SRX12679056 AF donor1 LA SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630516 SAMN22366334 AF donor1 LA RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679057 AF donor2 LA SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630517 SAMN22366335 AF donor2 LA RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679058 AF donor1 LV SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630518 SAMN22366344 AF donor1 LV RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679059 AF donor2 LV SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630519 SAMN22366345 AF donor2 LV RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679060 AF donor3 LV SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630520 SAMN22366346 AF donor3 LV RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679061 AF donor4 LV SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630521 SAMN22366347 AF donor4 LV RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679062 AF donor5 LV SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630522 SAMN22366348 AF donor5 LV RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679063 SR donor1 RA spike-in SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS7999226 SAMN17271740 SR donor1 RA spike-in RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679064 SR donor2 RA spike-in SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS7999227 SAMN17271741 SR donor2 RA spike-in RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679065 SR donor3 RA spike-in SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS7999228 SAMN17271742 SR donor3 RA spike-in RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679066 SR donor1 LA spike-in SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS7999220 SAMN17271734 SR donor1 LA spike-in RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679067 SR donor2 LA spike-in SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS7999221 SAMN17271735 SR donor2 LA spike-in RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679068 AF donor3 LA SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630523 SAMN22366336 AF donor3 LA RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679069 SR donor3 LA spike-in SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS7999222 SAMN17271736 SR donor3 LA spike-in RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679070 SR donor1 LV spike-in SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS7999223 SAMN17271737 SR donor1 LV spike-in RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679071 SR donor2 LV spike-in SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS7999224 SAMN17271738 SR donor2 LV spike-in RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679072 SR donor3 LV spike-in SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS7999225 SAMN17271739 SR donor3 LV spike-in RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679073 AF donor4 LA SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630524 SAMN22366337 AF donor4 LA RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679074 AF donor5 LA SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630525 SAMN22366338 AF donor5 LA RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679075 AF donor1 RA SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630526 SAMN22366339 AF donor1 RA RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679076 AF donor2 RA SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630527 SAMN22366340 AF donor2 RA RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679077 AF donor3 RA SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630528 SAMN22366341 AF donor3 RA RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679078 AF donor4 RA SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630529 SAMN22366342 AF donor4 RA RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX12679079 AF donor5 RA SRP342015 PRJNA771631 Total RNA was isolated from all samples using the Direct-zol RNA Microprep Kit (Zymo Research), followed by a DNase digestion step. The integrity of the isolated RNA was assessed using the Bioanalyzer RNA 6000 Nano Kit (Agilent). After ribosomal (r)RNA depletion, a directional library preparation was carried out with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). The quality of the resulting libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Library quantification was performed using the NEBNext Library Quant Kit for Illumina (NEB). Next, equimolar library pools were sequenced in paired-end mode using 75 cycles on a NextSeq 500 system (Illumina) with v2 and v2.5 chemistry. Since the sequencing of human SR and AF samples was performed in separate batches, the SR samples were re-sequenced in lower concentration as spike-ins together with the AF samples. This allowed using the spike-in samples as technical replicates to address potential batch effects. SRS10630530 SAMN22366343 AF donor5 RA RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500