title: biol rep 2, SW48 KRAS MT, Gln 0, E2 10 uM

description: Library name: Sample_MT2_G0E10

value: CRC


title: RL cells, DMSO treatment, 4 hours, bio rep 3

status: Public on Dec 11 2025

type: SRA

city: Stanford

first: Sai

last: Gourisankar

state: CA

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

country: USA

institute: Stanford

description: Library name: _RL_DMSO_3

library_source: transcriptomic

data_processing:
Raw reads were checked for quality using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed from adapters using cutadapt using parameters cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -b AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --nextseq-trim=20 --minimum-length 1.
Transcripts were quantified using kallisto against the human Gencode v33 indexed transcriptome and annotations.
Assembly: human Gencode v33
Supplementary files format and content: tab-delimited files include raw counts for each sample. TPM values should be ignored for 3' end counting-based data.

molecule: polyA RNA

organism: Homo sapiens

source_name: RL

extract_protocol:
Cells were plated at 1M/mL. For KP422 cells, cells were harvested in TRIsure (Bioline 38033). RNA was extracted using Direct-zol RNA MicroPrep columns (Zymo R2062) treated with DNAseI. For RL, SUDHL4, and OCILY19 cells, cells were harvested in Zymo DNA/RNA Shield (R1100).
For sequencing library preparation for KP422 cells, polyA-tailed mRNA was enriched (NEB E7490) and prepared into paired-end libraries (NEB E7765) and indexed (NEB E7335). Library size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent 5067) and concentrations determined by qPCR. For sequencing library preparation for RL, SUDHL4, and OCILY19 cells, 3' end counting was used (Plasmidsaurus): polyA mRNA was captured, reverse transcribed, and barcoded with a unique molecular identifier; then, double-stranded cDNA was generated and tagmented; finally, libraries were amplified using Illumina index primers for sequencing.

treatment_protocol: Treated at 1million cells/mL density at indicated timepoints and doses with final DMSO concentration of 0.1%

tag: cell line

value: RL

tag: cell type

value: DLBCL

tag: genotype

value: WT

tag: treatment

tag: time

value: 4 hours


title: OCILY19 cells, 1 nM TCIP3 treatment,4 hours, bio rep 2

description: Library name: _OCILY19_1nM4hTCIP3_2

value: 1 nM TCIP3


title: Ribo_sh-ABCE1_3

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

institute: Cornell University

library_source: other

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Normalized read density was calculated by custom python scripts.
Assembly: GRCm39.106
Supplementary files format and content: comma-delimited text files including normalized read density around start codons for each sample.
Supplementary files format and content: comma-delimited text files including normalized read density around stop codons for each sample.

molecule: other

extract_protocol:
For MRPA, fractions of 500 μl corresponding to monosome or polysome were collected for RNA extraction using TRIzol LS. RNA was purified using RNA Clean & Concentrator and eluted with 11 μl of nuclease-free water.  For Ribo-seq, RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.
For  Ribo-seq, 14 μl RNAs (10~200 ng) were mixed with 1 μl T4 PNK (NEB), 20 U SUPERase·In in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 65 °C for 20 min. After ethanol precipitation, 10 μl dissolved RNA were mixed with 1 μl homemade Ezra enzyme, 1 μl Poly(A) Polymerase (NEB) and 20 U SUPERase·In in 7 μl Ezra buffer. After incubation at 37 °C for 30 min followed by 65 °C for 20 min, 1 μl of 1 μM 5’ end adaptor, 1 μl of 1 μM biotinylated reverse transcription primer, 20 U SUPERase·In were added and incubated at 70 °C for 3 min followed by slowly cooling down (3 °C/min) to 25 °C. The hybridized RNA sample was mixed with 10 μl of pre-washed streptavidin beads and incubated at room temperature for 10 min. Beads were washed and re-suspended in 10 μl nuclease-free water. Ligation was performed for 60 min at 25 °C by mixing beads with a 10 μl reaction mixture (1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). After washing once with 2 × SSC, beads were re-suspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, RNaseOUT and SuperScript III) followed by incubation at 50 °C for 30 min. After washing once with 2 × SSC, beads were resuspended in 10 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR 5primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA). For MPRA, The purified RNA was reverse transcribed using SuperScript III and gene-specific primers. In brief, RNA samples were mixed with 1 μl of 10 mM dNTP, 2 pmol reverse primer and incubated at 65 °C for 5 min, then immediately placed on ice for 1 min. The reverse transcription was carried out by incubating with the 7 μl reaction mixture (5 × first strand buffer, 0.1 M DTT, RNaseOUT and SuperScript III) at 50 °C for 60 min followed by heating at 70 °C for 15 minutes. The products were then amplified with Illumina-based sequencing primers with barcode. PCR were performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR primers and 0.025 U Phusion polymerase. The PCR was initiated at 98 °C, 30 s; then (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. The PCR products with the expected size 190 bp were excised from a 8% polyacrylamide TBE gel. The DNA products were recovered from DNA elution buffer.


title: RL cells, 1 nM TCIP3 treatment, 4 hours, bio rep 3

description: Library name: _RL_1nMTCIP3_4h_3


title: SUDHL4 cells, 1 nM TCIP3 treatment, 4 hours, bio rep 3

description: Library name: _SUDHL4_1nM4hTCIP3_3


title: RL cells, DMSO treatment, 4 hours, bio rep 1

description: Library name: _RL_DMSO_1


title: RNA_9N_mono

molecule: total RNA


title: Ribo_18SrRNA_mut2-OE

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Normalized read density was calculated by custom python scripts.
Assembly: GRCm39.106
Supplementary files format and content: comma-delimited text files including normalized read density around start codons for each sample.

extract_protocol:
RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.
14 μl RNAs (10~200 ng) were mixed with 1 μl T4 PNK (NEB), 20 U SUPERase·In in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 65 °C for 20 min. After ethanol precipitation, 10 μl dissolved RNA were mixed with 1 μl homemade Ezra enzyme, 1 μl Poly(A) Polymerase (NEB) and 20 U SUPERase·In in 7 μl Ezra buffer. After incubation at 37 °C for 30 min followed by 65 °C for 20 min, 1 μl of 1 μM 5’ end adaptor, 1 μl of 1 μM biotinylated reverse transcription primer, 20 U SUPERase·In were added and incubated at 70 °C for 3 min followed by slowly cooling down (3 °C/min) to 25 °C. The hybridized RNA sample was mixed with 10 μl of pre-washed streptavidin beads and incubated at room temperature for 10 min. Beads were washed and re-suspended in 10 μl nuclease-free water. Ligation was performed for 60 min at 25 °C by mixing beads with a 10 μl reaction mixture (1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). After washing once with 2 × SSC, beads were re-suspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, RNaseOUT and SuperScript III) followed by incubation at 50 °C for 30 min. After washing once with 2 × SSC, beads were resuspended in 10 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR 5primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA).


title: KP422 cells, 1 nM TCIP3 treatment,4 hours, bio rep 2

description: Library name: _KP_5


title: OCILY19 cells, DMSO treatment, 4 hours, bio rep 2

description: Library name: _OCILY19_DMSO_2


title: Ribo_input_+CHX


title: Ribo_18SrRNA_mut1-OE


title: KP422 cells, 1 nM TCIP3 treatment, 4 hours, bio rep 1

description: Library name: _KP_4


title: Ribo_sh-ABCE1_1


title: SUDHL4 cells, DMSO treatment, 4 hours, bio rep 3

description: Library name: _SUDHL4_DMSO_3


title: RL cells, 1 nM TCIP3 treatment,4 hours, bio rep 2

description: Library name: _RL_1nMTCIP3_4h_2


title: KP422 cells, DMSO treatment, 4 hours, bio rep 3

description: Library name: _KP_3


title: Ribo_eRF1IP_-CHX


title: KP422 cells, DMSO treatment, 4 hours, bio rep 1

description: Library name: _KP_1


title: CR_BHB_NMN_NG3

city: Johnson City

first: Lev

middle: Y

last: Yampolsky

state: Tennessee

address: 811 Lazywood Dr

department: Biological sciences

institute: East Tennessee State University

description:
Library name: S14
raw sense reads

data_processing:
quality check of Indexed sequences was performed by Fastqc
indexed sequences were trimmed using an adaptor sequence by TrimGalore-0.4.5.
reads mapped to D. magna Xinb3 reference transcriptome (BioProject ID: PRJNA624896; D. Ebert and P. Fields, personal communication; Fields et al., in preparation) using STAR (Dobin et al. 2013)
and genes with differential expression (DE) among treatments and between clones were identified using DEseq2 (Love et al. 2014).
Assembly: Xinb3 reference transcriptome BioProject ID: PRJNA624896
Supplementary files format and content: raw read counts per transcript per library

organism: Daphnia magna

source_name: whole organism

growth_protocol: Daphnia maintained in the lab for over 5 years in modified ADaM zooplankton medium (Klüttgen et al. 1994; https://evolution.unibas.ch/ebert/lab/adam.htm) at 20 ºC on the diet of the green alga Scenedesmus acutus (synonym: Tetradesmus obliquus) grown in the lab on constant light in Jüttner et al. (1983) algal medium.

extract_protocol:
Qiagen Rneasy +
NEBNext Ultra II Directional RNA Library prep Kit

treatment_protocol: Racks containing tubes with Daphnia were removed from the holding aquaria for 2 hours every day and placed, after rinsing in fresh ADaM medium, into trays containing either 2.5 mM BHB, or 0.1mM NMN solutions in ADaM, or a solution of both chemicals together, at the same concentrations. Control cohorts in each of the diet treatments were placed for the same amount of time into identical trays containing ADaM medium. Thus, individuals from the two clones shared the exposure handling and solution, and all treatments shared the medium and food outside of exposure times. This resulted in the following treatments: Control400 (full diet), full diet with BHB exposure, full diet with NMN exposure, full diet with exposure to both BHB and NMN, and Control100 (CR diet).

tag: tissue

value: whole organism


title: Ribo_sh-Scram


title: Ribo_18SrRNA_WT-OE


title: KP422 cells, 1 nM TCIP3 treatment, 4 hours, bio rep 3

description: Library name: _KP_6


title: CR_BHB_NMN_LI3

description:
Library name: S22
raw sense reads


title: FLAG-BCL6 SUDHL5 cells, input for FLAG ChIP-seq, DMSO (0.1%) for 1 hr, bio rep 1

description: Library name: 1_DMSO_0hr_Input

library_source: genomic

data_processing:
The data quality was checked using fastq (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The raw reads were trimmed from adapters with cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
Raw reads were aligned to hg38 human genome assembly using bowtie2 (parameters: --local --maxins 1000).
Low quality reads, duplicated reads and reads with multiple alignments were removed using samtools and Picard (https://broadinstitute.github.io/picard/).
macs2 was used to map position of peaks with FDR cutoff of 0.05.
Bedtools was used to find a consensus set of peaks by merging peaks across multiple conditions (bedtools merge), count number of reads in peaks (bedtools intersect -c) and generate genome coverage (bedtools genomecov -bga).
deepTools was used to generate coverage densities across multiple experimental conditions (deeptools computeMatrix and deeptools plotProfile) and to generate bigwig files (deeptools bamCoverage), where reads mapping to ENCODE blacklist regions were excluded.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

extract_protocol:
Cells were washed in PBS containing TCIP3 or DMSO and crosslinked for 11 min in CiA Fix Buffer (50 mM HEPES pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl) with addition of formaldehyde to a final concentration of 1%. The crosslinking reaction was quenched by glycine added at 0.125 M final concentration. Crosslinked cells were centrifuged at 1,000 x g for 5 min. Nuclei were prepared by 10 min incubation of resuspended pellet in CiA NP-Rinse 1 buffer (50 mM HEPES pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IPEGAL CA-630, 0.25% Triton X100) followed by wash in CiA NP-Rinse 2 buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). The pellet was resuspended in CiA Covaris Shearing Buffer (0.1% SDS,1 mM EDTA pH 8.0, 10 mM Tris HCl pH 8.0) with protease inhibitors and sonicated for 20 min with a Covaris E220 sonicator (Peak Power 140, Duty Factor 5.0, Cycles/Burst 200). The distribution of fragments was confirmed with D1000 Tapestation or by agarose gel electrophoresis. 15 ug of chromatin per ChIP was used with anti-p300 antibodies (Bethyl Labs, cat#: A300-358A), with 12 ng Drosophila chromatin (53083, ActiveMotif) spiked in. 40 ug of chromatin per ChIP was used with anti-FLAG antibodies (Sigma, cat#: F1804) with 32 ng of Drosophila chromatin (53803, ActiveMotif) spiked in. After overnight incubation at 4 C in IP buffer (50 mM HEPES pH 7.5, 300mM NaCl, 1mM EDTA, 1% Triton X100, 0.1% sodium deoxycholic acid salt (DOC), 0.1% SDS), IPs were washed twice with IP buffer, once with DOC buffer (10 mM Tris pH 8, 0.25 M LiCl, 0.5% IPEGAL CA-630, 0.5% sodium deoxycholic acid salt (DOC), 1mM EDTA), and once with 10 mM Tris/1 mM EDTA buffer (TE) pH 8. IPs and inputs were reverse-crosslinked in TE/0.5% SDS/0.5 µg/µL proteinase K for 55 C /3 h then 65 C /18 h, then DNA was purified using a PCR cleanup spin column (Takara #74609).
Paired-end sequencing libraries were constructed using an NEBNext Ultra II DNA kit (E7645S) and indexed (NEB E7335). Library size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent 5067) and concentrations determined by qPCR.


