title: TCR Sample 4

city: Guangzhou

first: Ting

last: Xu

address: No. 106, Zhongshan Second Road

institute: Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences

description: Library name: TCR Sample 4

data_processing:
The Cell Ranger software pipeline(version 5.0.0) provided by 10x Genomics was used to demultiplex cellular barcodes, map reads to the reference genome
The data were derived by extracting CD8+ T cells based on gene expression. The files barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz were generated to represent the single-cell RNA sequencing data of these cells.
Assembly: GRCh38
Supplementary files format and content: The raw counts matrix, gene features, and cell barcodes were extracted from the Seurat object and saved as CD8_matrix.mtx, CD8_features.tsv, and CD8_barcodes.tsv, respectively, along with the metadata, which was saved as CD8_metadata.csv, for GEO submission.

source_name: LG and PBMC

extract_protocol:
Single cells were suspended with PBS + 0.04% BSA and loaded to 10× chromium controller to generated Gel beads in emulsion using 10× genomics Single Cell 5’ Library & Gel Bead Kit
RNA libraries were prepared using Chromium Single Cell V(D)J Reagent Kits with Feature Barcoding technology for Cell Surface Protein according to the instructions of 10x genomics.

value: LG and PBMC

value: primary Sjögren’s syndrome

value: female


title: SCAF1AID_4sUSeq_Control_Rep2

status: Public on Dec 20 2024

type: SRA

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

country: Germany

institute: Christian-Albrechts-University Kiel

library_source: other

data_processing:
After adapter trimming, and removing reads mapping to rRNA, the remaining reads were aligned to a combined human+mouse genome (Ensembl v90) using STAR (version 2.5.3a) with the parameters “–outFilterMismatchNmax 20 –outFilterScoreMinOverLread 0.4 –outFilterMatchNminOverLread 0.4 –alignEndsType Extend5pOfReads12 –outSAMattributes nM MD NH'. The reads mapped to the mouse genome were counted for each library for normalization and then discarded. Human mapped read pairs, mapping inside of a gene body on the plus or minus strand were determined using the Ensembl (v90) annotation, and reads having T>C mismatches in the forward read or A>G mismatches in the reverse read were then saved. Spike normalization factors were calculated using mouse mapped reads.
Assembly: hg38
Supplementary files format and content: Bedgraphs were made with Bedtools genomeCoverageBed (v2.27.1) using the T>C coverted reads containing bam files, and applying the calculated spike factor and '-bga', '-split' options.
Library strategy: 4sU-seq

molecule: other

organism: Homo sapiens

growth_protocol: U2OS SCAF1-AID cells were grown in DMEM suplemented with 10 % FCS and 1% Penicillin/Streptomycin.

extract_protocol:
Cells were lysed using QIAzol and lysates were spiked with 4sU-treated mouse T-cell lysates. Total RNA was purified with the miRNeasy mini kit, precipitated to reduce volume, and then subject to fragmentation. Fragmented RNA was biotinylated. This was followed by 4sU-RNA pulldown using MyOne streptavidin beads, followed by purification with the RNeasy MinElute cleanup kit. The 4sU-RNA was subject to alkylation using iodoacetamide, and then alkylated-4sU-RNA was sequenced.
4sU-RNA was used for library preparation with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep kit. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform. Base calling was performed using Illumina’s BaseSpace platform.

treatment_protocol: Cells were treated with 1 µM auxin for 6 hours prior to harvest, and nascent-RNA was metabolically-labelled with 4-thio-uracil (4sU) 15 min prior to harvest.

tag: cell line

tag: cell type

value: Osteosarcoma

tag: genotype

tag: treatment

value: Control


title: SCAF1AID_4sUSeq_Auxin_Rep2

value: Auxin


title: SCAF1AID_4sUSeq_Auxin_Rep1


title: TCR Sample 2

country: China

description: Library name: TCR Sample 2

library_source: transcriptomic single cell

molecule: polyA RNA

tag: tissue

tag: disease state

tag: Sex


title: SCAF1AID_4sUSeq_Control_Rep1


title: TCR Sample 1

description: Library name: TCR Sample 1

source_name: PBMC

value: PBMC

value: healthy control


title: Gene expression Sample 3

description: Library name: Gene expression Sample 3


title: Gene expression Sample 2

description: Library name: Gene expression Sample 2


title: PBMC, S031162

type: RNA

city: Edinburgh

first: Max

last: Bylesjo

state: Scotland

address: BioCube 1, Edinburgh BioQuarter, 13 Little France Road

country: United Kingdom

institute: Fios Genomics Ltd

hyb_protocol: The samples were hybridized to Clariom S Human Array Plates according to standard Affymetrix GeneTitan protocol

scan_protocol: Array plates were scanned using the Affymetrix GeneTitan Scanner with AGCC and exported as CEL files

data_processing: CEL files were imported into R and the input data was normalized using RMA separately for high- and low-risk patients, resulting in normalized expression levels in log base 2

label: biotin

molecule: total RNA

label_protocol: Samples were labeled with biotin using the GeneChip WT Plus Reagent Kit according to the manufacturer's instructions.

extract_protocol: RNA was extracted from whole blood collected with PAXgene RNA tubes according to the manufacturer's recommendations

tag: pid

tag: time

value: 6 months

tag: centre

value: NANT

tag: transplant type

value: Full Thickness

tag: risk group

value: High

tag: rejection

value: No

tag: gender

value: F


title: 22Rv1 CPSF1 sh2 BR3

city: Minneapolis

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

country: USA

institute: Masonic Cancer Center, University of Minnesota

description:
CDS_PACcounts.tsv
Introns_PACcounts.tsv
TenKb3pNoExons_PACcounts.tsv
ThreePrimeUTR_PACcounts.tsv

library_source: transcriptomic

data_processing:
Fastq files containing 150 bp single-end reads were aligned to the GRCh37 reference genome using HiSat2 (v. 2.1.0). Subread (v. 2.0.3) was used to quantify gene expression using the version 87 GRCh37 annotation from Ensembl. Count data were filtered to only keep genes that had a cpm (counts per million) value greater than 1 cpm in at least two samples across all experimental conditions.
Assembly: GRCh37
Supplementary files format and content: Read counts as tab separated values
Library strategy: PAC-seq

source_name: Cell Line

growth_protocol: LNCaP and 22Rv1 cells were maintained in RPMI 1640 media with 10% FBS, LNCaP95 cells were maintained in RPMI 1640 phenol red free media with 10% FBS

extract_protocol:
Total RNA was extracted from cells using the ReliaPrep RNA miniprep system (Promega).
RNA was submitted to Click Seq Technologies for PAC-seq library synthesis using a Mid Output 400 M, v2 sequencing kit according to manufacturer’s instructions.

treatment_protocol: LNCaP, LNCaP95, 22Rv1 cells were transduced with lentivirus encoding shCTRL, shCPSF1-1, or shCPSF1-2, followed by two sequential rounds of selection with 2 μg/mL puromycin dihydrochloride for 22Rv1 and LNCaP and 1 μg/mL puromycin dihydrochloride  (Gibco, A11138-03). Infected cells were expanded and seeded in 6-well plates at 500,000 cells per well and grown for 72 h in normal RPMI 1640 + 10% FBS media for 22Rv1 and LNCaP and  RPMI 1640 phenol red free + 10% FBS for LNCaP95.

value: Cell Line

value: Prostate Cancer

value: shRNA targeting CPSF1 (2)


title: 22Rv1 CTRL sh BR3

value: CTRL shRNA


title: 22Rv1 CPSF1 sh1 BR3

value: shRNA targeting CPSF1 (1)


title: DNAm from healthy control sample2

type: genomic

city: Atlanta

first: Dawn

middle: Marie

last: Jensen

state: Georgia

address: 55 Park Place

department: TReNDS Center

institute: Georgia State University

description: DNAm from healthy control

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing:
RnBeads package in R environment (v4.1.1)
DT1 and DT2 are the deltaT1 and deltaT2 difference maps from the brain imaging and cognitive data for the analyses.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Saliva

label_protocol: Standard Illumina Protocol

extract_protocol: DNAm was extracted from saliva according to standard instructions

tag: ursi

value: Healthy

value: Saliva


title: 22Rv1 CPSF1 sh2 BR2


title: TCR Sample 3

description: Library name: TCR Sample 3

value: LG and PBMC

value: primary Sjögren’s syndrome

value: female


title: 22Rv1 CPSF1 sh2 BR1


title: ACSL4 Knockdown MDA-MB-231 cell line Replicate 3

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: Library name: ACSL4_KD_3

data_processing:
HQ trimmed and filtered raw data was provided as input to NF-CORE RNA Seq computational pipeline to sentively Identify expressed transcript and its representative gene with their mRNA copy numbers represented as read count
Raw read count along with gene annotation was provided to iDEP 2.0 web based analysis tool for down stream processing and analysis.
Assembly: GRch38
Supplementary files format and content: Whole-Genome_Genes_Read_Count_All_Samples.tsv

source_name: Breast

extract_protocol:
Total RNA was extracted using Trizol Method as per recommende procedure
As per Illumina recommended protocol

value: Breast

value: Breast Adenocarcinoma

value: Knockdown


title: ACSL4 Knockdown MDA-MB-231 cell line Replicate 2

description: Library name: ACSL4_KD_2


title: PRGL493 Treated MDA-MB-231 cell line Replicate 3

description: Library name: PRGL493_3


title: ACSL4 Knockdown MDA-MB-231 cell line Replicate 1

description: Library name: ACSL4_KD_1


title: PRGL493 Treated MDA-MB-231 cell line Replicate 1

description: Library name: PRGL493_1


title: Control MDA-MB-231 cell line Replicate 3

description: Library name: Control_3


title: 22Rv1 CTRL sh BR2


title: Day 100 SNO, scRNAseq

city: Philadelphia

first: Yusha

last: Sun

state: PA

address: 415 Curie Boulevard, Clinical Research Building, Room 105

institute: University of Pennsylvania Perelman School of Medicine

description: in-house modified Smart-seq3

data_processing:
To process single-cell RNA sequencing data, raw files were demultiplexed with bcl2fastq (Illumina) without adapter trimming and with the option for --create-fastq-for-index-reads. A combined fastq file consisting of a 22-bp cell barcode (composed of 8-bp index 1, 8-bp index 2, and 6-bp barcode) was then generated. Alignment was performed using STARsolo as part of STAR v2.7.10b with GRCh38 as the reference genome and gencode v.41 GTF as the annotation file, and with the following additional parameters: --alignIntronMax 1000000 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --limitOutSJcollapsed 4000000 --soloType CB_UMI_Simple --soloCBstart 1 --soloCBlen 22 --soloUMIstart 23 --soloUMIlen 8 --soloBarcodeMate 1  --clip5pNbases 30  --soloCBmatchWLtype 1MM_multi  --soloCellFilter EmptyDrops_CR  --soloStrand Reverse. A cell barcode text file was supplied, and multimapping alignments were discarded.
Note that the raw fastq.gz files are structured where the first 22 base pairs are the cell barcode, then the next 8 base pairs the UMI.
Assembly: hg38
Supplementary files format and content: Tab-separated value files, matrix files, and samplesheet csv files with barcode whitelist

