F_{min})/(F_{max}-F_{min})$ where $F_{min}$ and $F_{max}$ are, respectively, the minimal and maximal fluorescence values of the raw data (see Figure S3 for an illustration).

Smart-Seq2 scRNA-Seq was performed using the protocol described by Picelli et al.^{59 (link)}. Briefly, single cells were sorted into cell lysis buffer containing 0. μL RNase inhibitor (Clontech), 1.9 μL Triton X-100 solution (0.2%), 1 μL dNTP mix (10 mM), and 1 μL oligo-dT primer (5 μM). Reverse transcription was performed containing 0.5 μL SuperScript II reverse transcriptase (200 U/μL, Invitrogen), 0.25 μL RNase inhibitor (40 U/μL, Clontech), 2;μL Superscript II First-Strand Buffer (5×, Invitrogen), 0.25 μL DTT (100 mM, Invitrogen), 2 μL betain (5 M, Sigma), 0.9 μL MgCl₂ (100 mM, Sigma), 1 μL TSO (10 μM). Reverse transcription was carried out at 42 °C for 90 min, followed by 10 cycles of 50 °C for 2 min and 42 °C for 2 min. PCR was performed using KAPA HiFi HotStart ReadyMIX (KAPA Biosystems) with 28 cycles of PCR and the IS PCR primer reduced to 50 nM. Sequencing libraries were prepared using the Nextera XT Library Preparation Kit (Illumina) and sequencing was performed on the Illumina NextSeq platform (150 bps, paired-end) at ~1 million reads per sample. Following sequencing, reads were processed using the VDJPuzzle algorithm^{13 (link)} to determine TCR sequences.