title: FLAG-BCL6 SUDHL5 cells, FLAG ChIP-seq, 10 nM TCIP3 (0.1% DMSO) for 1 hr, bio rep 1

description: Library name: 3_TCIP3_1hr_FLAG

tag: chip antibody

value: Sigma, cat#:F1804


title: CR_BHB_NMN_LG3

description:
Library name: S17
raw sense reads


title: CR_BHB_NMN_LI1

description:
Library name: S18
raw sense reads


title: FLAG-BCL6 SUDHL5 cells, FLAG ChIP-seq, DMSO (0.1%) for 1 hr, bio rep 1

description: Library name: 1_DMSO_0hr_FLAG


title: CR_BHB_NMN_CI2

description:
Library name: S11
raw sense reads


title: CR_BHB_NMN_LG1

description:
Library name: S19
raw sense reads


title: Ribo_vector1


title: SUDHL5 cells, p300 ChIP-seq, 1 nM TCIP3 (0.1% DMSO) for 2 hrs, bio rep 3

description: Library name: DHL5_6a_TCIP3_2hr_p300

value: Bethyl Labs, cat#:A300-358A


title: CR_BHB_NMN_NI2

description:
Library name: S15
raw sense reads


title: CR_BHB_NMN_CI3

description:
Library name: S12
raw sense reads


title: RL cells, DMSO treatment, 4 hours, bio rep 2

description: Library name: _RL_DMSO_2


title: SUDHL5 cells, p300 ChIP-seq, 1 nM TCIP3 (0.1% DMSO) for 2 hrs, bio rep 2

description: Library name: DHL5_5a_TCIP3_2hr_p300


title: RNA_9N-TAGT_heavy


title: CR_BHB_NMN_CG3

description:
Library name: S09
raw sense reads


title: SUDHL5 cells, p300 ChIP-seq, 1 nM TCIP3 (0.1% DMSO) for 2 hrs, bio rep 1

description: Library name: DHL5_4a_TCIP3_2hr_p300


title: CR_BHB_NMN_CG2

description:
Library name: S10
raw sense reads


title: Ribo_sh-Rps26


title: CR_BHB_NMN_NG1

description:
Library name: S08
raw sense reads


title: SUDHL5 cells, p300 ChIP-seq, DMSO (0.1%) for 2 hrs, bio rep 2

description: Library name: DHL5_2a_DMSO_2hr_p300


title: CR_BHB_NMN_NI3

description:
Library name: S16
raw sense reads


title: CR_BHB_NMN_BI1

description:
Library name: S06
raw sense reads


title: CR_BHB_NMN_BG2

description:
Library name: S04
raw sense reads


title: CR_BHB_NMN_BG3

description:
Library name: S05
raw sense reads


title: CR_BHB_NMN_LG2

description:
Library name: S20
raw sense reads


title: FLAG-BCL6 SUDHL5 cells, input for FLAG ChIP-seq, DMSO (0.1%) for 1 hr, bio rep 2

description: Library name: 5_DMSO_0hr_Input


title: FLAG-BCL6 SUDHL5 cells, FLAG ChIP-seq, DMSO (0.1%) for 1 hr, bio rep 2

description: Library name: 5_DMSO_0hr_FLAG


title: Talaporfin-treated xenograft tumor sample 3 (MIA PaCa-2)

city: Kitakyushu

first: Junko

last: Takahashi

state: Fukuoka

address: 2-7 Hibikino, Wakamatsu-ku

department: Graduate School of Information, Production and Systems

country: Japan

institute: Waseda University

description:
Library name: Talaporfin_3
Column name in gene_expression_human.csv: TS-3-h, Column name in gene_expression_mouse.csv: TS-3-m

data_processing:
Raw sequence data (FASTQ files) were quality-checked using FastQC, and adapter trimming was performed with Trim Galore. Transcript quantification was performed with Salmon v1.10.1 in quasi-mapping mode separately against the human (GENCODE release 42, GRCh38.p13) and mouse (GENCODE release M35, GRCm39) transcriptome references.
For human samples, TPM (Transcripts Per Million) and NumReads values were obtained from the Salmon output (quant.sf) and summarized to gene-level expression values using tximport v1.30.0 in R v4.3.2. For mouse samples, the same procedure was applied independently using the corresponding GENCODE M35 annotation. Processed data files contain gene-level TPM values for both species. All analyses were performed using default parameters unless otherwise specified.
Assembly: Human: GENCODE release 42 (GRCh38.p13); Mouse: GENCODE release M35 (GRCm39)
Supplementary files format and content: Processed data are provided as tab-delimited text files containing gene-level expression values summarized from Salmon quantification results. Each row represents a gene, and each column represents a sample. Expression values are reported as TPM (Transcripts Per Million). Separate files are provided for human (GENCODE release 42, GRCh38.p13) and mouse (GENCODE release M35, GRCm39) datasets. The first column contains gene identifiers (Ensembl gene IDs), followed by TPM values for each sample.  Processed data file: gene_expression_human.csv (columns: Control_1_human, Control_2_human, Control_3_human, Talaporfin_1_human, Talaporfin_2_human, Talaporfin_3_human, Xray_1_human, Xray_2_human, Xray_3_human, Talaporfin_Xray_1_human, Talaporfin_Xray_2_human, Talaporfin_Xray_3_human)
Supplementary files format and content: Processed data file: gene_expression_mouse.csv (columns: Control_1_mouse, Control_2_mouse, Control_3_mouse, Talaporfin_1_mouse, Talaporfin_2_mouse, Talaporfin_3_mouse, Xray_1_mouse, Xray_2_mouse, Xray_3_mouse, Talaporfin_Xray_1_mouse, Talaporfin_Xray_2_mouse, Talaporfin_Xray_3_mouse)

source_name: xenograft tumor (human pancreatic cancer)

growth_protocol: Human pancreatic cancer MIA PaCa-2 cells were cultured in DMEM supplemented with 10% fetal bovine serum under standard conditions (37°C, 5% CO₂). Approximately 3 × 10⁶ cells were suspended in PBS and subcutaneously inoculated into the right flank of BALB/c nu/nu nude mice. Tumors were allowed to grow to a volume of approximately 400 mm³ before initiating treatments.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit from MIA PaCa-2 xenograft tumor preserved in RNAlater (Qiagen). Isolation was performed according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA-seq libraries were prepared from total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Poly(A)+ RNA was purified from total RNA and converted into strand-specific cDNA libraries. Libraries were quantified, pooled, and sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads.

treatment_protocol: Mice were randomly divided into four groups: (1) no treatment (NT); (2) talaporfin sodium only (TS); (3) X-ray irradiation only (XT); and (4) combined radiodynamic therapy (TS-XT). Talaporfin sodium was administered intravenously at 10 mg/kg, 2 hours prior to each irradiation. X-ray irradiation was delivered at 3 Gy per day for three consecutive days (total 9 Gy) . Tumor tissues were collected 25 days after the final irradiation, immersed in RNAlater solution, and stored at -80 °C until RNA extraction.

value: MIA PaCa-2

value: talaporfin sodium (10 mg/kg, i.p.) only, no irradiation

tag: batch

value: batch 1


title: Talaporfin + X-ray treated xenograft tumor sample 2 (MIA PaCa-2)

description:
Library name: Talaporfin_Xray_2
Column name in gene_expression_human.csv: TS-XT-2-h, Column name in gene_expression_mouse.csv: TS-XT-2-m

value: xenograft tumor (human pancreatic cancer)

value: talaporfin sodium (10 mg/kg, i.p.) administered 2 h before each X-ray irradiation (3 Gy/day × 3 days, total 9 Gy)


title: rpsL_6h_005_rep3

city: Boston

first: Jaryd

last: Sullivan

address: 185 Cambridge St

institute: Massachusetts General Hospital

description:
Library name: Sample 342
Experiment16

data_processing:
Reads were demultiplexed based on their associated barcode. Up to 1 mismatch in the barcode was allowed. Barcode sequences and terminal G's that were added during template switching were trimmed.
Assembly: Pseudomonas aeruginosa UCBPP-PA14 GCF_000014625.1
Supplementary files format and content: tsv file includes raw counts for each sample

organism: Pseudomonas aeruginosa

growth_protocol: Cells were grown in 96-well plates in LB until mid-log phase

extract_protocol:
50ul of treated cells were mixed with 25ul 3X RNAgem Blue Buffer, incubated at 75C for 10mins and flashfrozen. RNA was extracted using the Direct-zol RNA Miniprep Plus Kit.
cDNA libraries were generated using a modified version of the RNAtag-seq protocol. 500ng of RNA was fragmented, depleted of genomic DNA, dephosphorylated, and ligated to DNA adapters. Barcoded RNAs were pooled and depleted of rRNA. Pools were converted to cDNA using reverse transcriptase template switching with PCR amplification of the Illumina P5 and P7 sequences. cDNA libraries were sequenced on Illumina Nextseq 500 platorm for paired end reads

treatment_protocol: 30ul of mid-log phase cells were mixed with 30ul of 2X rhamnose to a final OD of 0.1. Cells were grown for 6, or 10 hours.


title: Talaporfin-treated xenograft tumor sample 2 (MIA PaCa-2)

description:
Library name: Talaporfin_2
Column name in gene_expression_human.csv: TS-2-h, Column name in gene_expression_mouse.csv: TS-2-m


title: CR_BHB_NMN_BI2

description:
Library name: S13
raw sense reads


title: rpsL_10h_0_rep3

description:
Library name: Sample 339
Experiment13


title: SUDHL5 cells, p300 ChIP-seq, DMSO (0.1%) for 2 hrs, bio rep 3

description: Library name: DHL5_3a_DMSO_2hr_p300


title: SUDHL5 cells, input for p300 ChIP-seq, DMSO (0.1%) for 2 hrs

description: Library name: DHL5_1_DMSO_2hr_Input


title: FLAG-BCL6 SUDHL5 cells, FLAG ChIP-seq, 10 nM TCIP3 (0.1% DMSO) for 1 hr, bio rep 2

description: Library name: 7_TCIP3_1hr_FLAG


title: KP422 cells, DMSO treatment, 4 hours, bio rep 2

description: Library name: _KP_2


title: CR_BHB_NMN_LI2

description:
Library name: S21
raw sense reads


title: Talaporfin + X-ray treated xenograft tumor sample 3 (MIA PaCa-2)

description:
Library name: Talaporfin_Xray_3
Column name in gene_expression_human.csv: TS-XT-3-h, Column name in gene_expression_mouse.csv: TS-XT-3-m


title: SUDHL5 cells, input for p300 ChIP-seq, 1 nM TCIP3 (0.1% DMSO) for 2 hrs

description: Library name: DHL5_4_TCIP3_2hr_Input


title: rpsL_10h_0_rep2

description:
Library name: Sample 338
Experiment12


title: Talaporfin-treated xenograft tumor sample 1 (MIA PaCa-2)

description:
Library name: Talaporfin_1
Column name in gene_expression_human.csv: TS-1-h, Column name in gene_expression_mouse.csv: TS-1-m


title: Control xenograft tumor sample 3 (MIA PaCa-2)

description:
Library name: Control_3
Column name in gene_expression_human.csv: NT-3-h, Column name in gene_expression_mouse.csv: NT-3-m

value: no treatment (control)


title: rpsL_10h_0_rep1

description:
Library name: Sample 337
Experiment11


title: rpsL_10h_005_rep3

description:
Library name: Sample 336
Experiment10


title: CR_BHB_NMN_CI1

description:
Library name: S02
raw sense reads


title: Control xenograft tumor sample 1 (MIA PaCa-2)

description:
Library name: Control_1
Column name in gene_expression_human.csv: Control_1-human, Column name in gene_expression_mouse.csv: Control_1-mouse


title: BT549, TRMT112 OE Polysomes -2

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: AB1170 1720 2nd Ave. South

institute: University of Alabama at Birmingham

description:
Library name: BT549-OE-2
Illumina NovaSeq 6000

data_processing:
Initial processing of the FASTQ-format sequencing outputs included adaptor sequence removal using Trimmomatic, alignment with HISAT2, and elimination of PCR duplicates via SAMtools, resulting in BAM or SAM files. These files were subsequently analyzed using the Partek Genomics Suite (PGS, St. Louis, MO, USA). Reads per Kilobase of transcript per Million mapped reads (RPKM) normalization was applied prior to statistical evaluations to identify differentially expressed genes based on fold change and significance levels.
Assembly: GRCh38/hg38
Supplementary files format and content: txt file, with summarized fpkm-normalized counts.