source_name: human iPSC-derived cortical organoid

extract_protocol:
GBOs were first dissociated into a single-cell suspension with a brain tumor dissociation kit (Miltenyi Biotech, 130-0950929). In brief, 5-10 GBOs were washed with DPBS and incubated in 1 mL of dissociation mix according to the manufacturer’s protocol. GBOs were placed on a tube rotator in a 37°C incubator for 30 minutes to 1 hour with occasional pipetting to mechanically disrupt large tissue chunks. Cells were then strained through a 70 μm filter (Miltenyi Biotech, 130-110-916), centrifuged at 300g for 5 minutes and resuspended in 1 mL of GBO culture medium. Cell viability and cell concentration were measured with an automated cell counter (Thermo Fisher Scientific, Countess 3 Automated Cell Counter) with trypan blue staining (Thermo Fisher Scientific, C10312). An ideal cell viability following dissociation is typically > 80%. Cells were then resuspended in FACS pre-sort buffer (BD, 563503) with 0.2 μg/mL DAPI (BD, 564907). For sliced neocortical organoid (SNO) scRNAseq, 100-day old SNOs cultured as described above were dissociated in a similar manner as GBOs but with the addition of 50 μL Enzyme P (Miltenyi, 130-107-677) per 1 mL of dissociation mix. Single cells were sorted on a BD Influx (100 μm nozzle) with FACSDiva software into low-profile 96-well PCR plates (USA Scientific, 1402-9500) containing 3 μL of SMART-seq3 lysis buffer (0.5 μL PEG 8000 (40% solution, Sigma Aldrich, P1458), 0.03 μL Triton X-100 (10% solution), 0.02 μL of 100 μM Oligo-dT30VN, 0.2 μL of 10 mM dNTPs (Roche, 50-196-5273), 0.02 μL Protector RNase inhibitor (Sigma Aldrich, 3335402001), 0.02 μL recombinant RNase inhibitor (Takara, 2313B) and 2.21 μL nuclease-free water per reaction (Thermo Fisher Scientific, AM9932)) and 3 μL Vapor-Lock (Qiagen, 981611). Plates after sorting were briefly centrifuged, frozen on dry ice, and stored at -80°C for later processing.
For library preparation, plates were thawed, heated to 72°C for 10 minutes, and subsequently kept at 4°C for cell lysis. 3 μL of RT mix, containing 0.1 μL of 1 M Tris-HCl pH 8.3 (Hampton Research, HR2-900-14), 0.024 μL of 5 M NaCl (Thermo Fisher Scientific, AM9759), 0.01 μL of 1 M MgCl2 (Thermo Fisher Scientific, AM9530G), 0.04 μL of 1 mM GTP (Thermo Fisher Scientific, R1461), 0.32 μL of 100 mM DTT (Millipore Sigma, 3483-12-3), 0.016 μL of nuclease-free water, 0.025 μL Protector RNase inhibitor (Millipore Sigma, C852A14), 0.025 μL recombinant RNase inhibitor (Takara, 2313B), 0.04 μL reverse transcriptase (Thermo Fisher Scientific, EP0753), and 0.4 μL of 20 μM TSO, was added to each well of the 96-well plate. To enable multiplexing and enhance throughput, we designed 48 unique TSOs consisting of an additional 6-bp cell barcode directly adjacent to the 5’-end of the Smart-seq3 UMI. Reverse transcription was performed with the following thermocycling conditions: 42°C for 90 minutes, 10 cycles of 50°C for 2 minutes and 42°C for 2 minutes, 85°C for 5 minutes, and 4°C indefinitely. Next, for cDNA amplification, 6 μL of PCR mix, consisting of 2 μL 5X KAPA HiFi HotStart Buffer (Roche, KK2502), 0.3 μL of 10 mM dNTPs, 0.005 μL of 1 M MgCl2, 0.01 μL of 1mM PCR forward primer, 0.01 μL of 100 μM PCR reverse primer, 3.475 μL of nuclease-free water, and 0.2 μL of KAPA HiFi HotStart polymerase (Roche, KK2502), was added to each well. cDNA amplification was performed with the following thermocycling conditions: 98°C for 3 minutes, 18 cycles of 98°C for 20 seconds then 65°C for 30 seconds then 72°C for 4 minutes, 72°C for 5 minutes, and 4°C indefinitely. cDNA from 48 wells was then pooled together into one sample (2 samples per plate), and samples were then purified twice with 0.6X then 0.8X AMPure XP beads (Thermo Fisher Scientific, A63881) and eluted in 10 μL of nuclease-free water. cDNA was quantified using Qubit dsDNA HS assay kit (Life Technologies, Q32851). Each sample was then tagmented by mixing 2 μL of 0.5 ng/μL cDNA, 4 μL of 2X TD buffer (20 mM Tris pH 8.0, 10 mM MgCl2, 20% dimethylformamide (Sigma, D4551)), and 2 μL of Tn5 (Thermo Fisher Scientific, TNP92110) and incubating at 55°C for 20 minutes with reaction termination upon addition of 2 μL of 0.2% SDS (Invitrogen, 15553-035) at room temperature for 5 minutes. We chose to use i5-only Tn5 to enrich for the 5’-ends of mRNA, although full-length sequencing can be achieved using i5/i7 Tn5. Fragments were amplified by adding 1 μL of 10 μM Nextera i7 primer, 1 μL 10 μM Nextera i5 primer, 5 μL of 5X Phusion Plus Buffer (Thermo Fisher Scientific, F630L), 0.5 μL of 10 mM dNTPs, 0.5 μL of 1% Tween-20, 6.8 μL nuclease-free water, and 0.2 μL of Phusion Plus polymerase (Thermo Fisher Scientific, F630L). Tagmentation PCR was performed with the following thermocycling conditions: 98°C for 3 minutes, 8 cycles of 98°C for 10 seconds then 60°C for 30 seconds then 72°C for seconds, 72°C for 5 minutes, and then indefinitely at 4°C. Resulting DNA was purified twice with 0.8X then 1.0X AMPure XP beads and eluted in 10 μL of 10 mM Tris, pH 8.0. Samples were then quantified by qPCR with library sizes quantified by Bioanalyzer (Agilent). Samples were sequenced on either a NovaSeq 6000 (Illumina) or NextSeq 550 (Illumina) at a final depth of roughly 100K-200K reads/cell.

value: human iPSC-derived cortical organoid

value: nonmalignant


title: LNCaP95 CPSF1 sh2 BR3


title: Control MDA-MB-231 cell line Replicate 2

description: Library name: Control_2


title: Gene expression Sample 4

description: Library name: Gene expression Sample 4


title: K562 ML324 treated rep2

city: Beijing

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

description: Sample 26

data_processing:
(Sample 21~26) For RNA-seq: All reads were aligned to human genome (Ensembl GRCh38.83) using STAR and uniquely mapped reads were retained for further analysis.
FeatureCounts was used for calculating gene counts, and normalized for transcripts per million (TPM) using in-house scripts.
Differential gene expression analysis was conducted using DESeq2 with the p-value < 0.05, and all genes with non-zero counts in any sample were considered.
Assembly: Human GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: (Sample 21~26) For RNA-seq: Human erythroleukemia cell line K562 was maintained in RPMI1640 supplemented with 10% FBS (Gibco, 16140089), 100 IU/ml penicillin and 100 μg/ml streptomycin (Gibco, 15070063).

extract_protocol:
(Sample 21~26) For RNA-seq: K562 cell precipitation was collected and total RNA was harvested using Trizol reagent respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: (Sample 21~26) For RNA-seq: K562 cells were cultured with 0.1% DMSO (for untreated), 2.5µM 1,10-Phen (for 1,10-Phen treated), 5µM ML324 (for ML324 treated) at 37°C, 5% CO2 for 48~72h.

value: ML324 treated


title: Gene expression Sample 1

description: Library name: Gene expression Sample 1

value: PBMC

value: healthy control


title: UP-10072, baseline and ACh, scRNAseq

description: in-house modified Smart-seq3

source_name: human glioblastoma

value: human glioblastoma

value: malignant


title: K562 ML324 treated rep1

description: Sample 25


title: LNCaP95 CPSF1 sh1 BR3

value: Cell Line

value: Prostate Cancer


title: LNCaP95 CTRL sh BR3

value: CTRL shRNA


title: UP-9121 and UP-9096, baseline and ACh, scRNAseq

description: in-house modified Smart-seq3


title: PRGL493 Treated MDA-MB-231 cell line Replicate 2

description: Library name: PRGL493_2


title: LNCaP95 CPSF1 sh2 BR2

value: shRNA targeting CPSF1 (2)


title: K562 1,10-Phen treated rep2

description: Sample 24

value: 1,10-Phen treated


title: LNCaP95 CPSF1 sh1 BR2

value: shRNA targeting CPSF1 (1)


title: 22Rv1 CPSF1 sh1 BR2


title: K562 1,10-Phen treated rep1

description: Sample 23


title: LNCaP95 CTRL sh BR2


title: 22Rv1 CPSF1 sh1 BR1


title: K562 Ctrl rep2

description: Sample 22

value: untreated


title: K562 Ctrl rep1

description: Sample 21


title: LNCaP95 CPSF1 sh1 BR1


title: K562 P1-KD polysomes rep2

description: Sample 20

data_processing:
(Sample 13~20) For Polysome-seq: For analysis, the ERCC sequences were download from Thermofisher website (https://www.thermofisher.com).
All reads were mapped to human genome (Ensembl GRCh38.83) and ERCC sequences by STAR and uniquely mapped reads were counted by featureCounts. DESeq2 was used to calculate ERCC spike-in RNA size factors, which were then applied to normalize library size in each replicate.
EdgeR was used to estimate differential gene expression in Polysome-seq and RNA-seq respectively. Then, we calculated the translation efficiency (TE) by taking log2 (the ratio of Polysome-seq over RNA-seq) and considered a gene differentially translated when it met P-value < 0.05 and |log2 (ratio)| > log2 (1.5).
Assembly: Human GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Library strategy: Polysome-seq

growth_protocol: (Sample 13~20) For Polysome-seq: Human erythroleukemia cell line K562 was maintained in RPMI1640 supplemented with 10% FBS (Gibco, 16140089), 100 IU/ml penicillin and 100 μg/ml streptomycin (Gibco, 15070063).