source_name: Mammary

growth_protocol: SUM159 cells were cultured in DMEM/F-12 medium (ThermoFisher Scientific, Cat# 11330032) supplemented with 5% heat-inactivated fetal bovine serum (FBS) (ThermoFisher Scientific, Cat# A5256701), 5 µg/mL insulin (Millipore Sigma, Cat# I5500-500MG), and 1 µg/mL hydrocortisone (Millipore Sigma, Cat# H0888-1G). BT-549 cells were maintained in RPMI 1640 medium (ThermoFisher Scientific, Cat# 22400105) supplemented with 10% heat-inactivated FBS, while MDA-MB-231 cells were cultured in DMEM/F-12 medium supplemented with 5% heat-inactivated FBS.

extract_protocol:
Cells were washed twice with ice-cold PBS containing cycloheximide and lysed in polysome lysis buffer (20 mM Tris-HCl, 10 mM MgCl2, 300 mM NaCl, 1% Triton X-100, 100 µg/mL cycloheximide, 0.1 U/µL RNase inhibitor, 0.5 mg/mL heparin, and 1x Halt protease inhibitors). Lysates were clarified by centrifugation at 13,000 rpm for 10 minutes at 4°C. The protein concentration was measured, and 2.5 mg of total protein was loaded onto pre-prepared 10-50% sucrose gradients. Gradients were ultracentrifuged at 35,000 rpm for 3 hours 20 minutes at 4°C using a Beckman SW41Ti rotor. Following ultracentrifugation, gradients were fractionated using the Brandel SYN-202 Density Gradient Fractionation System. RNA was then isolated from the polysomes using the RNeasy Mini Kit, and 1 ug of total RNA was used for library construction and sequencing.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Cells were maintained at 37°C in a humidified environment with 5% CO2.

value: Mammary

value: Triple negative breast cancer cell line

value: TRMT112 OE

value: no treatment


title: BT549, TRMT112 OE Polysomes -1

description:
Library name: BT549-OE-1
Illumina NovaSeq 6000


title: rpsL_6h_005_rep2

description:
Library name: Sample 341
Experiment15


title: CR_BHB_NMN_BI3

description:
Library name: S07
raw sense reads


title: rpoB_6h_005_rep2

description:
Library name: Sample 332
Experiment6


title: X-ray-irradiated xenograft tumor sample 2 (MIA PaCa-2)

description:
Library name: Xray_2
Column name in gene_expression_human.csv: XT-2-h, Column name in gene_expression_mouse.csv: XT-2-m

value: X-ray irradiation only (3 Gy/day × 3 days, total 9 Gy)


title: CR_BHB_NMN_CG1

description:
Library name: S01
raw sense reads


title: BT549, EV CTRL Polysomes -1

description:
Library name: BT549-EV-1
Illumina NovaSeq 6000

value: EV CTRL


title: rpoB_6h_005_rep1

description:
Library name: Sample 331
Experiment5


title: SUDHL5 cells, p300 ChIP-seq, DMSO (0.1%) for 2 hrs, bio rep 1

description: Library name: DHL5_1a_DMSO_2hr_p300

value: DLBCL


title: SUM159, TRMT112 KD Polysomes -1

description:
Library name: 159-KD-1
Illumina NovaSeq 6000

value: TRMT112 KD


title: rpoB_10h_0_rep1

description:
Library name: Sample 328
Experiment2


title: rpoB_10h_0_rep3

description:
Library name: Sample 330
Experiment4


title: Talaporfin + X-ray treated xenograft tumor sample 1 (MIA PaCa-2)

description:
Library name: Talaporfin_Xray_1
Column name in gene_expression_human.csv: TS-XT-1-h, Column name in gene_expression_mouse.csv: TS-XT-1-m


title: X-ray-irradiated xenograft tumor sample 1 (MIA PaCa-2)

description:
Library name: Xray_1
Column name in gene_expression_human.csv: XT-1-h, Column name in gene_expression_mouse.csv: XT-1-m


title: MDA-MB-231, TRMT112 KD Polysomes -2

description:
Library name: 231-KD-2
Illumina NovaSeq 6000


title: CR_BHB_NMN_BG1

description:
Library name: S03
raw sense reads

value: whole organism


title: rpsL_6h_005_rep1

description:
Library name: Sample 340
Experiment14


title: X-ray-irradiated xenograft tumor sample 3 (MIA PaCa-2)

description:
Library name: Xray_3
Column name in gene_expression_human.csv: XT-2-h, Column name in gene_expression_mouse.csv: XT-3-m


title: MDA-MB-231, EV CTRL Polysomes -2

description:
Library name: 231-EV-2
Illumina NovaSeq 6000


title: Control xenograft tumor sample 2 (MIA PaCa-2)

description:
Library name: Control_2
Column name in gene_expression_human.csv: NT-2-h, Column name in gene_expression_mouse.csv: NT-2-m


title: MDA-MB-231, EV CTRL Polysomes -1

description:
Library name: 231-EV-1
Illumina NovaSeq 6000


title: rpsL_10h_005_rep1

description:
Library name: Sample 334
Experiment8


title: Patient_19_6 Months

city: Santiago de Compostela

first: David

last: Sánchez-López

state: A Coruña

address: Travesía Da Choupana S/n

country: Spain

institute: Institute of Health Research of Santiago de Compostela: Instituto de Investigacion Sanitaria de Santigao de Compostela

description:
Library name: X22
Column name in "Processed_data_ALL.txt" : "22"

data_processing:
FastQs generated from the bcl output of the NovaSeq 6000 with bcl2fastq v2.20.0.422
FastQs quality was studied with the following tools: FastQC v0.11.9 and multiqc v1.13.dev0
Trimming, alignment and generation of the GTF files were performed with NIMGenetics RNASeq_Pipeline v1.1
Counts’ files generated with NIMGenetics prepDE v1.0
Assembly: Genome assembly GRCh38
Supplementary files format and content: Tab delimited text file includes raw counts for each sample.

source_name: Primary Granulocytes

growth_protocol: Primary cells from patients

extract_protocol:
The granulocytes layer was carefully taken, and lysed for RNA isolation by AllPrep DNA/RNA/protein mini kit (Qiagen, Hilden, Germany), following the manufacturer’s protocol. 10 ng of total RNA from each sample was used as input for first-strand cDNA synthesis and subsequent cDNA amplification.
Illumina sequencing libraries were prepared using the SMART-Seq mRNA LP protocol from Takara Bio (Takara Bio Inc, San Jose, USA), following the manufacturer's instructions.

treatment_protocol: Primary cells from patients

value: Primary Granulocytes

value: After semaglutide treatment for 6 months


title: rpoB_10h_005_rep2

description:
Library name: Sample 326
Experiment2


title: Patient_21_6 Months

description:
Library name: X24
Column name in "Processed_data_ALL.txt" : "24"


title: rplJ_10h_0_rep3

description:
Library name: Sample 321
Experiment2


title: Patient_18_6 Months

description:
Library name: X20
Column name in "Processed_data_ALL.txt" : "20"


title: BT549, EV CTRL Polysomes -2

description:
Library name: BT549-EV-2
Illumina NovaSeq 6000


title: rplJ_10h_005_rep3

description:
Library name: Sample 318
Experiment2


title: rplJ_10h_0_rep1

description:
Library name: Sample 319
Experiment2


title: rpoB_10h_0_rep2

description:
Library name: Sample 329
Experiment3


title: rplJ_6h_005_rep3

description:
Library name: Sample 324
Experiment2


title: rpoB_6h_005_rep3

description:
Library name: Sample 333
Experiment7


title: SUM159, TRMT112 KD Polysomes -2

description:
Library name: 159-KD-2
Illumina NovaSeq 6000


title: SUM159, EV CTRL Polysomes -1

description:
Library name: 159-EV-1
Illumina NovaSeq 6000


title: rpsL_10h_005_rep2

description:
Library name: Sample 335
Experiment9


title: rpoB_10h_005_rep1

description:
Library name: Sample 325
Experiment2


title: rpoB_10h_005_rep3

description:
Library name: Sample 327
Experiment2


title: SUM159, EV CTRL Polysomes -2

description:
Library name: 159-EV-2
Illumina NovaSeq 6000


title: Patient_18_Basal

description:
Library name: X19
Column name in "Processed_data_ALL.txt" : "19"

value: Basal condition


title: MDA-MB-231, TRMT112 KD Polysomes -1

description:
Library name: 231-KD-1
Illumina NovaSeq 6000


title: Patient_21_Basal

description:
Library name: X23
Column name in "Processed_data_ALL.txt" : "23"


title: Patient_12_Basal

description:
Library name: X17
Column name in "Processed_data_ALL.txt" : "17"


title: Patient_11_Basal

description:
Library name: X15
Column name in "Processed_data_ALL.txt" : "15"


title: rplJ_10h_005_rep1

description:
Library name: Sample 316
Experiment2


title: rplJ_10h_005_rep2

description:
Library name: Sample 317
Experiment2


title: rhlR_6h_005_rep2

description:
Library name: Sample 314
Experiment2


title: rplJ_6h_005_rep2

description:
Library name: Sample 323
Experiment2


title: rplJ_10h_0_rep2

description:
Library name: Sample 320
Experiment2


title: rplJ_6h_005_rep1

description:
Library name: Sample 322
Experiment2


title: Patient_11_6 Months

description:
Library name: X16
Column name in "Processed_data_ALL.txt" : "16"


title: rhlR_6h_005_rep1

description:
Library name: Sample 313
Experiment2


title: Patient_12_6 Months

description:
Library name: X18
Column name in "Processed_data_ALL.txt" : "18"


title: rhlR_10h_0_rep3

description:
Library name: Sample 312
Experiment2


title: Patient_7_6 Months

description:
Library name: X10
Column name in "Processed_data_ALL.txt" : "10"


title: rhlR_10h_005_rep3

description:
Library name: Sample 309
Experiment2


title: pbpA_6h_005_rep1

description:
Library name: Sample 304
Experiment2


title: Patient_5_Basal

description:
Library name: X5
Column name in "Processed_data_ALL.txt" : "5"


title: Patient_6_Basal

description:
Library name: X7
Column name in "Processed_data_ALL.txt" : "7"


title: pbpA_6h_005_rep3

description:
Library name: Sample 306
Experiment2


title: rhlR_10h_005_rep2

description:
Library name: Sample 308
Experiment2


title: Patient_5_6 Months

description:
Library name: X6
Column name in "Processed_data_ALL.txt" : "6"


title: Patient_19_Basal

description:
Library name: X21
Column name in "Processed_data_ALL.txt" : "21"


title: pbpA_10h_0_rep2

description:
Library name: Sample 302
Experiment2


title: pbpA_10h_005_rep3

description:
Library name: Sample 300
Experiment2


title: rhlR_6h_005_rep3

description:
Library name: Sample 315
Experiment2


title: pbpA_10h_0_rep3

description:
Library name: Sample 303
Experiment2


title: Ci10076 CD8s cultured with various conditions - GEX and FB combined for multi demultiplexing pipeline [FB]

first: Kevin

middle: James

last: Maroney

state: Alabama

address: 1001 20th Street S, 1501, Ascend Apartments

description:
Library name: Ci10076FB_S56
Ci10076FB_S56
Feature barcoding library containing gene expression (polyA RNA), antibody-derived tags (ADT), and hashtag oligonucleotides (HTO): read1 contains cell barcode and UMI; read2 contains mRNA, ADT, and HTO sequences. Libraries were generated using 10x Genomics 5′ v2 chemistry and sequenced on the Illumina NovaSeq 6000. "polyA RNA" was selected for the "Molecule" column because the bulk of the data for read 2 encoded for GEX. This combined file represents the output for the cellranger "multi" multi-omics and demultiplexing pipeline from a multiplexed input containing 10 multiplexed conditions.  After demultiplexing, processed files were generated - descriptions provided in supplemental file.