extract_protocol:
(Sample 13~20) For Polysome-seq: 450 µl lysate was prepared as described (Analysis of mRNA Translation by Polysome Profiling. Methods Mol Biol 2404, 69-81, 2022.). 100 µl lysate was used to prepare input (shCtrl, PABPC1 KD). 350 µl lysate was used to prepare heveay polysomes (shCtrl, PABPC1 KD). Total RNA of input, polysomes were harvested using LS Trizol reagent respectively, dissolved using equal volume of nuclease free water, ERCC per component and removed rRNA in them.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: (Sample 13~20) For Polysome-seq: After being transfected with shCtrl (for untreated), shPABPC1 (for PABPC1 KD) lentivirus for 4~5 days, K562 cells were incubated with 100 µg /ml cycloheximide (CHX, CST) at 37°C, 5%CO2 for 10 min, washed twice with ice-cold PBS containing 100 µg/ml of CHX and lysed in lysis buffer.

value: PABPC1 knockdown


title: K562 P1-KD polysomes rep1

description: Sample 19


title: Control MDA-MB-231 cell line Replicate 1

description: Library name: Control_1

value: Breast

value: Breast Adenocarcinoma


title: LNCaP95 CTRL sh BR1


title: LNCaP CPSF1 sh2 BR3

value: LNCaP


title: 22Rv1 CTRL sh BR1


title: LNCaP CPSF1 sh1 BR3


title: K562 P1-KD input rep1

description: Sample 17


title: K562 Polysomes rep1

description: Sample 15


title: LNCaP CTRL sh BR2


title: K562 input rep1

description: Sample 13


title: K562 input rep2

description: Sample 14


title: K562 P1-KD input rep2

description: Sample 18


title: K562 Polysomes rep2

description: Sample 16


title: K562 RIP input rep2 (ML324 treated)

description: Sample 12

data_processing:
(Sample 1~12) For RIP-seq: All reads were aligned to human genome (Ensembl GRCh38.83) using STAR and uniquely mapped reads were retained for further analysis.
FeatureCounts was used for calculating gene counts, and normalized for transcripts per million (TPM) using in-house scripts.
The protein-bound transcripts were identified by DESeq2 with P-value < 0.05 and fold change (IP versus input) > 1.2. All genes with TPM ≥ 1 in any sample were considered.
Assembly: Human GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: (Sample 1~12) For RIP-seq: Human erythroleukemia cell line K562 was maintained in RPMI1640 supplemented with 10% FBS (Gibco, 16140089), 100 IU/ml penicillin and 100 μg/ml streptomycin (Gibco, 15070063).

extract_protocol:
(Sample 1~12) For RIP-seq: K562 cell precipitation was collected and lysed in lysis buffer to perform input and PABPC1 Immunoprecipitation (untreated, 1,10-Phen treated, ML324 treated). Total RNA of input, PABPC1 Immunoprecipitation was harvested using Trizol reagent respectively and removed rRNA in them.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: (Sample 1~12) For RIP-seq: K562 cells were cultured with 0.1% DMSO (for untreated), 2.5µM 1,10-Phen (for 1,10-Phen treated), 5µM ML324 (for ML324 treated) at 37°C, 5% CO2 for 48~72h.


title: LNCaP CPSF1 sh1 BR2


title: LNCaP CPSF1 sh2 BR1


title: LNCaP CPSF1 sh1 BR1


title: K562 RIP input rep1 (ML324 treated)

description: Sample 11


title: LNCaP CTRL sh BR1


title: K562 PABPC1 IP rep2 (ML324 treated)

description: Sample 10


title: K562 PABPC1 IP rep1 (ML324 treated)

description: Sample 9


title: LNCaP95 CPSF1 sh2 BR1


title: K562 RIP input rep2 (1,10-Phen treated)

description: Sample 8


title: K562 RIP input rep1 (1,10-Phen treated)

description: Sample 7


title: LNCaP CTRL sh BR3


title: K562 PABPC1 IP rep2 (1,10-Phen treated)

description: Sample 6


title: K562 RIP input rep2 (untreated)

description: Sample 4


title: LNCaP CPSF1 sh2 BR2


title: K562 RIP input rep1 (untreated)

description: Sample 3


title: K562 PABPC1 IP rep2 (untreated)

description: Sample 2


title: K562 PABPC1 IP rep1 (untreated)

description: Sample 1


title: BAP1_HEK293T

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg19,mm9
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: The SCLC cell lines NCI-H526 was obtained from ATCC, and were maintained with ATCC-formulated RPMI-1640 medium containing 10% FBS (Sigma).

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. For ATAC-seq, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience). 50K to 100K nuclei were then centrifuge (pre-chilled) at 500 g for 10 min. Supernatant was then removed and the nuclei were resuspended in 50 uL of tagmentated DNA by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer shaking at 1,000 rpm, and then cleaned up by the MiniElute reaction clean up kit (Qiagen).
ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter). for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE.
ATAC-seq: Tagmentated DNA was amplified with barcode primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 50M PE reads (25M in each direction) per sample.

value: kidney

value: wild type


title: Beclin_cKO_2mo 2

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from Becn1 conditional KO sciatic nerve from 2 months old mice

hyb_protocol: 5.5ug of sscDNA were fragmentated and 5.2 ug were hybridized for 16 hr at 45°C on GeneChip Mouse Clariom S Array (GPL23038 Platform). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using TAC software using RMA

organism: Mus musculus

source_name: murine sciatic nerve

label_protocol: Biotinylated cRNA were prepared according to the standardThermoFisher protocol starting  from 100ng of Total RNA using the ThermoFisher WTA Kit

growth_protocol: Sciatic nerves were dissected from control and Schwann cell conditional Becn1 knockout mice at P10 and 2 months of age.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen), according to the manufacturer’s instructions.

value: Becn1 cKO

value: 2 months old


title: Beclin_cKO_2mo 1


title: HEK293T_BAP1_KO_BAP1_Rep1

value: infected with BAP1_WT


title: Beclin_wt_2mo 4

description: Gene expression data from Becn1 wild-type sciatic nerve from 2 months old mice

value: Becn1 wild-type


title: K562 PABPC1 IP rep1 (1,10-Phen treated)

description: Sample 5


title: HEK293T_BAP1_KO_GFP_Rep2

value: infected with GFP


title: Beclin_cKO_2mo 3


title: HEK293T_BAP1_WT_GFP_Rep2


title: Beclin_cKO_2mo 4


title: HEK293T_BAP1_KO_GFP_Rep1


title: Beclin_cKO_P10 1

description: Gene expression data from Becn1 conditional KO sciatic nerve from 10 days old mice

value: 10 days old


title: HEK293T_BAP1_KO_C91S_Rep1

value: infected with BAP1_C91S


title: Beclin_cKO_P10 4


title: Beclin_wt_2mo 3


title: Beclin_cKO_P10 2


title: Beclin_wt_P10 2

description: Gene expression data from Becn1 wild-type sciatic nerve from 10 days old mice


title: Huh7.5.1 Cas9-P2A-blasticidin cells, ZEBOV minigenome replicon cells, d19, low-GFP sorted, replicate 1

city: San Francisco

first: Amy

middle: L

last: Kistler

state: CA

address: 499 Illinois St, 4th floor

institute: Chan Zuckerberg Biohub

description: Library name: Sample 9

data_processing:
Demultiplexed FASTQ files were analyzed using the 'count' subcommand of MAGeCK software (v0.5.9.4; Li et al., 2014) to quantify sgRNA abundance by matching reads to the sgRNA library sequences, with the normalization method set to 'total'. The sgRNA count tables were subsequently analyzed using the ‘test’ subcommand (RRA) of MAGeCK software (v0.5.9.4; Li et al., 2014) to calculate positive enrichment scores for each gene. The two-step process was automated using Nextflow (v21.10.6). The analysis workflow standardizes metadata conventions. (Available at https://github.com/czbiohub-sf/CRISPRflow/blob/main/modules.nf)
Assembly: Brunello sgRNA library (Available at https://media.addgene.org/cms/filer_public/8b/4c/8b4c89d9-eac1-44b2-bb2f-8fea95672705/broadgpp-brunello-library-contents.txt)
Supplementary files format and content: Tab-delimited text file provides statistics for gene enrichment in GFP-low population compared to unsorted or high population, calculated from replicate 1 and replicate 2 data combined.
Supplementary files format and content: Tab-delimited text file provides statistics for sgRNA enrichment in GFP-low population compared to unsorted or high population, calculated from replicate 1 and replicate 2 data combined.
Library strategy: CRISPR Screen

source_name: cell line

growth_protocol: Huh7.5.1 cell lines stably transduced with spCas9-P2A-blasticidinR genes and a ZEBOV minigenome replicon system was maintained in DMEM media supplemented with 10% FBS and 200ug/mL zeocin antibiotic at 37C in a humidified atmosphere with 5% CO2. Cells were transitioned to antibiotic free media 24h prior to transduction with pooled lentiviral library of Brunello sgRNAs, and transitioned to media supplemented with 4ug/mL puromycin for 2-4 days post transduction, then cultured without antibiotics throughout the course of the screen.

extract_protocol:
Genomic DNA was extracted from the cell pellets of the sorted cells using the Zymo Quick-DNA Miniprep Plus kit and from cell pellets of the unsorted cells using the Qiagen Blood Maxi Kit. The genomic DNA preps were further purified from contaminants using the Zymo OneStep PCR Inhibitor Removal Kit.
Sequencing libraries were prepared from extracted genomic DNA by PCR amplification using barcoded Illumina P7 and P5 primers of the sgRNA cassettes. The entire prep of extracted gDNA was barcoded and amplified (1 µg gDNA/ 50 µl PCR reaction) for each screen condition.

treatment_protocol: pooled genome-wide sgRNA library-mediated gene depletions. Cells were harvested directly after puromycin selection, or incubated further, and subjected to FACS to harvest cells in the bottom 20% (GFP-low) or top 10% (GFP-high) range of population fluorescence on day 20 post-transduction.

value: cell line

value: human hepatoma cells

value: Brunello lentiviral sgRNA KO library pool transduction


title: Beclin_wt_P10 3


title: Beclin_wt_2mo 1


title: Beclin_wt_2mo 2


title: HEK293T_BAP1_WT_GFP_Rep1


title: Beclin_wt_P10 4


title: Huh7.5.1 Cas9-P2A-blasticidin cells, ZEBOV minigenome replicon cells, d0, unsorted, replicate 1

description: Library name: Sample 10


title: HEK293T_C91S_Clone 2_Rep2


title: Beclin_cKO_P10 3


title: Huh7.5.1 Cas9-P2A-hygromycin cells, DENV2 replicon cells, d19, low-GFP sorted, replicate 1

description: Library name: Sample 1


title: Huh7.5.1 Cas9-P2A-hygromycin cells, DENV2 replicon cells, d19, low-GFP sorted, replicate 2

description: Library name: Sample 3


title: Huh7.5.1 Cas9-P2A-hygromycin cells, DENV2 replicon cells, d19, high-GFP sorted, replicate 1

description: Library name: Sample 2


title: HEK293T_C91S_Clone 1_Rep2


title: THP1, ∆EccCa1-Rv Uninfected, 16h_sorted, rep 2

city: Cambridge

middle: K.

last: Barczak

state: MA

address: The Ragon Institute, 400 Technology Square

department: Medicine/Infectious Diseases

institute: Massachusetts General Hospital

data_processing:
Raw reads were aligned to the human genome using TopHat
Cufflinks was used to estimate the transcript abundance
Assembly: GRCh37
Supplementary files format and content: Cufflinks_FPKM values for each sample is provided in escel file

source_name: THP1 differentiated to macrophages with PMA

growth_protocol: THP1 monocytes were differentiated to macrophage with PMA stimulation

extract_protocol:
Poly(A) containing mRNA was isolated from the RNA extracted from the flow sorted samples using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina Index Primers

treatment_protocol: Macrophages were infected with H37Rv-GFP and ∆EccCa1-Rv-GFP strains and incubated for 4 hours. Cells were washed with PBS and media was replaced. Thereafter, the cells were sorted to GFP+(Infected) and GFP-(Unifected samples and total RNA was extracted every 2hrs, 4hrs, 8hrs and 16 hrs post infection

value: 16hrs ∆EccCa1-Rv bystanders


title: HEK293T_C91S_Clone 1_Rep1


title: THP1, ∆EccCa1-Rv infected, 16h_sorted, rep 2

value: THP1 differentiated to macrophages with PMA

value: 16hrs ∆EccCa1-Rv infected


title: HEK293T_WT_Rep1


title: THP1, ∆EccCa1-Rv Uninfected, 16h_sorted, rep 1


title: THP1, ∆EccCa1-Rv infected, 16h_sorted, rep 1


title: THP1, H37Rv Uninfected, 16h_sorted, rep 2

value: 16hrs H37Rv bystanders


title: THP1, H37Rv Uninfected, 16h_sorted, rep 1


title: MP65_BAP1_WT_Rep1

value: melanoma


title: THP1, H37Rv infected, 16h_sorted, rep 1

value: 16hrs H37Rv infected


title: MP65_GFP_Rep2

value: wild type


title: MP65_BAP1_C91S_Rep2


title: THP1, H37Rv infected, 16h_sorted, rep 2


title: THP1, ∆EccCa1-Rv Uninfected, 8h_sorted, rep 2

value: 8hrs ∆EccCa1-Rv bystanders


title: MP65_GFP_Rep1


title: Beclin_wt_P10 1


title: UP-10072, UP-9121, UP-9096, time course variations

description:
Bulk ACh time course
in-house modified Smart-seq3 for bulk RNA seq

data_processing:
Raw files were demultiplexed with bcl2fastq (Illumina) without adapter trimming and with the option for --create-fastq-for-index-reads. A combined fastq file consisting of a 22-bp cell barcode (composed of 8-bp index 1, 8-bp index 2, and 6-bp barcode) was then generated. Alignment was performed using STARsolo as part of STAR v2.7.10b with GRCh38 as the reference genome and gencode v.41 GTF as the annotation file, and with the following additional parameters: --alignIntronMax 1000000 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --limitOutSJcollapsed 4000000 --soloType CB_UMI_Simple --soloCBstart 1 --soloCBlen 22 --soloUMIstart 23 --soloUMIlen 8 --soloBarcodeMate 1  --clip5pNbases 30  --soloCBmatchWLtype 1MM_multi  --soloCellFilter EmptyDrops_CR  --soloStrand Reverse --soloUMIdedup NoDedup. A sample barcode text file was supplied, and multimapping alignments were discarded. The NoDedup option was used to account for increased UMI complexity of these samples.
Note that the raw fastq.gz files are structured where the first 22 base pairs are the cell barcode, then the next 8 base pairs the UMI.
Assembly: hg38
Supplementary files format and content: Tab-separated value files, matrix files, and samplesheet csv files with barcode whitelist.

extract_protocol:
GBOs were reaggregated into organoids of 2000 cells in 96-well U-bottomed plates. For ACh experiments, ACh (acetylcholine chloride, Sigma Aldrich, A6625) was applied to a final concentration of 1 mM for various durations prior to removal of medium and sample lysis. If any condition required a waiting period prior to lysis, GBOs were washed once with GBO medium prior to complete replacement with fresh GBO medium. For sequencing of CHRM3 knockdown GBOs, GBO cells were directly infected with either scrambled or knockdown lentivirus prior to reaggregation as described above for retroviral infection, and cells were subjected to 1-hour ACh treatment 7 days following shRNA transduction. Sample lysis was performed by adding 30 μL of SMART-seq3 lysis buffer (5 μL PEG 8000 (40% solution, Sigma Aldrich, P1458), 0.3 μL Triton X-100 (10% solution), 0.2 μL of 100 μM Oligo-dT30VN, 2 μL of 10 mM dNTPs (Roche, 50-196-5273), 0.2 μL Protector RNase inhibitor (Sigma Aldrich, 3335402001), 0.2 μL recombinant RNase inhibitor (Takara, 2313B) and 22.1 μL nuclease-free water (Thermo Fisher Scientific, AM9932)) to each well.
For library preparation, the plate was heated to 72°C for 10 minutes, and subsequently kept at 4°C for cell lysis. 30 μL of RT mix, containing 1 μL of 1 M Tris-HCl pH 8.3 (Hampton Research, HR2-900-14), 0.24 μL of 5 M NaCl (Thermo Fisher Scientific, AM9759), 0.1 μL of 1 M MgCl2 (Thermo Fisher Scientific, AM9530G), 0.4 μL of 1 mM GTP (Thermo Fisher Scientific, R1461), 3.2 μL of 100 mM DTT (Millipore Sigma, 3483-12-3), 0.16 μL of nuclease-free water, 0.25 μL Protector RNase inhibitor (Millipore Sigma, C852A14), 0.25 μL recombinant RNase inhibitor (Takara, 2313B), 0.4 μL reverse transcriptase (Thermo Fisher Scientific, EP0753), and 4 μL of 20 μM TSO, was added to each well of the 96-well plate. To enable multiplexing and enhance throughput, we designed 48 unique TSOs consisting of an additional 6-bp cell barcode directly adjacent to the 5’-end of the Smart-seq3 UMI. Reverse transcription was performed with the following thermocycling conditions: 42°C for 90 minutes, 10 cycles of 50°C for 2 minutes and 42°C for 2 minutes, 85°C for 5 minutes, and 4°C indefinitely. Next, for cDNA amplification, 6 μL of PCR mix, consisting of 20 μL 5X KAPA HiFi HotStart Buffer (Roche, KK2502), 3 μL of 10 mM dNTPs, 0.05 μL of 1 M MgCl2, 0.1 μL of 1mM PCR forward primer, 0.1 μL of 100 μM PCR reverse primer, 34.75 μL of nuclease-free water, and 2 μL of KAPA HiFi HotStart polymerase (Roche, KK2502), was added to each well. cDNA amplification was performed with the following thermocycling conditions: 98°C for 3 minutes, 16 cycles of 98°C for 20 seconds then 65°C for 30 seconds then 72°C for 4 minutes, 72°C for 5 minutes, and 4°C indefinitely. cDNA from 48 wells was then pooled together into one sample (2 samples per plate), and samples were then purified twice with 0.6X then 0.8X AMPure XP beads (Thermo Fisher Scientific, A63881) and eluted in 100 μL of nuclease-free water. cDNA was quantified using Qubit dsDNA HS assay kit (Life Technologies, Q32851). Each sample was then tagmented by mixing 10 μL of 0.5 ng/μL cDNA, 20 μL of 2X TD buffer (20 mM Tris pH 8.0, 10 mM MgCl2, 20% dimethylformamide (Sigma, D4551)), and 10 μL of diluted Tn5 (Thermo Fisher Scientific, TNP92110) and incubating at 55°C for 20 minutes with reaction termination upon addition of 10 μL of 0.2% SDS (Invitrogen, 15553-035) at room temperature for 5 minutes. We chose to use i5-only Tn5 to enrich for the 5’-ends of mRNA, although full-length sequencing can be achieved using i5/i7 Tn5. Fragments were amplified by adding 5 μL of 10 μM Nextera i7 primer, 5 μL 10 μM Nextera i5 primer, 25 μL of 5X Phusion Plus Buffer (Thermo Fisher Scientific, F630L), 2.5 μL of 10 mM dNTPs, 2.5 μL of 1% Tween-20, 17 μL nuclease-free water, and 1 μL of Phusion Plus polymerase (Thermo Fisher Scientific, F630L). Tagmentation PCR was performed with the following thermocycling conditions: 98°C for 3 minutes, 10 cycles of 98°C for 10 seconds then 60°C for 30 seconds then 72°C for seconds, 72°C for 5 minutes, and then indefinitely at 4°C. Resulting DNA was purified twice with 0.8X then 1.0X AMPure XP beads and eluted in 10 μL of 10 mM Tris, pH 8.0. Samples were then quantified by qPCR with library sizes quantified by Bioanalyzer (Agilent). Samples were sequenced on  a NovaSeq 6000 (Illumina) at a final depth of roughly 12-15M reads/sample (with one sample being one well/barcode).

value: human glioblastoma

value: malignant


title: Huh7.5.1 Cas9-P2A-hygromycin cells, DENV2 replicon cells, d19, high-GFP sorted, replicate 2

description: Library name: Sample 4


title: THP1, ∆EccCa1-Rv Uninfected, 8h_sorted, rep 1


title: HEK293T_C91S_Clone 2_Rep1

value: kidney


title: UP-10072, UP-9121, UP-9096, 1h ACh variations

description:
Bulk ACh 1 hour
in-house modified Smart-seq3 for bulk RNA seq


title: THP1, ∆EccCa1-Rv infected, 8h_sorted, rep 1

value: 8hrs ∆EccCa1-Rv infected


title: THP1, ∆EccCa1-Rv infected, 8h_sorted, rep 2


title: Serum_Patient_22_Post-Op

first: Felipe

last: Takaesu

address: 1562 Haygood Drive

institute: Emory University

description:
p23186-s045_Patient-22-Post-Op-TotalRNA_S325_L001_R1_001.fastq.gz
human_serum_counts.txt

data_processing:
Raw data from Illumina was converted to fastq format. Total RNA sequences were cleaned using
the TrimGalore wrapper package. Cleaned reads were then  further processed using the bbduk.sh package in the BBMap suite. Reads were analyzed for  polybase sequences and ribosomal RNA contaminants and removed. The subsequent reads  underwent alignment using the STAR aligner.
miRNA sequences were processed using a similar pipeline. QIAseq miRNA adapters from 3’
and 5’ ends were trimmed using the TrimGalore wrapper package, followed by quality trimming.
Alignment of the miRNA was preformed using miRDeep2
Assembly: GRCh38
Supplementary files format and content: Excel files containing miRNA and total RNA raw counts for sEV samples
Supplementary files format and content: Excel file containing raw count for Serum samples

source_name: Serum

extract_protocol:
serum or EV RNAs were isolated using a Plasma/Serum RNA  Purification Mini Kit and an Exosomal RNA Isolation Kit per the manufacturer’s instructions. Quality control of the isolated RNAs was  performed using an Agilent Bioanalyzer
Total RNA libraries were prepared using SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian protocol. miRNA libraries were prepared using the QIAseq miRNA Library Kit.