data_processing:
Initially, 3 sets of paired reads fasta files were obtained for the 3 types of data (RNA EXPRESSION, TCR, and CITE-seq/multiplex hashtag antibody feature barcodes (FB)) for each multiplexed donor for a total of 18 files and 112 GB of gzipped data. Initial de-multiplexing was performed on these 3 donor multiplexed data using the RNA EXPRESSION and hashtags of the FB fasta files adopting a modified version of the strategy described here so as to in the most unbiased manner use the 5’ Biolegend hashtagging oligos with the 3’ CMO Biolegend demultiplexing pipeline to assign cells to different samples within each donor:https://www.10xgenomics.com/resources/analysis-guides/demultiplexing-and-analyzing-5%E2%80%99-immune-profiling-libraries-pooled-with-hashtags. A hashing_demux_HMO-set.csv targets file as well as a demultiplex config file were used for this purpose. After initial QC of the number of cells and reads returned for every sample, it became apparent that the elite controller PBMC-KF11 stimulated condition was either not sorted or not amplified. Bam files generated in the demultiplexing process were then converted back to fastq within donor sample folders under condition folders and TCR and CITE-seq data was then extracted using the cell id’s assigned to each sample from demultiplexing using cellranger multi and a new config file for each sample within each donor directory. This resulted in 87 unique fasta files, 3 each RNA EXPRESSION, TCR, and FB for the 10 conditions per donor sample under donor/condition directory folder, then used for downstream Seurat analysis.
All demultiplexed multi-omic data was imported into a single Seurat file by linking the TCR clonotypes, TCR filtered contic annotations, matrix, barcodes, and features files to each sample in a separate Seurat file through use of a complex folder structure (Patient -> condition -> GEXFB or TCR -> processed data files) before merging into a master Seurat file which was used for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: CellRanger multi pipeline output files: GEXFB_barcodes.tsv.gz, GEXFB_matrix.mtx.gz, GEXFB_features.tsv.gz
Supplementary files format and content: CellRanger multi pipeline output files: clonotypes.csv, filtered_contig_annotations.csv

source_name: 41A3.CD4, 41A3.CD4.B57, 41A3.CD4.E01, 41A3.CD4.E03, none (PBMC) - (multiplexed conditions)

extract_protocol:
CD8+ T cells from 3 PWH, 1 from each control status (n = 1 NC, ART+ NC, and C) of the previous n = 8 cohort, were co-cultured with CD8+ T cells as described for that set of experiments.. These co-cultures were performed in wells of a 24-well plate as per instruction of the Single Cell and Flow Cytometry Core at UAB. After 18 hrs co-incubation, cells were washed and first stained with the Hashing antibodies 1-10 (C0251-C0260) from Biolegend (cat # of C0251 is 394661 for reference to set) per manufacturer instructions post initial titration of both hashtagging antibodies(data not shown). After washing off, cells were stained using the same panel as previously outlined in addition to the following CITE-seq antibodies with the exact same staining protocol (TotalSeq-C a-CD3, CD4, CD8, TCRαβ, CD56, CD69, CD137, CD107a, PE, APC, FITC, CD45RA, CD45RO, and CCR7). Unactivated (CD69+/137+) CD56- CD8+ cells from the unstimulated (no KF11 loading for 41A3 lines or pulse for PBMCs) as well as both unactivated and activated CD8+ T cells from stimulated conditions were sorted using the BD Symphony S6 cell sorter into a single tube, multiplexed for all 10 samples for one of the 3 PWH per day.
Libraries of these cells were then generated on that same day for RNA EXPRESSION (gene expression), TCR, and CITE-seq before these separate hashtagged libraries were then all sequenced on the NovaSeq using an S1 flow cell to cover 1.6 billion reads across the estimated 22,172 cells sorted post manual quality control pre-library generation. Specifically, Cell suspension, 10x barcoded gel beads, and oil were loaded into 10x Chromium™ Single Cell Chip K (PN# 1000287). Using Chromium Next GEM Single Cell 5' v2 Kit (PN#1000263) kit to capture single cells in nanoliter-scale oil droplets by 10xChromium™ Controller and generate Gel Bead-In-EMulsions (GEMs). The 5’-biased gene expression, TCR and feature barcoding libraries were generated following the instruction. All libraries   were sequenced by Illumina Novaseq6000 machine, targeting read pairs 20,000 /cell for gene expression and 20,000/cell for TCR libraries and 5000 /cell for feature barcoding libraries , and the sequencing cycles consists of 26bp for read 1, 90bp for read 2 and 10bp for i7 and i5.

value: CD8 T cells


title: Patient_10_Basal

description:
Library name: X13
Column name in "Processed_data_ALL.txt" : "13"


title: pbpA_10h_005_rep2

description:
Library name: Sample 299
Experiment2


title: pbpA_10h_005_rep1

description:
Library name: Sample 298
Experiment2


title: Ci10074 CD8s cultured with various conditions - TCR data

description:
Library name: Ci10074TCR_S58
Ci10074TCR_S58
TCR library: read1 file contains cell barcode and UMI; read2 file contains T-cell receptor (V(D)J) sequences for immune profiling. Libraries were prepared using the 10x Genomics 5′ v2 kit and sequenced on the Illumina NovaSeq 6000. After demultiplexing, processed files were generated - descriptions provided in supplemental file.

data_processing:
Initially, 3 sets of paired reads fasta files were obtained for the 3 types of data (RNA EXPRESSION, TCR, and CITE-seq/multiplex hashtag antibody feature barcodes (FB)) for each multiplexed donor for a total of 18 files and 112 GB of gzipped data. Initial de-multiplexing was performed on these 3 donor multiplexed data using the RNA EXPRESSION and hashtags of the FB fasta files adopting a modified version of the strategy described here so as to in the most unbiased manner use the 5’ Biolegend hashtagging oligos with the 3’ CMO Biolegend demultiplexing pipeline to assign cells to different samples within each donor:https://www.10xgenomics.com/resources/analysis-guides/demultiplexing-and-analyzing-5%E2%80%99-immune-profiling-libraries-pooled-with-hashtags. A hashing_demux_HMO-set.csv targets file as well as a demultiplex config file were used for this purpose. After initial QC of the number of cells and reads returned for every sample, it became apparent that the elite controller PBMC-KF11 stimulated condition was either not sorted or not amplified. Bam files generated in the demultiplexing process were then converted back to fastq within donor sample folders under condition folders and TCR and CITE-seq data was then extracted using the cell id’s assigned to each sample from demultiplexing using cellranger multi and a new config file for each sample within each donor directory. This resulted in 87 unique fasta files, 3 each RNA EXPRESSION, TCR, and FB for the 10 conditions per donor sample under donor/condition directory folder, then used for downstream Seurat analysis.
All demultiplexed multi-omic data was imported into a single Seurat file by linking the TCR clonotypes, TCR filtered contic annotations, matrix, barcodes, and features files to each sample in a separate Seurat file through use of a complex folder structure (Patient -> condition -> GEXFB or TCR -> processed data files) before merging into a master Seurat file which was used for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: CellRanger multi pipeline output files: GEXFB_barcodes.tsv.gz, GEXFB_matrix.mtx.gz, GEXFB_features.tsv.gz
Supplementary files format and content: CellRanger multi pipeline output files: clonotypes.csv, filtered_contig_annotations.csv
Library strategy: TCR-Seq

value: 41A3.CD4, 41A3.CD4.B57, 41A3.CD4.E01, 41A3.CD4.E03, none (PBMC) - (multiplexed conditions)


title: Patient_10_6 Months

description:
Library name: X14
Column name in "Processed_data_ALL.txt" : "14"


title: Ci10074 CD8s cultured with various conditions - GEX and FB combined for multi demultiplexing pipeline [GEX]

description:
Library name: Ci10074_S57
Ci10074_S57
Feature barcoding library containing gene expression (polyA RNA), antibody-derived tags (ADT), and hashtag oligonucleotides (HTO): read1 contains cell barcode and UMI; read2 contains mRNA, ADT, and HTO sequences. Libraries were generated using 10x Genomics 5′ v2 chemistry and sequenced on the Illumina NovaSeq 6000. "polyA RNA" was selected for the "Molecule" column because the bulk of the data for read 2 encoded for GEX. This combined file represents the output for the cellranger "multi" multi-omics and demultiplexing pipeline from a multiplexed input containing 10 multiplexed conditions.  After demultiplexing, processed files were generated - descriptions provided in supplemental file.

library_source: transcriptomic single cell


title: parC_10h_0_rep2

description:
Library name: Sample 293
Experiment2


title: Ci10004 CD8s cultured with various conditions - GEX and FB combined for multi demultiplexing pipeline [FB]

description:
Library name: Ci10004FB_S62
Ci10004FB_S62
Feature barcoding library containing gene expression (polyA RNA), antibody-derived tags (ADT), and hashtag oligonucleotides (HTO): read1 contains cell barcode and UMI; read2 contains mRNA, ADT, and HTO sequences. Libraries were generated using 10x Genomics 5′ v2 chemistry and sequenced on the Illumina NovaSeq 6000. "polyA RNA" was selected for the "Molecule" column because the bulk of the data for read 2 encoded for GEX. This combined file represents the output for the cellranger "multi" multi-omics and demultiplexing pipeline from a multiplexed input containing 10 multiplexed conditions.  After demultiplexing, processed files were generated - descriptions provided in supplemental file.


title: parC_10h_0_rep3

description:
Library name: Sample 294
Experiment2


title: rhlR_10h_0_rep1

description:
Library name: Sample 310
Experiment2


title: Patient_8_Basal

description:
Library name: X11
Column name in "Processed_data_ALL.txt" : "11"


title: parC_10h_0_rep1

description:
Library name: Sample 292
Experiment2


title: parC_10h_005_rep3

description:
Library name: Sample 291
Experiment2


title: sJAG1-expressing LN229-4

city: Augusta

first: Balveen

last: Kaur

state: GA

address: CN-3205, 1410 Laney-Walker Blvd

department: Pathology

institute: Augusta University

description: Library name: J4

data_processing:
cutadapt (for adapter trimming and quality filtering)
Alignment using STAR aligner
Normalization, quality control, and differential gene expression analysis were performed in R using DESeq2.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Count matrix in CSV format with rows as genes and columns as samples, values represent raw read counts.

source_name: cell line

growth_protocol: LN229 cells were maintained in 150 mm TC-treated Culture Dishes with 10%FBS DMEM

extract_protocol:
Total RNA was isolated using the Rneasy Plus kit from Qiagen and samples were submitted for bulk RNA sequencing
Library preparation was performed with the SMARTer® Stranded Total RNA Sample Prep Kit (Takara Bio USA, Inc., cat# 634878). This process incorporated RiboGone™ and SMART® (Switching Mechanism at the 5' end of RNA Template) technologies, along with PCR amplification, to generate Illumina-compatible libraries without adapter ligation. RiboGone efficiently depleted rRNA from total RNA before library construction. Library quality was assessed using the TapeStation 2000 (Agilent Technologies), and concentrations were measured with Qubit (Thermo Fisher Scientific) before sequencing. Dual-indexed i5/i7 paired-end libraries were sequenced on the NovaSeq 6000 system (Illumina) with a minimum coverage of 50-60 million reads per sample.