value: Serum

value: Post-Op


title: THP1, H37Rv Uninfected, 8h_sorted, rep 2

value: 8hrs H37Rv bystanders


title: Serum_Patient_19_Post-Op

description:
p23186-s043_Patient-19-Post-Op-TotalRNA_S323_L001_R1_001.fastq.gz
human_serum_counts.txt


title: HEK293T_WT_Rep2


title: MP65_BAP1_C91S_Rep1

value: infected with BAP1_C91S


title: THP1, H37Rv Uninfected, 8h_sorted, rep 1


title: Serum_Patient_18_Post-Op

description:
p23186-s042_Patient-18-Post-Op-TotalRNA_S322_L001_R1_001.fastq.gz
human_serum_counts.txt


title: THP1, ∆EccCa1-Rv Uninfected, 4h_sorted, rep 1

value: 4hrs ∆EccCa1-Rv bystanders


title: THP1, ∆EccCa1-Rv Uninfected, 4h_sorted, rep 2


title: Serum_Patient_16_Post-Op

description:
p23186-s040_Patient-16-Post-Op-TotalRNA_S320_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_13_Post-Op

description:
p23186-s038_Patient-13-Post-Op-TotalRNA_S318_L001_R1_001.fastq.gz
human_serum_counts.txt


title: THP1, ∆EccCa1-Rv infected, 4h_sorted, rep 2

value: 4hrs ∆EccCa1-Rv infected


title: THP1, H37Rv infected, 8h_sorted, rep 2

value: THP1 differentiated to macrophages with PMA

value: 8hrs H37Rv infected


title: THP1, H37Rv Uninfected, 4h_sorted, rep 2

value: 4hrs H37Rv bystanders


title: MP65_BAP1_WT_Rep2

value: melanoma

value: infected with BAP1_WT


title: Serum_Patient_10_Post-Op

description:
p23186-s035_Patient-10-Post-Op-TotalRNA_S315_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_11_Post-Op

description:
p23186-s036_Patient-11-Post-Op-TotalRNA_S316_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_12_Post-Op

description:
p23186-s037_Patient-12-Post-Op-TotalRNA_S317_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_21_Post-Op

description:
p23186-s044_Patient-21-Post-Op-TotalRNA_S324_L001_R1_001.fastq.gz
human_serum_counts.txt


title: THP1, H37Rv infected, 4h_sorted, rep 2

value: 4hrs H37Rv infected


title: Serum_Patient_14_Post-Op

description:
p23186-s039_Patient-14-Post-Op-TotalRNA_S319_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_9_Post-Op

description:
p23186-s034_Patient-9-Post-Op-TotalRNA_S314_L001_R1_001.fastq.gz
human_serum_counts.txt


title: THP1, H37Rv infected, 8h_sorted, rep 1


title: Serum_Patient_8_Post-Op

description:
p23186-s033_Patient-8-Post-Op-TotalRNA_S313_L001_R1_001.fastq.gz
human_serum_counts.txt


title: THP1, H37Rv infected, 4h_sorted, rep 1


title: Serum_Patient_7_Post-Op

description:
p23186-s032_Patient-7-Post-Op-TotalRNA_S312_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_6_Post-Op

description:
p23186-s031_Patient-6-Post-Op-TotalRNA_S311_L001_R1_001.fastq.gz
human_serum_counts.txt


title: THP1, ∆EccCa1-Rv Uninfected, 2h_sorted, rep 1

value: 2hrs ∆EccCa1-Rv bystanders


title: Serum_Patient_5_Post-Op

description:
p23186-s030_Patient-5-Post-Op-TotalRNA_S310_L001_R1_001.fastq.gz
human_serum_counts.txt


title: THP1, ∆EccCa1-Rv Uninfected, 2h_sorted, rep 2


title: THP1, ∆EccCa1-Rv infected, 2h_sorted, rep 2

value: 2hrs ∆EccCa1-Rv infected


title: Serum_Patient_3_Post-Op

description:
p23186-s029_Patient-3-Post-Op-TotalRNA_S309_L001_R1_001.fastq.gz
human_serum_counts.txt


title: THP1, ∆EccCa1-Rv infected, 4h_sorted, rep 1


title: Serum_Patient_1_Post-Op

description:
p23186-s028_Patient-1-Post-Op-TotalRNA_S308_L001_R1_001.fastq.gz
human_serum_counts.txt


title: THP1, ∆EccCa1-Rv infected, 2h_sorted, rep 1


title: Serum_Patient_22_Pre-Op

description:
p23186-s027_Patient-22-Pre-Op-TotalRNA_S307_L001_R1_001.fastq.gz
human_serum_counts.txt

value: Pre-Op


title: Serum_Patient_21_Pre-Op

description:
p23186-s026_Patient-21-Pre-Op-TotalRNA_S306_L001_R1_001.fastq.gz
human_serum_counts.txt


title: THP1, H37Rv Uninfected, 2h_sorted, rep 1

value: 2hrs H37Rv bystanders


title: THP1, H37Rv infected, 2h_sorted, rep 2

value: 2hrs H37Rv infected


title: Serum_Patient_20_Pre-Op

description:
p23186-s025_Patient-20-Pre-Op-TotalRNA_S305_L001_R1_001.fastq.gz
human_serum_counts.txt

value: Serum


title: Serum_Patient_19_Pre-Op

description:
p23186-s024_Patient-19-Pre-Op-TotalRNA_S304_L001_R1_001.fastq.gz
human_serum_counts.txt


title: H3K27me3_BAP1_KO_HEK293T

value: kidney

value: wild type


title: Serum_Patient_17_Pre-Op

description:
p23186-s022_Patient-17-Pre-Op-TotalRNA_S302_L001_R1_001.fastq.gz
human_serum_counts.txt


title: H3K27me3_BAP1_WT_HEK293T


title: Serum_Patient_18_Pre-Op

description:
p23186-s023_Patient-18-Pre-Op-TotalRNA_S303_L001_R1_001.fastq.gz
human_serum_counts.txt


title: H2AK119Ub_BAP1_KO_HEK293T


title: Serum_Patient_16_Pre-Op

description:
p23186-s021_Patient-16-Pre-Op-TotalRNA_S301_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_15_Pre-Op

description:
p23186-s020_Patient-15-Pre-Op-TotalRNA_S300_L001_R1_001.fastq.gz
human_serum_counts.txt


title: H2AK119Ub_BAP1_WT_HEK293T


title: Serum_Patient_14_Pre-Op

description:
p23186-s019_Patient-14-Pre-Op-TotalRNA_S299_L001_R1_001.fastq.gz
human_serum_counts.txt


title: 0150-B-18

city: Durban

first: Emily

middle: Beth

last: Wong

state: KwaZulu-Natal

address: 719 Umbilo Road

department: Basic science laboratory

country: South Africa

institute: Africa Health research Institute

data_processing:
The `RNASeqPipelineR` was used to perform alignment, quantification and annotation of the RNA sequencing data (RNA-seq) from the whole and mini population RNA-Seq libraries. The RNA-seq data were aligned against the human genome (hg38) using STAR (v2.4.2a), and gene expression quantification was performed using RSEM (v1.2.22).
Assembly: hg38
Supplementary files format and content: mraw_counts.csv

source_name: BAL

extract_protocol:
RNA from mini sorted populations of BAL samples were extracted using SMARTSeqI&II RNA extraction methods
Libraries were prepared using the same SMARTSeqI&II protocol.

value: BAL

value: MAIT

tag: disease status

value: LTBI and HIV-positive


title: Serum_Patient_13_Pre-Op

description:
p23186-s018_Patient-13-Pre-Op-TotalRNA_S298_L001_R1_001.fastq.gz
human_serum_counts.txt


title: 0150-B-17


title: 0150-B-16


title: THP1, H37Rv Uninfected, 2h_sorted, rep 2

value: THP1 differentiated to macrophages with PMA


title: Serum_Patient_11_Pre-Op

description:
p23186-s016_Patient-11-Pre-Op-TotalRNA_S296_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_12_Pre-Op

description:
p23186-s017_Patient-12-Pre-Op-TotalRNA_S297_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_10_Pre-Op

description:
p23186-s015_Patient-10-Pre-Op-TotalRNA_S295_L001_R1_001.fastq.gz
human_serum_counts.txt


title: 0134-B-16


title: 0134-B-18


title: THP1, H37Rv infected, 2h_sorted, rep 1


title: Serum_Patient_8_Pre-Op

description:
p23186-s013_Patient-8-Pre-Op-TotalRNA_S293_L001_R1_001.fastq.gz
human_serum_counts.txt


title: 0150-B-02


title: 0150-B-03


title: Serum_Patient_9_Pre-Op

description:
p23186-s014_Patient-9-Pre-Op-TotalRNA_S294_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_6_Pre-Op

description:
p23186-s011_Patient-6-Pre-Op-TotalRNA_S291_L001_R1_001.fastq.gz
human_serum_counts.txt


title: 0150-B-01


title: Serum_Patient_7_Pre-Op

description:
p23186-s012_Patient-7-Pre-Op-TotalRNA_S292_L001_R1_001.fastq.gz
human_serum_counts.txt


title: WT Col-0 long-read

city: Toronto

first: Satyaki

last: Rajavasireddy

state: ON

address: 1265 Military Trail, Toronto,, SY246

department: Biological Sciences (Scarborough)

country: Canada

institute: University of Toronto

description: Library name: Col_9

data_processing:
Sequencing and basecalling was performed with: MinKNOW 23.04.6, Bream 7.5.10, Configuration 5.5.14, Guppy 6.5.7, and MinKNOW Core 5.5.5
Reads were filtered using Filtlong v0.2.1 to select the best reads in terms of length and quality, up to a max coverage of 50x (parameters: --min_length 1000 --min_window_q 40 --trim --split 1500 --target_bases 6605000000)
Filtered reads were aligned to the Col-CEN v1.2 genome using Vulcan dual-mode alignment (parameters: -ont)
Structural variants in each sample were called with cuteSV (parameters: --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 --min_size 30 --max_size -1 –genotype). All SVs from all samples were merged with SURVIVOR (parameters: merge 1000 1 1 1 0 30) and genotyped again with cuteSV (parameters: --min_mapq 20 --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 --min_size 30 --max_size -1).
Final filtering step removed any structural variant that was present in the DMSO or WT Col-0 controls, present in more than one phenotypic line, or had a quality score less than 20.
Assembly: Col-CEN v1.2
Supplementary files format and content: vcf file contains information for each structural variant and a matrix of genotypes for each sample and variant

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown in a Conviron growth chamber under long day conditions (16h 120 µmol fluorescent light) at 22C.

extract_protocol:
Two leaves from each sample were flash-frozen in liquid nitrogen. Frozen tissue was ground into powder with a QIAGEN Tissuelyser II (30 beats/sec for 1min). High molecular weight DNA was extracted using a Promega Wizard HMW DNA Extraction Kit. DNA was sheared by passing through a 23G needle twice. Contaminating RNA and proteins were removed by treating with RNase A and Proteinase K (New England Biolabs). DNA was further cleaned and small fragments removed by performing a 0.7x bead cleanup using a modified SPRI bead mixture in which the buffer of Agencourt AMPure XP beads was exchanged with a custom buffer of 10 mM Tris-HCl, 1mM EDTA pH8, 1.6M NaCl, 11% w/v PEG 8000.
Batch A was prepared using ONT Rapid Barcoding Kit V10 and sequenced on R9.4.1 flow cell. Batch B was prepared using ONT Native Barcoding Kit V14 and sequenced on R10.4.1 flow cell.

treatment_protocol: M1 plants were grown on 0.5X MS Media containing 160 µM of etoposide or DMSO for two weeks, after which they were transferred to soil. M1 plants were self-fertilized to yield M2 plants, which were self-fertilized to yield M3 plants.

value: leaf

tag: generation

tag: batch

value: B


title: short-internode dwarf rep 2 long-read

description: Library name: 34C_7_22

value: etoposide


title: Serum_Patient_4_Pre-Op

description:
p23186-s009_Patient-4-Pre-Op-TotalRNA_S289_L001_R1_001.fastq.gz
human_serum_counts.txt


title: 0134-B-03

tag: cell type


title: short-internode dwarf rep 1 long-read

description: Library name: 34C_6_24


title: Serum_Patient_2_Pre-Op

description:
p23186-s007_Patient-2-Pre-Op-TotalRNA_S287_L001_R1_001.fastq.gz
human_serum_counts.txt


title: Serum_Patient_1_Pre-Op

description:
p23186-s006_Patient-1-Pre-Op-TotalRNA_S286_L001_R1_001.fastq.gz
human_serum_counts.txt


title: 0134-B-02


title: DMSO rep 2 long-read

description: Library name: C23_30

value: DMSO

value: A


title: 0150-B-06


title: EV_Patient_16_Post-Op_miRNA

description:
p23097-s034_Patient-16-Post-Op-miRNA_S165
human_ev_counts_miRNA.txt

value: Post-Op


title: EV_Patient_17_Post-Op_miRNA

description:
p23097-s035_Patient-17-Post-Op-miRNA_S166
human_ev_counts_miRNA.txt


title: 0150-B-05


title: EV_Patient_15_Post-Op_miRNA

description:
p23097-s033_Patient-15-Post-Op-miRNA_S164
human_ev_counts_miRNA.txt


title: virescent rep 2 long-read

description: Library name: 13B_46_23


title: EV_Patient_14_Post-Op_miRNA

description:
p23097-s032_Patient-14-Post-Op-miRNA_S163
human_ev_counts_miRNA.txt


title: EV_Patient_12_Post-Op_miRNA

description:
p23097-s030_Patient-12-Post-Op-miRNA_S162
human_ev_counts_miRNA.txt


title: 0150-B-04


title: EV_Patient_11_Post-Op_miRNA

description:
p23097-s029_Patient-11-Post-Op-miRNA_S161
human_ev_counts_miRNA.txt


title: Serum_Patient_5_Pre-Op

description:
p23186-s010_Patient-5-Pre-Op-TotalRNA_S290_L001_R1_001.fastq.gz
human_serum_counts.txt


title: EV_Patient_10_Post-Op_miRNA

description:
p23097-s028_Patient-10-Post-Op-miRNA_S160
human_ev_counts_miRNA.txt


title: virescent relative without phenotype long-read

description: Library name: 13B_18_20


title: Serum_Patient_3_Pre-Op

description:
p23186-s008_Patient-3-Pre-Op-TotalRNA_S288_L001_R1_001.fastq.gz
human_serum_counts.txt


title: 0134-B-06


title: DMSO rep 1 long-read

description: Library name: C13_5


title: EV_Patient_9_Post-Op_miRNA

description:
p23097-s027_Patient-9-Post-Op-miRNA_S159
human_ev_counts_miRNA.txt


title: EV_Patient_8_Post-Op_miRNA

description:
p23097-s026_Patient-8-Post-Op-miRNA_S158
human_ev_counts_miRNA.txt


title: 0134-B-05


title: EV_Patient_7_Post-Op_miRNA

description:
p23097-s025_Patient-7-Post-Op-miRNA_S157
human_ev_counts_miRNA.txt


title: EV_Patient_6_Post-Op_miRNA

description:
p23097-s024_Patient-6-Post-Op-miRNA_S156
human_ev_counts_miRNA.txt


title: 0113-B-05


title: green plant producing variegated progeny long-read

description: Library name: 5A_58_18


title: EV_Patient_5_Post-Op_miRNA

description:
p23097-s023_Patient-5-Post-Op-miRNA_S155
human_ev_counts_miRNA.txt


title: EV_Patient_4_Post-Op_miRNA

description:
p23097-s022_Patient-4-Post-Op-miRNA_S154
human_ev_counts_miRNA.txt


title: BR-like dwarf rep 2 long-read

description: Library name: 1A_20_8


title: short-internode dwarf relative without phenotype long-read

description: Library name: 34C_9_3


title: 0150-B-12


title: virescent rep 1 long-read

description: Library name: 13B_25_26


title: EV_Patient_2_Post-Op_miRNA

description:
p23097-s020_Patient-2-Post-Op-miRNA_S152
human_ev_counts_miRNA.txt


title: EV_Patient_3_Post-Op_miRNA

description:
p23097-s021_Patient-3-Post-Op-miRNA_S153
human_ev_counts_miRNA.txt


title: BR-like dwarf rep 1 long-read

description: Library name: 1A_14_25


title: 0150-B-11


title: EV_Patient_1_Post-Op_miRNA

description:
p23097-s019_Patient-1-Post-Op-miRNA_S151
human_ev_counts_miRNA.txt


title: 0150-B-10


title: EV_Patient_17_Pre-Op_miRNA

description:
p23097-s017_Patient-17-Pre-Op-miRNA_S149
human_ev_counts_miRNA.txt


title: BR-like dwarf relative without phenotype long-read

description: Library name: 1A_4_11


title: EV_Patient_18_Pre-Op_miRNA

description:
p23097-s018_Patient-18-Pre-Op-miRNA_S150
human_ev_counts_miRNA.txt


title: 0134-B-12


title: EV_Patient_16_Pre-Op_miRNA

description:
p23097-s016_Patient-16-Pre-Op-miRNA_S148
human_ev_counts_miRNA.txt


title: EV_Patient_14_Pre-Op_miRNA

description:
p23097-s014_Patient-14-Pre-Op-miRNA_S146
human_ev_counts_miRNA.txt


title: LibG.d

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

country: France

institute: CNRS

description:
Sample name: LibG.d (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
LibG.d

data_processing:
Quality of the raw data was assessed by FastQC High Throughput Sequence QC Report (version 0.10.1). Raw sequenced reads were pre-processed by removing the adaptors (5’ adapter: 5’-GUUCAGAGUUCUACAGUCCGACGAUCNNNN-3’ and 3’adapter: 5’-NNNNTGGAATTCTCGGGTGCCAAGG-3’) and filtered based on phred qualityfastx_quality_filter and fastq_clipper (fastx_toolkit package, version 0.0.13).
Only reads with non-ambiguous bases and 15 to 29 nts in length were kept for further analysis - Final quality analysis - Retrieving of all filtered out reads
Sequence alignment was performed using Bowtie  (version 0.12.8 or 1.1.1, 0 mismatches allowed).
Reads were aligned to Drosophila genome (version v6.06, downloaded from flybase.org). Non-assigned reads were matched to viral genome (Drosophila C virus or Cricket Paralysis Virus: NCBI RefSeq NC_001834.1 and NC_003924.1)Parameters of the alignment: -v 0 (for viruses) and -v 1 (for Drosophila derived smallRNAs)
Reads with different nucleotide lengths were independently aligned on viral genome and antigenome and counted using in-house perl script, which generate _count file
21 long siRNAs were aligned on nucleotide sequence of the virus of interest. The number of siRNa was counted for each position, resulting in _alignment file. The script was generated in-house.
Genome_build: Drosophila genome: version v6.06. Drosophila C virus (DCV): NCBI RefSeq NC_001834. Cricket Paralysis Virus (CrPV): NC_003924.1
Supplementary_files_format_and_content: [count.tab] Number of Reads aligned on viral genome (column 2: Nb(+)) and on viral antigenome (column 3: Nb(-)) for each Read Size (column 1: Length)
Supplementary_files_format_and_content: [alignment.tab] Read Number (column 2: Reads) for each first nucleotide Position (column 1: Position)

organism: Drosophila melanogaster

source_name: Drosophila adult flies

growth_protocol: Flies were fed on standard cornmeal–agar medium at 25°C and used in infection experiments.

extract_protocol:
Samples of 12 flies (6 males and 6 females) were homogenized in 500 µl of TRIZOL reagent (INVITROGEN) with Precellys®24 tissue homogenizer. After tissues disruption, total RNA was extracted following the manufacturer’s instructions.
Small RNAs under 30 nucleotides in size were electrophoretically purified using 15% polyacrylamide gels and subsequently cloned following the protocol in Sorefan et al, 2012
small RNA-Seq. Sequence strategy was 1 x 50 base pairs (bp) performed using Illumina HiSeq 2000
Cloned small RNAs were sequenced by the “IGBMC Microarray and Sequencing platform”, member of “France Génomic” consortium (ANR-10-INBS-0009)

treatment_protocol: Infections were performed with 3-5 days old adult flies by intrathoracic injection (4.6 nL; Nanoject II apparatus, Drummond Scientific) with previously indicated amount of virus.