value: cell line

value: glioblastoma


title: sJAG1-expressing LN229-3

description: Library name: J3


title: parC_10h_005_rep2

description:
Library name: Sample 290
Experiment2


title: rhlR_10h_0_rep2

description:
Library name: Sample 311
Experiment2


title: Patient_8_6 Months

description:
Library name: X12
Column name in "Processed_data_ALL.txt" : "12"


title: sJAG1-expressing LN229-1

description: Library name: J1


title: noguide_6h_005_rep3

description:
Library name: Sample 288
Experiment2


title: noguide_6h_005_rep2

description:
Library name: Sample 287
Experiment2


title: Parental LN229-4

description: Library name: P4


title: rhlR_10h_005_rep1

description:
Library name: Sample 307
Experiment2


title: Patient_7_Basal

description:
Library name: X9
Column name in "Processed_data_ALL.txt" : "9"


title: pbpA_6h_005_rep2

description:
Library name: Sample 305
Experiment2


title: Patient_6_6 Months

description:
Library name: X8
Column name in "Processed_data_ALL.txt" : "8"


title: noguide_10h_0_rep3

description:
Library name: Sample 285
Experiment2


title: parC_6h_005_rep2

description:
Library name: Sample 296
Experiment2


title: noguide_10h_0_rep1

description:
Library name: Sample 283
Experiment2


title: hSGO

city: Shanghai

first: Jinkui

last: Zhu

state: Shanghai

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.

department: School of Life Science and Technology

country: China

institute: ShanghaiTech University

description: Library name: hSGO-scRNA

data_processing:
Cell Ranger (v6.1.2) were employed to get gene count matrices with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix file

source_name: organoid

extract_protocol:
Organoids were collected and dissociated into single cells. Briefly, organoids were isolated by mincing the freshly obtained surgical specimens into 1-mm cubic pieces followed by enzymatic digestion using 2mg/ml collagenase II, 2mg/ml collagenase IV, and 0.1mg/ml DNase I, and were incubated on a rocker for 30 min at 37 °C.
The digested cells were then passed through a 40 µm cell strainer and washed twice with PBS. Cell concentration were determined using AO/PI fluorescent staining dyes and cell survival rate should be above 80%. The isolated cells were then loaded directly into the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl (Single Cell 3′ library V3) as described in the manufacturer’s protocol. GEMs (Gel Bead in Emulsion) were constructed for single-cell separation according to the number of cells to be harvested. After GEMs were formed, GEMs were collected for reverse transcription in a PCR machine for labeling. Then, the GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads and then subjected to cDNA amplification and quality inspection. The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation, adaptor ligation, sample index PCR, etc., the library was quantitatively examined and sequenced on the Illumina Novaseq 6000 instrument using 150-base-pair paired-end reads.

value: organoid

value: hESC H9


title: Patient_4_6 Months

description:
Library name: X4
Column name in "Processed_data_ALL.txt" : "4"


title: Patient_4_Basal

description:
Library name: X3
Column name in "Processed_data_ALL.txt" : "3"


title: Ci10074 CD8s cultured with various conditions - GEX and FB combined for multi demultiplexing pipeline [FB]

description:
Library name: Ci10074FB_S59
Ci10074FB_S59
Feature barcoding library containing gene expression (polyA RNA), antibody-derived tags (ADT), and hashtag oligonucleotides (HTO): read1 contains cell barcode and UMI; read2 contains mRNA, ADT, and HTO sequences. Libraries were generated using 10x Genomics 5′ v2 chemistry and sequenced on the Illumina NovaSeq 6000. "polyA RNA" was selected for the "Molecule" column because the bulk of the data for read 2 encoded for GEX. This combined file represents the output for the cellranger "multi" multi-omics and demultiplexing pipeline from a multiplexed input containing 10 multiplexed conditions.  After demultiplexing, processed files were generated - descriptions provided in supplemental file.


title: parC_6h_005_rep1

description:
Library name: Sample 295
Experiment2


title: T47D Everolimus-Resistant, Everolimus, Bio rep 1

city: Duarte

first: Aritro

last: Nath

state: California

address: 1500 E Duarte Rd

department: Medical Oncology & Therapeutics Research

institute: City of Hope

description:
Library name: T47D_everR_ever_rep_1
T47D_everR_ever_rep_1

data_processing:
2 x paired-end raw RNA-seq FASTQ files were processed with BETSY workflow manager, which aligned reads to hg19 using STAR (v1.26) and quantified transcripts by RSEM (v1.3.1).
Assembly: GRCh37 (hg19)
Supplementary files format and content: Tab-delimited text (.txt) files with counts or transcripts per million. First column is gene symbols and subsequent columns are samples.

source_name: T47D Everolimus-Resistant

growth_protocol: CAMA1 and MCF7 breast cancer cells were maintained in DMEM while T47D breast cancer cells were maintained in RPMI. Media was supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic and incubated in 5% CO2 at 37°C.

extract_protocol:
Cells were collected for bulk RNA-seq  after 12 hours of treatment. Cells were pooled, washed with PBS, and pellets were frozen at -80°C for subsequent RNA isolation. RNA was isolated using the Qiagen RNeasy® Plus Mini Kit (Cat. No: 74136) following the manufacturer’s protocol.
Library preparation was performed on the samples using the Illumina TruSeq Stranded mRNA Kit following the manufacturer’s protocol.

treatment_protocol: CAMA1, MCF7 and T47D breast cancer cells were treated with 10nM everolimus (Selleck Chemicals, Cat. No: S1120). Cells were treated for 12 hours.

value: T47D Everolimus-Resistant

value: ER+ Breast Cancer

value: WT

value: Everolimus

value: Day0 Hr12


title: sJAG1-expressing LN229-2

description: Library name: J2


title: murA_6h_005_rep3

description:
Library name: Sample 279
Experiment2


title: noguide_6h_005_rep1

description:
Library name: Sample 286
Experiment2


title: T47D Everolimus-Resistant, DMSO, Bio rep 2

description:
Library name: T47D_everR_DMSO_rep_2
T47D_everR_DMSO_rep_2

value: DMSO


title: parC_6h_005_rep3

description:
Library name: Sample 297
Experiment2


title: murA_10h_0_rep3

description:
Library name: Sample 276
Experiment2


title: T47D Everolimus-Resistant, DMSO, Bio rep 1

description:
Library name: T47D_everR_DMSO_rep_1
T47D_everR_DMSO_rep_1


title: Ci10076 CD8s cultured with various conditions - GEX and FB combined for multi demultiplexing pipeline [GEX]

description:
Library name: Ci10076_S54
Ci10076_S54
Feature barcoding library containing gene expression (polyA RNA), antibody-derived tags (ADT), and hashtag oligonucleotides (HTO): read1 contains cell barcode and UMI; read2 contains mRNA, ADT, and HTO sequences. Libraries were generated using 10x Genomics 5′ v2 chemistry and sequenced on the Illumina NovaSeq 6000. "polyA RNA" was selected for the "Molecule" column because the bulk of the data for read 2 encoded for GEX. This combined file represents the output for the cellranger "multi" multi-omics and demultiplexing pipeline from a multiplexed input containing 10 multiplexed conditions.  After demultiplexing, processed files were generated - descriptions provided in supplemental file.


title: parC_10h_005_rep1

description:
Library name: Sample 289
Experiment2


title: murA_10h_0_rep2

description:
Library name: Sample 275
Experiment2


title: Ci10004 CD8s cultured with various conditions - GEX and FB combined for multi demultiplexing pipeline [GEX]

description:
Library name: Ci10004_S60
Ci10004_S60
Feature barcoding library containing gene expression (polyA RNA), antibody-derived tags (ADT), and hashtag oligonucleotides (HTO): read1 contains cell barcode and UMI; read2 contains mRNA, ADT, and HTO sequences. Libraries were generated using 10x Genomics 5′ v2 chemistry and sequenced on the Illumina NovaSeq 6000. "polyA RNA" was selected for the "Molecule" column because the bulk of the data for read 2 encoded for GEX. This combined file represents the output for the cellranger "multi" multi-omics and demultiplexing pipeline from a multiplexed input containing 10 multiplexed conditions.  After demultiplexing, processed files were generated - descriptions provided in supplemental file.


title: Ci10004 CD8s cultured with various conditions - TCR data

description:
Library name: Ci10004TCR_S61
Ci10004TCR_S61
TCR library: read1 file contains cell barcode and UMI; read2 file contains T-cell receptor (V(D)J) sequences for immune profiling. Libraries were prepared using the 10x Genomics 5′ v2 kit and sequenced on the Illumina NovaSeq 6000. After demultiplexing, processed files were generated - descriptions provided in supplemental file.


title: Parental LN229-2

description: Library name: P2


title: pbpA_10h_0_rep1

description:
Library name: Sample 301
Experiment2


title: murA_10h_005_rep3

description:
Library name: Sample 273
Experiment2


title: Parental LN229-3

description: Library name: P3


title: noguide_10h_005_rep1

description:
Library name: Sample 280
Experiment2


title: noguide_10h_0_rep2

description:
Library name: Sample 284
Experiment2


title: noguide_10h_005_rep2

description:
Library name: Sample 281
Experiment2


title: noguide_10h_005_rep3

description:
Library name: Sample 282
Experiment2


title: Parental LN229-1

description: Library name: P1


title: T47D Sensitive, Everolimus, Bio rep 2

description:
Library name: T47D_ever_rep_2
T47D_ever_rep_2

source_name: T47D Sensitive

value: T47D Sensitive


title: mreB_6h_005_rep2

description:
Library name: Sample 269
Experiment2


title: MCF7 Everolimus-Resistant, Everolimus, Bio rep 2

description:
Library name: MCF7_everR_ever_rep_2
MCF7_everR_ever_rep_2

source_name: MCF7 Everolimus-Resistant

value: MCF7 Everolimus-Resistant


title: murA_6h_005_rep1

description:
Library name: Sample 277
Experiment2


title: T47D Everolimus-Resistant, Everolimus, Bio rep 3

description:
Library name: T47D_everR_ever_rep_3
T47D_everR_ever_rep_3


title: hHFO

description: Library name: hHFO-scRNA


title: mreB_10h_0_rep3

description:
Library name: Sample 267
Experiment2


title: T47D Everolimus-Resistant, Everolimus, Bio rep 2

description:
Library name: T47D_everR_ever_rep_2
T47D_everR_ever_rep_2


title: murA_10h_0_rep1

description:
Library name: Sample 274
Experiment2


title: mreB_10h_0_rep2

description:
Library name: Sample 266
Experiment2


title: murA_10h_005_rep2

description:
Library name: Sample 272
Experiment2


title: T47D Everolimus-Resistant, DMSO, Bio rep 3

description:
Library name: T47D_everR_DMSO_rep_3
T47D_everR_DMSO_rep_3


title: T47D Sensitive, Everolimus, Bio rep 3

description:
Library name: T47D_ever_rep_3
T47D_ever_rep_3


title: MCF7 Everolimus-Resistant, DMSO, Bio rep 2

description:
Library name: MCF7_everR_DMSO_rep_2
MCF7_everR_DMSO_rep_2


title: MCF7 Everolimus-Resistant, DMSO, Bio rep 1

description:
Library name: MCF7_everR_DMSO_rep_1
MCF7_everR_DMSO_rep_1


title: mreB_10h_005_rep2

description:
Library name: Sample 263
Experiment2


title: mreB_10h_005_rep1

description:
Library name: Sample 262
Experiment2


title: T47D Sensitive, Everolimus, Bio rep 1

description:
Library name: T47D_ever_rep_1
T47D_ever_rep_1


title: MCF7 Sensitive, DMSO, Bio rep 3

description:
Library name: MCF7_DMSO_rep_3
MCF7_DMSO_rep_3

source_name: MCF7 Sensitive

value: MCF7 Sensitive


title: murA_10h_005_rep1

description:
Library name: Sample 271
Experiment2


title: mreB_6h_005_rep1

description:
Library name: Sample 268
Experiment2


title: CAMA1 Everolimus-Resistant, Everolimus, Bio rep 3

description:
Library name: CAMA1_everR_ever_rep_3
CAMA1_everR_ever_rep_3

source_name: CAMA1 Everolimus-Resistant

value: CAMA1 Everolimus-Resistant


title: MCF7 Everolimus-Resistant, Everolimus, Bio rep 3

description:
Library name: MCF7_everR_ever_rep_3
MCF7_everR_ever_rep_3


title: murA_6h_005_rep2

description:
Library name: Sample 278
Experiment2


title: T47D Sensitive, DMSO, Bio rep 3

description:
Library name: T47D_DMSO_rep_3
T47D_DMSO_rep_3


title: T47D Sensitive, DMSO, Bio rep 2

description:
Library name: T47D_DMSO_rep_2
T47D_DMSO_rep_2


title: T47D Sensitive, DMSO, Bio rep 1

description:
Library name: T47D_DMSO_rep_1
T47D_DMSO_rep_1


title: MCF7 Everolimus-Resistant, DMSO, Bio rep 3

description:
Library name: MCF7_everR_DMSO_rep_3
MCF7_everR_DMSO_rep_3


title: MCF7 Everolimus-Resistant, Everolimus, Bio rep 1

description:
Library name: MCF7_everR_ever_rep_1
MCF7_everR_ever_rep_1


title: lpxC_10h_0_rep2

description:
Library name: Sample 257
Experiment2


title: lpxC_10h_0_rep1

description:
Library name: Sample 256
Experiment2


title: lpxC_6h_005_rep3

description:
Library name: Sample 261
Experiment2


title: CAMA1 Everolimus-Resistant, Everolimus, Bio rep 1

description:
Library name: CAMA1_everR_ever_rep_1
CAMA1_everR_ever_rep_1


title: Ci10076 CD8s cultured with various conditions - TCR data

description:
Library name: Ci10076TCR_S55
Ci10076TCR_S55
TCR library: read1 file contains cell barcode and UMI; read2 file contains T-cell receptor (V(D)J) sequences for immune profiling. Libraries were prepared using the 10x Genomics 5′ v2 kit and sequenced on the Illumina NovaSeq 6000. After demultiplexing, processed files were generated - descriptions provided in supplemental file.