tag: host strain

tag: infection

value: Cricket Paralysis Virus (CrPV) 5pfu

tag: infection methods

value: 3-5 days old flies were intrathoracically infected

value: RNA was extracted 2 days post infection


title: 0134-B-11

tag: tissue


title: EV_Patient_13_Pre-Op_miRNA

description:
p23097-s013_Patient-13-Pre-Op-miRNA_S145
human_ev_counts_miRNA.txt

tag: treatment

value: Pre-Op


title: EV_Patient_12_Pre-Op_miRNA

description:
p23097-s012_Patient-12-Pre-Op-miRNA_S144
human_ev_counts_miRNA.txt

value: Serum


title: Lib8.R

description:
Sample name: Lib8.R (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib8.R


title: EV_Patient_11_Pre-Op_miRNA

description:
p23097-s011_Patient-11-Pre-Op-miRNA_S143
human_ev_counts_miRNA.txt


title: Lib8.d

description:
Sample name: Lib8.d (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib8.d


title: EV_Patient_9_Pre-Op_miRNA

description:
p23097-s009_Patient-9-Pre-Op-miRNA_S141
human_ev_counts_miRNA.txt


title: EV_Patient_8_Pre-Op_miRNA

description:
p23097-s008_Patient-8-Pre-Op-miRNA_S140
human_ev_counts_miRNA.txt


title: 0113-B-12


title: EV_Patient_10_Pre-Op_miRNA

description:
p23097-s010_Patient-10-Pre-Op-miRNA_S142
human_ev_counts_miRNA.txt


title: HEK293T_BAP1_KO_C91S_Rep2

tag: cell line

value: kidney

tag: genotype

value: infected with BAP1_C91S


title: 0113-B-11

value: BAL


title: EV_Patient_7_Pre-Op_miRNA

description:
p23097-s007_Patient-7-Pre-Op-miRNA_S139
human_ev_counts_miRNA.txt


title: LibCs

description:
Sample name: Lib Cs (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib Cs

value: Drosophila C virus (DCV) 500pfu

tag: time

value: RNA was extracted 4 days post infection


title: Libyw

description:
Sample name: Lib YW (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib YW

value: yw


title: 0113-B-10

value: LTBI and HIV-positive


title: EV_Patient_6_Pre-Op_miRNA

description:
p23097-s006_Patient-6-Pre-Op-miRNA_S138
human_ev_counts_miRNA.txt


title: G31R/df or dcr-2G31R/df

description:
Sample name: Lib 7 (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib 7

value: RNA was extracted 5 days post infection


title: EV_Patient_5_Pre-Op_miRNA

description:
p23097-s005_Patient-5-Pre-Op-miRNA_S137
human_ev_counts_miRNA.txt


title: 0150-B-09


title: G31R/df,Rescue or dcr-2G31R/df,rescue

description:
Sample name: Lib 6 (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib 6


title: IL13Rα2-targeted CAR T cells treated with ICG001 first then CART replicate 2

city: Duarte

first: Yate-Ching

last: Yuan

address: 1500 East Duarte

institute: City of Hope

hyb_protocol: RNA was hybridized with the Codeset from the gene panel at 65°C for 16 h. The post-hybridization probe-target mixture was quantified using the nCounter Digital Analyzer, and all data analyses were performed on nSolver (NanoString Technologies).

scan_protocol: Scanning was done using NanoString nCounter system, following manufacturer's instructions.

data_processing:
Raw gene count was averaged across three brain tissue samples from CAR T treated mice and across two brain tissue samples from CAR T + ICG001 treated groups.
All raw data were first normalized with internal positive and negative controls to eliminate variability unrelated to the samples, then normalized to the selected housekeeping genes using Geometric Means methods. Statistically significant (p<0.05) and|fold change|≥1.5 differential expressed genes  were analyzed and clustered as described below.

source_name: primary mouse tumor cell lines

label_protocol: Samples were labeled according to the treatment received ICG001+ CAR Ts [MIC]; CAR T +ICG001 [MCI] and ICG001 only [MI]; CAR T only [MC]

extract_protocol: Total RNA was isolated from K-Luc tumor tissue and analyzed by NanoString (NanoString nCount mouse PanCancer Immune profiling paneled assays (https://nanostring.com/products/ncounter-assays-panels/oncology/pancancer-immune-profiling).Brain tissue was dissected to isolate tumors and tumors were snap frozen for RNA isolation and used for Nanostring analysis.

treatment_protocol: Mice were either treated with ICG001 [MI], CARTs [MC], CART and then ICG001 [MCI], or ICG001 and then CAR Ts [MIC].

tag: sample type

value: immunocompetent mouse derived glioma model engineered with IL13Rα2-targeted CAR T cells

value: ICG001 + CAR T


title: EV_Patient_4_Pre-Op_miRNA

description:
p23097-s004_Patient-4-Pre-Op-miRNA_S136
human_ev_counts_miRNA.txt


title: null/df,Rescue or dcr-2L811fsX/Df,Rescue

description:
Sample name: Lib 5 (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib 5


title: 0150-B-08


title: null/df or dcr-2L811fsX/Df

description:
Sample name: Lib 1 (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib 1


title: IL13Rα2-targeted CAR T cells treated with ICG001 first then CART replicate 1


title: EV_Patient_3_Pre-Op_miRNA

description:
p23097-s003_Patient-3-Pre-Op-miRNA_S135
human_ev_counts_miRNA.txt


title: IL13Rα2-targeted CAR T cells treated with ICG001 only

value: ICG001 only


title: 0134-B-09


title: II/Df,Rescue

description:
Sample name: Lib 4 (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib 4

value: wIR;II/Df,Rescue;III


title: EV_Patient_2_Pre-Op_miRNA

description:
p23097-s002_Patient-2-Pre-Op-miRNA_S134
human_ev_counts_miRNA.txt


title: IL13Rα2-targeted CAR T cells treated with CART first then ICG001 replicate 2

value: CAR T + ICG001


title: II/Df

description:
Sample name: Lib 3 (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib 3

value: wIR;II/Df;III

value: 3-5 days old flies were intrathoracically infected


title: EV_Patient_1_Pre-Op_miRNA

description:
p23097-s001_Patient-1-Pre-Op-miRNA_S133
human_ev_counts_miRNA.txt

value: Pre-Op


title: IL13Rα2-targeted CAR T cells treated with CART first then ICG001 replicate 1


title: II/II

description:
Sample name: Lib 2 (Refer to Extended Data Figure 3)
Sample Title: refer to the text and abbreviations in figures
small RNAs (15-29nt)
Lib 2

value: wIR;II;III


title: EV_Patient_17_Post-Op

description:
p23097-s035_Patient-17-Post-Op-TotalRNA_S56
human_ev_counts.txt

value: Serum

value: Post-Op


title: 0134-B-08

value: BAL


title: CD206pos_E14.5_18_3

city: Freiburg

first: Lukas

last: Amann

address: Breisacher Straße 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

data_processing:
Image analysis and base calling resulted in .bcl files, which were converted into fastq files with either the CASAVA1.8.2 software or with the bcl2fastq v2.18 software.
The RNA-seq data was aligned with STAR v2.7.8a to the mouse reference genome Gencode M26. Counts were obtained using FeatureCounts v2.0.2.
Assembly: Gencode M26
Supplementary files format and content: Processed counts are provided in the file Counts_dural_macrophages.txt

source_name: Dura mater

growth_protocol: SPF beeding facility

extract_protocol:
Cells were sorted into RNAprotect Cell Reagend (QIAGEN) according to the manufacturers recommendations. RNA was extracted using Picopure RNA extraction kit (Life Technologies) according to manufacturer’s protocol. The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 500 pg total-RNA.
Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3.

tag: strain

value: Dura mater

value: dural macrophages

tag: time point


title: IL13Rα2-targeted CAR T cells control replicate 3

value: CAR T only


title: 0134-B-15

value: AM

value: LTBI and HIV-positive


title: 0134-B-14


title: EV_Patient_15_Post-Op

description:
p23097-s033_Patient-15-Post-Op-TotalRNA_S54
human_ev_counts.txt


title: 0150-B-07


title: 0134-B-13


title: IL13Rα2-targeted CAR T cells control replicate 2

value: immunocompetent mouse derived glioma model engineered with IL13Rα2-targeted CAR T cells


title: IL13Rα2-targeted CAR T cells control replicate 1


title: HuH7 cells,HIR_RK-4

city: MACAU

first: HONG

last: SHEN

state: MACAU

address: Room 6034, Building N22, Avenida da Universidade, Taipa

department: Institute of Chinese Medical Sciences

institute: UNIVERSITY OF MACAU

description: Library name: Sample8

data_processing:
SOAPnuke software (v 2.0) was used to perform the filtering function including trimming (adapter, low quality end and etc.) and discarding (adapter, low quality, high N base ratio and etc.).
The FastQC (v0.11.5) software was used to evaluate the quality of sequencing reads.
The HISAT2 software (v2.2.1) was employed in the process of aligning the sequencing-generated  reads with the reference genomes.
The assembly and quantification of transcripts derived from aligned RNA-seq reads were conducted using the StringTie software (v1.3.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text file includes fpkm values for all samples

source_name: HuH7 cells

growth_protocol: HuH7 cells were cultured in DMEM with 10% fetal bovine serum. Cell cultures were maintained in a humidified atmosphere of 5% CO2 at 37℃. To simulate the hypoxia/reoxygenation (H/R) model in vitro, HuH7 cells were exposed to hypoxic conditions (1% oxygen) in glucose-free DMEM for 6 h, followed by culture under normoxic conditions.

extract_protocol:
Total RNA was isolated using a TRIzol reagent (Life Technologies) and 250 ng of quantified RNA from each sample was used for cDNA library construction.
RNA libraries for RNA-seq were prepareed using an MGIEasy RNA Library Prep Kit (MGI Tech Co., Ltd., Shenzhen, China).

treatment_protocol: HuH7 cell were treated with DMEM containing DMSO or  ginsenoside Rk2 (20 μM) for 6h after hypoxic conditions (during the reoxygenation period).