title: MCF7 Sensitive, Everolimus, Bio rep 2

description:
Library name: MCF7_ever_rep_2
MCF7_ever_rep_2


title: MCF7 Sensitive, DMSO, Bio rep 1

description:
Library name: MCF7_DMSO_rep_1
MCF7_DMSO_rep_1


title: CAMA1 Everolimus-Resistant, DMSO, Bio rep 3

description:
Library name: CAMA1_everR_DMSO_rep_3
CAMA1_everR_DMSO_rep_3


title: lpxC_10h_0_rep3

description:
Library name: Sample 258
Experiment2


title: lpxC_10h_005_rep2

description:
Library name: Sample 254
Experiment2


title: CAMA1 Everolimus-Resistant, DMSO, Bio rep 2

description:
Library name: CAMA1_everR_DMSO_rep_2
CAMA1_everR_DMSO_rep_2


title: mreB_10h_0_rep1

description:
Library name: Sample 265
Experiment2


title: lpxC_10h_005_rep1

description:
Library name: Sample 253
Experiment2


title: MCF7 Sensitive, Everolimus, Bio rep 1

description:
Library name: MCF7_ever_rep_1
MCF7_ever_rep_1


title: CAMA1 Everolimus-Resistant, DMSO, Bio rep 1

description:
Library name: CAMA1_everR_DMSO_rep_1
CAMA1_everR_DMSO_rep_1


title: lpxC_6h_005_rep2

description:
Library name: Sample 260
Experiment2


title: CAMA1 Sensitive, Everolimus, Bio rep 3

description:
Library name: CAMA1_ever_rep_3
CAMA1_ever_rep_3

source_name: CAMA1 Sensitive

value: CAMA1 Sensitive


title: MCF7 Sensitive, Everolimus, Bio rep 3

description:
Library name: MCF7_ever_rep_3
MCF7_ever_rep_3


title: lptE_6h_005_rep3

description:
Library name: Sample 252
Experiment2


title: lptE_6h_005_rep2

description:
Library name: Sample 251
Experiment2


title: lpxC_6h_005_rep1

description:
Library name: Sample 259
Experiment2


title: lptE_6h_005_rep1

description:
Library name: Sample 250
Experiment2


title: CAMA1 Sensitive, Everolimus, Bio rep 1

description:
Library name: CAMA1_ever_rep_1
CAMA1_ever_rep_1


title: mreB_10h_005_rep3

description:
Library name: Sample 264
Experiment2


title: CAMA1 Sensitive, DMSO, Bio rep 2

description:
Library name: CAMA1_DMSO_rep_2
CAMA1_DMSO_rep_2


title: lptE_10h_0_rep1

description:
Library name: Sample 247
Experiment2


title: CAMA1 Sensitive, DMSO, Bio rep 1

description:
Library name: CAMA1_DMSO_rep_1
CAMA1_DMSO_rep_1


title: mreB_6h_005_rep3

description:
Library name: Sample 270
Experiment2


title: P10B-3

city: Atlanta

first: Youssef

middle: M

last: Zohdy

address: 1365 Clifton Road NE

department: Neurosurgery

institute: Emory University

description: Library name: Sample 40

data_processing:
Raw RNA reads processing was conducted following the validated nf-core bulk RNA-seq bioinformatics pipeline. Adapter sequences and low-quality sequences were analyzed using FastQC13 and trimmed from the reading using TrimGalore. The RNA-seq reads were aligned to the human reference genome hg38 using STAR v2.7.11 and quantified using Salmon. Differential expression values were calculated with DESeq2 in R (R Core Team, 2022).
Assembly: hg38
Supplementary files format and content: FPKM

source_name: Patient resected tumor

extract_protocol:
The frozen samples stored were thawed, and immediate steps were taken for RNA extraction. To ensure consistency, all samples were processed simultaneously to avoid any potential batch effects. RNA was extracted and purified from the patient specimens using the Direct-zol RNA Microprep Kit (Cat. #R2063), following the manufacturer’s protocol. Nuclease-free commercially available water was used during the RNA isolation process. The quality and quantity of the extracted RNA were immediately assessed using Nanodrop UV measurements. Following the measurements, all isolated RNA samples were stored at -80° C until sequencing.
An RNA-seq library was generated utilizing the Illumina mRNA sample prep kit (Cat. #RS-100-0801) according to the manufacturer's protocol in 3 technical replicates for each sample. The library constructs' size and concentration were verified with a bioanalyzer before sequencing on the Illumina NovaSeq6000. The raw reads' quality was evaluated to confirm the success of the library preparation and sequencing processes.

value: Patient resected tumor


title: lptE_10h_005_rep3

description:
Library name: Sample 246
Experiment2


title: lptE_10h_005_rep1

description:
Library name: Sample 244
Experiment2


title: P10B-1

description: Library name: Sample 38


title: lptD_10h_0_rep3

description:
Library name: Sample 240
Experiment2


title: CAMA1 Everolimus-Resistant, Everolimus, Bio rep 2

description:
Library name: CAMA1_everR_ever_rep_2
CAMA1_everR_ever_rep_2


title: P10A-2

description: Library name: Sample 36


title: lptD_10h_0_rep2

description:
Library name: Sample 239
Experiment2


title: P9-2

description: Library name: Sample 33


title: CAMA1 Sensitive, Everolimus, Bio rep 2

description:
Library name: CAMA1_ever_rep_2
CAMA1_ever_rep_2


title: MCF7 Sensitive, DMSO, Bio rep 2

description:
Library name: MCF7_DMSO_rep_2
MCF7_DMSO_rep_2


title: lptE_10h_0_rep2

description:
Library name: Sample 248
Experiment2


title: lptE_10h_0_rep3

description:
Library name: Sample 249
Experiment2


title: lptE_10h_005_rep2

description:
Library name: Sample 245
Experiment2


title: lpxC_10h_005_rep3

description:
Library name: Sample 255
Experiment2


title: lptD_10h_0_rep1

description:
Library name: Sample 238
Experiment2


title: P8-3

description: Library name: Sample 31


title: P8-2

description: Library name: Sample 30


title: lptD_6h_005_rep2

description:
Library name: Sample 242
Experiment2


title: CAMA1 Sensitive, DMSO, Bio rep 3

description:
Library name: CAMA1_DMSO_rep_3
CAMA1_DMSO_rep_3


title: P10B-2

description: Library name: Sample 39


title: lptD_10h_005_rep2

description:
Library name: Sample 236
Experiment2


title: lptD_6h_005_rep1

description:
Library name: Sample 241
Experiment2


title: P9-1

description: Library name: Sample 32


title: P9-3

description: Library name: Sample 34


title: P8-1

description: Library name: Sample 29


title: P7-1

description: Library name: Sample 26


title: P10A-3

description: Library name: Sample 37


title: lptD_6h_005_rep3

description:
Library name: Sample 243
Experiment2


title: P7-2

description: Library name: Sample 27


title: P10A-1

description: Library name: Sample 35


title: lptD_10h_005_rep3

description:
Library name: Sample 237
Experiment2


title: P7-3

description: Library name: Sample 28


title: lptA_6h_005_rep3

description:
Library name: Sample 234
Experiment2


title: lptA_10h_005_rep2

description:
Library name: Sample 227
Experiment2


title: leuS_6h_005_rep3

description:
Library name: Sample 225
Experiment2


title: P5A-2

description: Library name: Sample 18


title: P5A-1

description: Library name: Sample 17


title: leuS_10h_0_rep2

description:
Library name: Sample 221
Experiment2


title: P4-3

description: Library name: Sample 16


title: P4-2

description: Library name: Sample 15


title: lptA_6h_005_rep2

description:
Library name: Sample 233
Experiment2


title: leuS_10h_0_rep1

description:
Library name: Sample 220
Experiment2


title: lptA_10h_005_rep1

description:
Library name: Sample 226
Experiment2


title: leuS_10h_005_rep3

description:
Library name: Sample 219
Experiment2


title: leuS_10h_005_rep2

description:
Library name: Sample 218
Experiment2


title: lptA_6h_005_rep1

description:
Library name: Sample 232
Experiment2


title: P3-2

description: Library name: Sample 12


title: P6-3

description: Library name: Sample 25


title: gyrB_6h_005_rep3

description:
Library name: Sample 216
Experiment2


title: lptD_10h_005_rep1

description:
Library name: Sample 235
Experiment2


title: lptA_10h_0_rep3

description:
Library name: Sample 231
Experiment2


title: P2-3

description: Library name: Sample 10


title: gyrB_6h_005_rep2

description:
Library name: Sample 215
Experiment2


title: lptA_10h_0_rep2

description:
Library name: Sample 230
Experiment2


title: P2-2

description: Library name: Sample 9


title: D3-2

description: Library name: Sample 7

source_name: Patient resected meningies

value: Patient resected meningies


title: lptA_10h_005_rep3

description:
Library name: Sample 228
Experiment2


title: gyrB_6h_005_rep1

description:
Library name: Sample 214
Experiment2


title: gyrB_10h_0_rep3

description:
Library name: Sample 213
Experiment2


title: P6-2

description: Library name: Sample 24


title: gyrB_10h_0_rep2

description:
Library name: Sample 212
Experiment2


title: P5A-3

description: Library name: Sample 19


title: D3-1

description: Library name: Sample 6


title: P5B-3

description: Library name: Sample 22


title: P6-1

description: Library name: Sample 23


title: D2-3

description: Library name: Sample 5


title: leuS_6h_005_rep2

description:
Library name: Sample 224
Experiment2


title: leuS_10h_0_rep3

description:
Library name: Sample 222
Experiment2


title: P3-3

description: Library name: Sample 13


title: P5B-2

description: Library name: Sample 21


title: lptA_10h_0_rep1

description:
Library name: Sample 229
Experiment2


title: D2-2

description: Library name: Sample 4


title: gyrB_10h_005_rep2

description:
Library name: Sample 209
Experiment2


title: D1-2

description: Library name: Sample 2


title: D2-1

description: Library name: Sample 3


title: P4-1

description: Library name: Sample 14


title: D1-1

description: Library name: Sample 1


title: Cntl 23

city: Nashville

first: Kasey

last: Vickers

address: 2220 Pierce Ave, PRB 312

institute: VUMC

description: Library name: Cntl 23

data_processing:
TIGER (“Tools for Integrative Genome analysis of Extracellular sRNAs”), an in-house small RNA sequencing analysis pipeline, was used to quantify small RNAs (Allen, R. M., Zhao, S., Ramirez Solano, M. A., Zhu, W., et al., Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins. J Extracell Vesicles 2018, 7, 1506198.)
Briefly, Cutadapt (v4.5) was used to trim 3’ adapters for raw reads. All reads with less than 16 nucleotides were designated as “too short” and discarded. Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1)(www.bioinformatics.babraham.ac.uk/projects/fastqc).
The adaptor-trimmed reads were mapped to the GENCODE GRCh38.p13 genome, addition to rRNA and tRNA reference sequences, by Bowtie1 (v1.3.1) allowing only one mismatch
Significantly differential expressed features with absolute fold change >= 1.5 and p value <= 0.05 were detected by DESeq2 (v1.42.1) using total reads as normalization factor.
The reads with less than 20 nucleotides which were neither annotated as small RNA nor perfectly mapped to human genome were discarded. Remaining unmapped reads were then mapped in parallel to exogenous structural RNA databases and curated microbial genome databases allowing no mismatches. Reads that failed to align to any strategy were categorized as ‘unknown’.
Assembly: Human GRCh38.p13 genome
Supplementary files format and content: csv file containing reads per million of each sample

source_name: HDL

extract_protocol:
Total RNA was purified from the reaction use miRNeasy Mini kit (Qiagen).
Libraries were prepared using the NEXTFlex small RNA sequencing kit v3 (Revvity), using 1:8 adatper dilution, 22 PCR cycles and the no size selection bead cleanup.

treatment_protocol: RNA was demethylated in a 50 μL demethylation mixture containing 1 μM purified AlkB-wt, D135S and D135T enzymes, 25 mM MES buffer pH 6.0, 2 mM MgCl2, 270 mM KCl, 2 mM L-ascorbic acid, 300 μM α-ketoglutarate, 283 μM (NH4)2Fe(SO4)2, and 1 U/mL SUPERase•In RNase Inhibitor (Thermo). The demethylation reaction was conducted at 25ºC for 2h then stopped by addition of 5 mM EDTA and heated at 65ºC for 10 min to denature the AlkB enzymes.

value: HDL

value: Healthy


title: gyrA_6h_005_rep1

description:
Library name: Sample 205
Experiment2


title: leuS_6h_005_rep1

description:
Library name: Sample 223
Experiment2


title: CAC 25

description: Library name: CAC 25


title: gyrA_10h_005_rep1

description:
Library name: Sample 199
Experiment2


title: folA_6h_005_rep3

description:
Library name: Sample 198
Experiment2


title: CAC 23

description: Library name: CAC 23


title: P2-1

description: Library name: Sample 8


title: gyrA_10h_0_rep3

description:
Library name: Sample 204
Experiment2


title: CAC 22

description: Library name: CAC 22


title: gyrA_10h_0_rep1

description:
Library name: Sample 202
Experiment2


title: leuS_10h_005_rep1

description:
Library name: Sample 217
Experiment2


title: gyrA_6h_005_rep3

description:
Library name: Sample 207
Experiment2


title: folA_10h_0_rep3

description:
Library name: Sample 195
Experiment2


title: gyrB_10h_0_rep1

description:
Library name: Sample 211
Experiment2


title: gyrA_10h_005_rep2

description:
Library name: Sample 200
Experiment2


title: gyrA_10h_0_rep2

description:
Library name: Sample 203
Experiment2


title: folA_10h_0_rep2

description:
Library name: Sample 194
Experiment2


title: gyrB_10h_005_rep3

description:
Library name: Sample 210
Experiment2


title: folA_10h_0_rep1

description:
Library name: Sample 193
Experiment2


title: CAC 18

description: Library name: CAC 18


title: CAC 19

description: Library name: CAC 19


title: P3-1

description: Library name: Sample 11


title: gyrB_10h_005_rep1

description:
Library name: Sample 208
Experiment2


title: CAC 17

description: Library name: CAC 17


title: P5B-1

description: Library name: Sample 20


title: folA_10h_005_rep2

description:
Library name: Sample 191
Experiment2


title: gyrA_6h_005_rep2

description:
Library name: Sample 206
Experiment2


title: folA_10h_005_rep1

description:
Library name: Sample 190
Experiment2


title: Cntl 23 AlkB

description: Library name: Cntl 23 AlkB

value: Healthy, AlkB


title: Cntl 22

description: Library name: Cntl 22


title: dxr_6h_005_rep3

description:
Library name: Sample 189
Experiment2


title: Cntl 21 AlkB

description: Library name: Cntl 21 AlkB


title: Cntl 18

description: Library name: Cntl 18


title: Cntl 19

description: Library name: Cntl 19


title: Cntl 20 AlkB

description: Library name: Cntl 20 AlkB


title: dxr_10h_0_rep2

description:
Library name: Sample 185
Experiment2


title: Cntl 24

description: Library name: Cntl 24


title: dxr_10h_0_rep3

description:
Library name: Sample 186
Experiment2


title: CAC 24

description: Library name: CAC 24


title: Cntl 18 AlkB

description: Library name: Cntl 18 AlkB


title: dxr_10h_0_rep1

description:
Library name: Sample 184
Experiment2


title: CAC 24 AlkB

description: Library name: CAC 24 AlkB

value: CAC>21, AlkB


title: dxr_10h_005_rep2

description:
Library name: Sample 182
Experiment2


title: Cntl 17

description: Library name: Cntl 17


title: folA_6h_005_rep2

description:
Library name: Sample 197
Experiment2


title: ctrlg_6h_005_rep3

description:
Library name: Sample 180
Experiment2


title: Cntl 22 AlkB

description: Library name: Cntl 22 AlkB


title: CAC 22 AlkB

description: Library name: CAC 22 AlkB


title: folA_6h_005_rep1

description:
Library name: Sample 196
Experiment2


title: CAC 21

description: Library name: CAC 21


title: folA_10h_005_rep3

description:
Library name: Sample 192
Experiment2


title: CAC 20 AlkB

description: Library name: CAC 20 AlkB


title: ctrlg_6h_005_rep2

description:
Library name: Sample 179
Experiment2


title: gyrA_10h_005_rep3

description:
Library name: Sample 201
Experiment2


title: CAC 20

description: Library name: CAC 20


title: ctrlg_10h_0_rep2

description:
Library name: Sample 176
Experiment2


title: ctrlg_10h_0_rep3

description:
Library name: Sample 177
Experiment2


title: Cntl 19 AlkB

description: Library name: Cntl 19 AlkB


title: Cntl 24 AlkB

description: Library name: Cntl 24 AlkB


title: Cntl 15

description: Library name: Cntl 15


title: dxr_6h_005_rep2

description:
Library name: Sample 188
Experiment2


title: CAC 19 AlkB

description: Library name: CAC 19 AlkB


title: Cntl 17 AlkB

description: Library name: Cntl 17 AlkB


title: rpsL-0.05-rep3

description:
Library name: Sample 171
Experiment1


title: rpsL-0.05-rep2

description:
Library name: Sample 170
Experiment1


title: rpsL-0.0125-rep3

description:
Library name: Sample 168
Experiment1


title: rpsL-0.05-rep1

description:
Library name: Sample 169
Experiment1


title: Cntl 9

description: Library name: Cntl 9


title: CAC 16

description: Library name: CAC 16


title: ctrlg_10h_005_rep3

description:
Library name: Sample 174
Experiment2


title: rpsL-0-rep2

description:
Library name: Sample 164
Experiment1


title: CAC 14

description: Library name: CAC 14


title: CAC 13

description: Library name: CAC 13


title: CAC 23 AlkB

description: Library name: CAC 23 AlkB


title: Cntl 16

description: Library name: Cntl 16


title: rpoB-0.05-rep2

description:
Library name: Sample 161
Experiment1


title: CAC 11

description: Library name: CAC 11


title: CAC 21 AlkB

description: Library name: CAC 21 AlkB


title: dxr_6h_005_rep1

description:
Library name: Sample 187
Experiment2


title: rpoB-0.05-rep1

description:
Library name: Sample 160
Experiment1


title: CAC 10

description: Library name: CAC 10


title: rpoB-0.0125-rep3

description:
Library name: Sample 159
Experiment1


title: dxr_10h_005_rep1

description:
Library name: Sample 181
Experiment2


title: ctrlg_10h_0_rep1

description:
Library name: Sample 175
Experiment2


title: CAC 17 AlkB

description: Library name: CAC 17 AlkB


title: dxr_10h_005_rep3

description:
Library name: Sample 183
Experiment2


title: Cntl 13

description: Library name: Cntl 13


title: rpoB-0.05-rep3

description:
Library name: Sample 162
Experiment1


title: CAC 15

description: Library name: CAC 15


title: rpsL-0-rep3

description:
Library name: Sample 165
Experiment1


title: Cntl 11

description: Library name: Cntl 11


title: rpoB-0.0125-rep1

description:
Library name: Sample 157
Experiment1


title: Cntl 12 AlkB

description: Library name: Cntl 12 AlkB


title: CAC 9

description: Library name: CAC 9


title: ctrlg_10h_005_rep1

description:
Library name: Sample 172
Experiment2


title: rpsL-0.0125-rep2

description:
Library name: Sample 167
Experiment1


title: Cntl 16 AlkB

description: Library name: Cntl 16 AlkB


title: rpoB-0-rep3

description:
Library name: Sample 156
Experiment1


title: Cntl 10

description: Library name: Cntl 10


title: rpoB-0-rep1

description:
Library name: Sample 154
Experiment1


title: rplJ-0.05-rep3

description:
Library name: Sample 153
Experiment1


title: rpsL-0-rep1

description:
Library name: Sample 163
Experiment1


title: Cntl 12

description: Library name: Cntl 12


title: CAC 12

description: Library name: CAC 12


title: ctrlg_10h_005_rep2

description:
Library name: Sample 173
Experiment2


title: rpsL-0.0125-rep1

description:
Library name: Sample 166
Experiment1


title: Cntl 14

description: Library name: Cntl 14


title: CAC 15 AlkB

description: Library name: CAC 15 AlkB


title: rplJ-0.0125-rep3

description:
Library name: Sample 150
Experiment1


title: CAC 18 AlkB

description: Library name: CAC 18 AlkB


title: ctrlg_6h_005_rep1

description:
Library name: Sample 178
Experiment2


title: CAC 14 AlkB

description: Library name: CAC 14 AlkB


title: CAC 13 AlkB

description: Library name: CAC 13 AlkB


title: rplJ-0.0125-rep2

description:
Library name: Sample 149
Experiment1


title: rplJ-0.0125-rep1

description:
Library name: Sample 148
Experiment1


title: CAC 11 AlkB

description: Library name: CAC 11 AlkB


title: rplJ-0-rep3

description:
Library name: Sample 147
Experiment1


title: CAC 9 AlkB

description: Library name: CAC 9 AlkB


title: rplJ-0-rep2

description:
Library name: Sample 146
Experiment1


title: rplJ-0-rep1

description:
Library name: Sample 145
Experiment1


title: rhlR-0.05-rep3

description:
Library name: Sample 144
Experiment1


title: Cntl 6

description: Library name: Cntl 6


title: Cntl 9 AlkB

description: Library name: Cntl 9 AlkB


title: Cntl 5

description: Library name: Cntl 5


title: rhlR-0.0125-rep2

description:
Library name: Sample 140
Experiment1


title: Cntl 3

description: Library name: Cntl 3


title: Cntl 10 AlkB

description: Library name: Cntl 10 AlkB


title: rplJ-0.05-rep2

description:
Library name: Sample 152
Experiment1


title: Cntl 13 AlkB

description: Library name: Cntl 13 AlkB


title: Cntl 2

description: Library name: Cntl 2


title: rhlR-0.0125-rep1

description:
Library name: Sample 139
Experiment1


title: rhlR-0-rep3

description:
Library name: Sample 138
Experiment1


title: rpoB-0.0125-rep2

description:
Library name: Sample 158
Experiment1


title: CAC 7

description: Library name: CAC 7


title: CAC 16 AlkB

description: Library name: CAC 16 AlkB


title: rpoB-0-rep2

description:
Library name: Sample 155
Experiment1


title: CAC 6

description: Library name: CAC 6


title: rhlR-0.0125-rep3

description:
Library name: Sample 141
Experiment1


title: pbpA-0.05-rep2

description:
Library name: Sample 134
Experiment1


title: CAC 10 AlkB

description: Library name: CAC 10 AlkB


title: rplJ-0.05-rep1

description:
Library name: Sample 151
Experiment1


title: CAC 4

description: Library name: CAC 4


title: CAC 3

description: Library name: CAC 3


title: pbpA-0.0125-rep1

description:
Library name: Sample 130
Experiment1


title: CAC 1

description: Library name: CAC 1


title: CAC 12 AlkB

description: Library name: CAC 12 AlkB


title: rhlR-0.05-rep1

description:
Library name: Sample 142
Experiment1


title: Cntl 8

description: Library name: Cntl 8


title: pbpA-0-rep1

description:
Library name: Sample 127
Experiment1


title: CAC 5

description: Library name: CAC 5


title: Cntl 4

description: Library name: Cntl 4


title: pbpA-0.0125-rep3

description:
Library name: Sample 132
Experiment1


title: rhlR-0.05-rep2

description:
Library name: Sample 143
Experiment1


title: CAC 8

description: Library name: CAC 8


title: pbpA-0.05-rep3

description:
Library name: Sample 135
Experiment1


title: parC-0.05-rep2

description:
Library name: Sample 125
Experiment1


title: Cntl 4 AlkB

description: Library name: Cntl 4 AlkB


title: Cntl 5 AlkB

description: Library name: Cntl 5 AlkB


title: rhlR-0-rep2

description:
Library name: Sample 137
Experiment1


title: Wildtype Col-0 Arabidopsis roots, hypoxic, rep 2

city: Winnipeg

first: Claudio

last: Stasolla

state: MB

address: 66 Dafoe Road

department: Plant Science

country: Canada

institute: University of Manitoba

description:
Library name: Wt.Hypoxic.2
10X Genomics Chromium Next GEM Single Cell 3' Reagents Kit v3.1 (Dual Index)

data_processing:
Raw reads were pseudoaligned to the TAIR10 transcriptome and quantified with scKB (Hsu et al., 2022).
High-quality cells were selected with COPILOT (Hsu et al., 2022; default settings) and doublets were removed with DoubletFinder (McGinnis et al., 2019).
Cells were loaded into separate Seurat objects with Seurat v5.1.0 (Hao et al., 2024) and counts were normalized with SCTransform v0.4.1 (Hafemeister & Satija, 2019).
Each sample was integrated with the Shahan et al., 2022 Arabidopsis root atlas and annotation labels were transferred with Seurat [FindTransferAnchors, TransferData, AddMetaData].
Annotated samples were integrated into one Seurat object [SelectIntegrationFeatures, PrepSCTIntegration, FindIntegrationAnchors, IntegrateData].
PCA and UMAP dimension reductions were calculated (dims = 50).
Assembly: TAIR10
Supplementary files format and content: AtRootHypoxiaIntegrated.rds: Fully processed, integrated, and annotated dataset (Seurat v5 R object).
Supplementary files format and content: Gene counts output from COPILOT (Hsu et al., 2022); contains filtered high-quality cells with doublets removed. Sparse matrices in Market Exchange (MEX) format, consisting of gzipped tsv files of barcodes and features, and gzipped matrix files.

organism: Arabidopsis thaliana

source_name: Root tip, 1cm

growth_protocol: Arabidopsis (Arabidopsis thaliana) Col-0 seeds were sterilized in 70% ethanol containing 0.5% Triton X-100 for 15 min followed by 95% ethanol for 15 min (Mira et al. 2017). Seeds were plated in squared petri dishes containing agar germination medium [Murashige and Skoog (MS) salt with vitamins, 2.5% sucrose (w/v) and 0.8 % agar (w/v), pH 5.7], incubated for 24 h at 4 °C in the dark, and then transferred to a growth cabinet (22 °C, 16 h light/8 h dark).

extract_protocol:
Nuclei were isolated from fresh root tissue (1 cm root tips) using a modified protocol based on Guillotin et al. (Guillotin et al., 2023). Roots were collected from 5 different plates and immediately transferred into a pre-chilled Petri dish containing 300 µL of lysis buffer [0.3 M sucrose, 1.25% Ficoll, 2.5% Dextran T40, 15 mM Tris-HCl, 20 mM MES, 10 mM MgCl₂, 60 mM KCl, 15 mM NaCl, 0.5 mM spermine and spermidine, 0.05% Triton X-100, 5 mM DTT, 1 mM PMSF, 1% Protease Inhibitor Cocktail (Sigma P9599), 0.4 u/µl Protector RNase Inhibitor (Sigma), 0.4% BSA, 1% DEPC] and chopped on ice with two razor blades for 2–3 minutes. The homogenate was transferred to a chilled microcentrifuge tube, gently ground with a plastic micropestle, and incubated on ice for 2–3 minutes. The suspension was filtered through a 20 µm strainer into a chilled 1.5 ml Eppendorf tube, rinsed with 200 µL lysis buffer, and centrifuged at 1000 × g for 10 minutes. The supernatant was gently removed, and the pellet resuspended in 300 µL of wash buffer [0.3 M sucrose, 15 mM Tris-HCl, 15 mM MES, 60 mM KCl, 15 mM NaCl, 2 mM EDTA, 0.5 mM spermine and spermidine, 0.05% Triton X-100, 5 mM DTT, 1 mM PMSF, 1% Protease Inhibitor Cocktail, 0.2 u/µl Protector RNase Inhibitor, 0.4% BSA] and centrifuged at 1000 × g, 5 minutes. The pelleted nuclei were resuspended in 50–100 µL of final buffer [0.3 M sucrose, 15 mM Tris-HCl, 15 mM MES, 60 mM KCl, 15 mM NaCl, 0.5 mM spermine and spermidine, 5 mM DTT, 1% Protease Inhibitor Cocktail, 0.2 u/µl Protector RNase Inhibitor, 1% BSA]. The suspension was filtered through a 10 µm strainer into a fresh chilled tube.
Single-nuclei RNA-sequencing libraries were prepared using the 10X Genomics (Pleasanton, CA, USA) Chromium Next GEM Single Cell 3’ Reagents Kits v3.1 (Dual Index) protocol. A total of 902 million 100 bp paired-end reads were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA, USA) at Génome Québec (Montréal, QC, Canada).

treatment_protocol: Oxygen treatments were carried out on uniform 5-day-old seedlings as reported in Mira et al. (2024), with two replicates each. Briefly, plates were placed in acrylic desiccators flushed with either 4% oxygen (hypoxia) or 21% oxygen (normoxia) under dark conditions for 4 hours. Each biological replicate consisted of at least 50 plants across 5 plates.

value: Root tip, 1cm

value: Wildtype

tag: ecotype

value: 4hr hypoxia, 4% oxygen


title: pbpA-0.05-rep1

description:
Library name: Sample 133
Experiment1


title: Cntl 8 AlkB

description: Library name: Cntl 8 AlkB


title: Cntl 11 AlkB

description: Library name: Cntl 11 AlkB


title: pbpA-0-rep3

description:
Library name: Sample 129
Experiment1


title: pbpA-0.0125-rep2

description:
Library name: Sample 131
Experiment1


title: Cntl 1

description: Library name: Cntl 1


title: parC-0.0125-rep2

description:
Library name: Sample 122
Experiment1


title: Wildtype Col-0 Arabidopsis roots, normoxic, rep 2

description:
Library name: Wt.Normoxic.2
10X Genomics Chromium Next GEM Single Cell 3' Reagents Kit v3.1 (Dual Index)

value: 4hr normoxia, 21% oxygen


title: CAC 5 AlkB

description: Library name: CAC 5 AlkB


title: Cntl 7 AlkB

description: Library name: Cntl 7 AlkB


title: Wildtype Col-0 Arabidopsis roots, normoxic, rep 1

description:
Library name: Wt.Normoxic.1
10X Genomics Chromium Next GEM Single Cell 3' Reagents Kit v3.1 (Dual Index)


title: Cntl 2 AlkB

description: Library name: Cntl 2 AlkB


title: Cntl 6 AlkB

description: Library name: Cntl 6 AlkB


title: CAC 3 AlkB

description: Library name: CAC 3 AlkB


title: parC-0-rep3

description:
Library name: Sample 120
Experiment1


title: CAC 2 AlkB

description: Library name: CAC 2 AlkB


title: pbpA-0-rep2

description:
Library name: Sample 128
Experiment1


title: CAC 1 AlkB

description: Library name: CAC 1 AlkB


title: CAC 2

description: Library name: CAC 2


title: Cntl 1 AlkB

description: Library name: Cntl 1 AlkB


title: rhlR-0-rep1

description:
Library name: Sample 136
Experiment1


title: parC-0-rep2

description:
Library name: Sample 119
Experiment1


title: parC-0.0125-rep3

description:
Library name: Sample 123
Experiment1


title: parC-0.0125-rep1

description:
Library name: Sample 121
Experiment1


title: VTP, XPO1, rep2

city: HOUSTON

first: Margaret

last: Goodell

state: TX

address: 1 Baylor Plz, Rm N1030

institute: Baylor College of Medicine

data_processing:
Fastq files quality were controlled using fastqc/multizc
Cut-and-run paired-end reads were trimmed from 3' end using Trimmomatic and unique reads were mapped to the mouse genome (mm10) using Bowtie2
BigWig file for each biological replicates were generated using deepTools (bamCoverage) with counts-per-miillion (CPM) normalization and blacklist subtraction
Cut-and-run reads from biological replicates were then merged for peak calling using MACS3
Quantification of peaks for Cut-and-run sequencing was performed using Subread package (featureCounts)
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
100,000 counted cells were permeabalized with 0.01% Digtonin to perform antibody binding and Mnase digestion. The antibody-enriched DNA fragments were released and used for library construction
Cut-and-run sequencing library preparation was performed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645) according to the manufacturer’s protocol.

value: OCI-AML3 (NPM1c degron)

tag: cut-and-run antibody

value: VTP


title: parC-0.05-rep3

description:
Library name: Sample 126
Experiment1


title: VTP, NUP98, rep2


title: Rat lung CD31+ cells, Glenn surgery 3 weeks post-surgery, rep2

city: Milwaukee

first: Andrew

middle: D

last: Spearman

state: Wisconsin

address: 8701 Watertown Plank Rd

institute: Medical College of Wisconsin

description:
Library name: R2023-1435
10X Genomics

data_processing:
Default parameters using CellRanger (10X Genomics cloud analysis)
Assembly: Norway rat genome; Rnor_6.0.98
Supplementary files format and content: Raw counts matrix

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
Rat lung samples were dissociated using a gentleMACS OctoDissociator (Miltenyi) and multi-tissue dissociation kit 2 (Miltenyi). Cells were washed and resuspended in 0.04% BSA in sterile PBS.
Library preparation was performed using Chromium Next GEM single cell 3' reagent kits (10X Genomics).

value: Lung

value: Wild-type

value: Glenn surgery


title: parC-0-rep1

description:
Library name: Sample 118
Experiment1


title: VTP, Menin, rep2

value: Menin (CST, #6891)


title: VTP, MLL, rep2

value: MLL / HRX (Active Motif, #61295)


title: CAC 6 AlkB

description: Library name: CAC 6 AlkB


title: noguide-0.05-rep2

description:
Library name: Sample 116
Experiment1


title: Cntl 3 AlkB

description: Library name: Cntl 3 AlkB


title: CAC 7 AlkB

description: Library name: CAC 7 AlkB


title: VTP, IgG, rep2

value: mIgG (Abcam, #ab46540)


title: Rat lung CD31+ cells, sham surgery 3 weeks post-surgery, rep4

description:
Library name: R2023-1440
10X Genomics

value: Sham surgery


title: Wildtype Col-0 Arabidopsis roots, hypoxic, rep 1

description:
Library name: Wt.Hypoxic.1
10X Genomics Chromium Next GEM Single Cell 3' Reagents Kit v3.1 (Dual Index)


title: noguide-0.05-rep3

description:
Library name: Sample 117
Experiment1


title: CAC 8 AlkB

description: Library name: CAC 8 AlkB

value: HDL


title: parC-0.05-rep1

description:
Library name: Sample 124
Experiment1


title: CAC 4 AlkB

description: Library name: CAC 4 AlkB


title: Rat lung CD31+ cells, Glenn surgery 3 weeks post-surgery, rep4

description:
Library name: R2023-1439
10X Genomics


title: VTP, MLL, rep1


title: noguide-0.05-rep1

description:
Library name: Sample 115
Experiment1


title: Cntl 14 AlkB

description: Library name: Cntl 14 AlkB


title: Rat lung CD31+ cells, Glenn surgery 3 weeks post-surgery, rep3

description:
Library name: R2023-1437
10X Genomics


title: VTP, H3K27me3, rep1


title: VTP, H3K27me3, rep2


title: Rat lung CD31+ cells, sham surgery 3 weeks post-surgery, rep2

description:
Library name: R2023-1436
10X Genomics


title: Rat lung CD31+ cells, sham surgery 3 weeks post-surgery, rep1

description:
Library name: R2023-1434
10X Genomics


title: VTP, XPO1, rep1


title: Eltanexor, XPO1, rep2

value: Eltanexor


title: VTP, IgG, rep1


title: Eltanexor, NUP98, rep2


title: noguide-0-rep3

description:
Library name: Sample 111
Experiment1