value: HuH7 cells

value: Epithelial-like, tumorigenic cells

value: Wildtype

value: Ginsenoside Rk2 dissolved in DMSO


title: CD206pos_E14.5_18_1


title: EV_Patient_14_Post-Op

description:
p23097-s032_Patient-14-Post-Op-TotalRNA_S53
human_ev_counts.txt


title: HEK293T_BAP1_KO_BAP1_Rep2

value: kidney

value: infected with BAP1_WT


title: THP1, H37Rv Uninfected, 4h_sorted, rep 1

value: THP1 differentiated to macrophages with PMA

value: 4hrs H37Rv bystanders


title: CD206pos_d3_17_3


title: HuH7 cells,HIR_RK-3

description: Library name: Sample7


title: EV_Patient_13_Post-Op

description:
p23097-s031_Patient-13-Post-Op-TotalRNA_S52
human_ev_counts.txt

value: Serum


title: HuH7 cells,HIR_RK-2

description: Library name: Sample6


title: EV_Patient_12_Post-Op

description:
p23097-s030_Patient-12-Post-Op-TotalRNA_S51
human_ev_counts.txt

value: Post-Op


title: EV_Patient_16_Post-Op

description:
p23097-s034_Patient-16-Post-Op-TotalRNA_S55
human_ev_counts.txt


title: HuH7 cells,HIR_RK-1

description: Library name: Sample5


title: CD206pos_E14.5_18_2


title: CD206pos_d3_17_1


title: Serum_Patient_17_Post-Op

description:
p23186-s041_Patient-17-Post-Op-TotalRNA_S321_L001_R1_001.fastq.gz
human_serum_counts.txt


title: HuH7 cells,HIR-4

description: Library name: Sample4

value: DMSO


title: CD206pos_d10_16_3

value: Dura mater


title: CD206pos_d10_16_1

value: dural macrophages


title: HuH7 cells,HIR-2

description: Library name: Sample2


title: EV_Patient_9_Post-Op

description:
p23097-s027_Patient-9-Post-Op-TotalRNA_S48
human_ev_counts.txt


title: Triple Negative Breast Cancer Tumor [CM39]

city: Mexico City

first: Patricia

middle: Piña

last: Sánchez

state: CDMX

address: Cuauhtémoc Avenue

department: Medical Research Unit in Oncological Diseases

country: Mexico

institute: IMSS

description: Gene expression data from triple negative breast cancer

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed with  the Transcriptome Analysis Console (TAC 4.0.1, Applied Biosystems) to identify differentially expressed genes between TNBC and luminal samples.  Quality control and normalization were performed using Robust Multichip Average (RMA).

source_name: Triple Negative Breast Cancer Tumor

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was obtained and purified from tissue sections embedded in paraffin and fixed with formalin with the RNeasy FFPE Kit (QIAGEN, 73504), following the manufacturer's instructions

value: Formalin-fixed paraffin-embedded tissue sections

tag: population

value: Mexican Patient

tag: age


title: EV_Patient_8_Post-Op

description:
p23097-s026_Patient-8-Post-Op-TotalRNA_S47
human_ev_counts.txt


title: HuH7 cells,HIR-1

description: Library name: Sample1


title: CD206pos_d3_17_2


title: Triple Negative Breast Cancer Tumor [CM37]


title: Triple Negative Breast Cancer Tumor [CM36]


title: EV_Patient_11_Post-Op

description:
p23097-s029_Patient-11-Post-Op-TotalRNA_S50
human_ev_counts.txt


title: CD206pos_3W_15_2


title: EV_Patient_6_Post-Op

description:
p23097-s024_Patient-6-Post-Op-TotalRNA_S45
human_ev_counts.txt


title: mice, liver, HIR_RK-3

description: Library name: Sample6

data_processing:
SOAPnuke software (v 2.0) was used to perform the filtering function including trimming (adapter, low quality end and etc.) and discarding (adapter, low quality, high N base ratio and etc.).
The FastQC (v0.11.5) software was used to evaluate the quality of sequencing reads.
The HISAT2 software (v2.2.1) was employed in the process of aligning the sequencing-generated  reads with the reference genomes.
The assembly and quantification of transcripts derived from aligned RNA-seq reads were conducted using the StringTie software (v1.3.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text file includes fpkm values for all samples

source_name: liver

growth_protocol: Male mice with a C57BL/6 background, aged 8-10 weeks were kept in a specific pathogen-free (SPF) facility under a controlled 12-hour light/dark cycle environment with access to chow and water ad libitum. A 75% hepatic warm IR injury model was induced on mice.

extract_protocol:
Total RNA was isolated using a TRIzol reagent (Life Technologies) and 250 ng of quantified RNA from each liver sample was used for cDNA library construction.
RNA libraries for RNA-seq were prepareed using an MGIEasy RNA Library Prep Kit (MGI Tech Co., Ltd., Shenzhen, China).

treatment_protocol: Mice were administered with ginsenoside Rk2 or vehicle  two days before the surgery and at the initiation of perfusion.

value: liver

tag: Sex

value: male

tag: disease state

value: Ginsenoside Rk2 dissolved in the vehicle solution


title: Triple Negative Breast Cancer Tumor [CM30]


title: Triple Negative Breast Cancer Tumor [CM29]


title: EV_Patient_5_Post-Op

description:
p23097-s023_Patient-5-Post-Op-TotalRNA_S44
human_ev_counts.txt


title: EV_Patient_10_Post-Op

description:
p23097-s028_Patient-10-Post-Op-TotalRNA_S49
human_ev_counts.txt


title: HuH7 cells,HIR-3

description: Library name: Sample3

value: HuH7 cells

value: Epithelial-like, tumorigenic cells


title: CD206pos_d10_16_2

tag: batch


title: Triple Negative Breast Cancer Tumor [CM26]


title: EV_Patient_4_Post-Op

description:
p23097-s022_Patient-4-Post-Op-TotalRNA_S43
human_ev_counts.txt


title: CD206pos_3W_15_3

tag: cell type


title: EV_Patient_7_Post-Op

description:
p23097-s025_Patient-7-Post-Op-TotalRNA_S46
human_ev_counts.txt


title: CD206pos_8W_14_6


title: Triple Negative Breast Cancer Tumor [CM27]


title: mice, liver, HIR-3

description: Library name: Sample3

value: A 75% hepatic warm IR injury model was induced on mice.

value: vehicle solution


title: Triple Negative Breast Cancer Tumor [CM25]


title: EV_Patient_15_Pre-Op_miRNA

description:
p23097-s015_Patient-15-Pre-Op-miRNA_S147
human_ev_counts_miRNA.txt

value: Pre-Op


title: CD206pos_8W_14_5


title: EV_Patient_3_Post-Op

description:
p23097-s021_Patient-3-Post-Op-TotalRNA_S42
human_ev_counts.txt


title: mice, liver, HIR_RK-2

description: Library name: Sample5


title: CD206pos_8W_14_4


title: mice, liver, HIR-2

description: Library name: Sample2


title: mice, liver, HIR-1

description: Library name: Sample1


title: EV_Patient_2_Post-Op

description:
p23097-s020_Patient-2-Post-Op-TotalRNA_S41
human_ev_counts.txt


title: CD206pos_3W_15_1


title: EV_Patient_1_Post-Op

description:
p23097-s019_Patient-1-Post-Op-TotalRNA_S40
human_ev_counts.txt


title: mice, liver, HIR_RK-1

description: Library name: Sample4


title: line 9A rep 1 short-read

description: Library name: 9A_11_9

data_processing:
First 10 bp of each read as well as any adapters were removed with trimmomatic.
Trimmed reads were aligned to the Col-CEN v1.2 genome with BWA-MEM (bwa mem -R "@RG\tID:id\tSM:sample\tLB:lib" reference.fasta sample.R1.fastq sample.R2.fastq  | samblaster --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20)
SVs were identifed with LUMPY Express using a benchmarked pipeline described in Goktay et al. 2021.
SVs attributed to ChrC, ChrM, and the NOR on Chr2 were removed. SVs found within 2kb of an SV present in DMSO treated controls, or shared amongst four or more unrelated etoposide-treated lines were removed. Only deletions and duplications that were supported by split reads were retained in the final SV set.
Assembly: Col-CEN v1.2
Supplementary files format and content: vcf file contains information for each structural variant identified via lumpy express and which samples it was identified in.

extract_protocol:
DNA was extracted from rosette leaf tissue using a CTAB protocol.
Up to 15 ng of genomic DNA was used as input for the Nextera DNA Flex Library Preparation Kit.

value: leaf

value: etoposide

tag: generation


title: Triple Negative Breast Cancer Tumor [CM40]


title: Siglec-11 transgenic mouse 9, 24 months old, Sequencing Run 2

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

institute: University Hospital of Bonn

data_processing:
Adapters were trimmed from the reads using Bbmerge/BBDUK. Reads were then aligned to the mouse reference genome mm10 (GRCm38) with the ensemble gene annotation version 101 using STAR [v2.7.3a] (Dobin et al., 2013) with standard parameters. Read count generation was performed using featureCounts/Subread [v2.0.0] (Liao et al., 2014) ignoring multimapping reads.
Assembly: mm10
Supplementary files format and content: tab-deliminated text file including raw counts for each sample
Supplementary files format and content: Tab-delimited text file containing read count values for each gene across all samples. The data were generated using the featureCounts tool from the Subread package. Each row represents a gene, and each column corresponds to a sample. The values represent the number of reads mapped to each gene in each sample, without normalization

source_name: Brain

growth_protocol: Wildtype and transgenic mice were housed at a 12 hours dark/night cycle in a temperature-control facility with ad libitum water and food until reaching 6 and 24 months of age.

extract_protocol:
RNA was harvested from whole left-brain hemispheres that were homogenized in QIAzol Lysis reagent (Qiagen), afterwhich RNAeasy kit was utilized to isolate the RNA, which was sent for sequencing.
QuantSeq 3′ mRNA-Seq Library Prep Kit, Lexogen with an input of 100 ng total RNA

value: Brain

value: Siglec-11 transgenic


title: EV_Patient_18_Pre-Op

description:
p23097-s018_Patient-18-Pre-Op-TotalRNA_S39
human_ev_counts.txt

value: Serum


title: line 9A rep 2 short-read

description: Library name: 9A_11_23


title: EV_Patient_17_Pre-Op

description:
p23097-s017_Patient-17-Pre-Op-TotalRNA_S38
human_ev_counts.txt


title: DMSO rep 4 short-read

description: Library name: 4_8_8

value: DMSO


title: EV_Patient_16_Pre-Op

description:
p23097-s016_Patient-16-Pre-Op-TotalRNA_S37
human_ev_counts.txt


title: Siglec-11 transgenic mouse 6, 24 months old, Sequencing Run 2


title: 0134-B-10

value: BAL

tag: disease status

value: LTBI and HIV-positive


title: short-internode dwarf rep 2 short-read

description: Library name: 34C_7_32


title: short-internode dwarf relative without phenotype rep 1 short-read

description: Library name: 34C_9_20


title: Triple Negative Breast Cancer Tumor [CM20]

value: Formalin-fixed paraffin-embedded tissue sections

value: Mexican Patient


title: EV_Patient_14_Pre-Op

description:
p23097-s014_Patient-14-Pre-Op-TotalRNA_S35
human_ev_counts.txt


title: Wildtype mouse 8, 24 months old, Sequencing Run 2

value: WT


title: Siglec-11 transgenic mouse 7, 24 months old, Sequencing Run 2


title: short-internode dwarf rep 1 short-read

description: Library name: 34C_6_9


title: Triple Negative Breast Cancer Tumor [CM19]


title: Wildtype mouse 7, 24 months old, Sequencing Run 2


title: Luminal Breast Cancer Tumor [CM15]

description: Gene expression data from Luminal breast cancer

source_name: Luminal Breast Cancer Tumor


title: EV_Patient_13_Pre-Op

description:
p23097-s013_Patient-13-Pre-Op-TotalRNA_S34
human_ev_counts.txt


title: EV_Patient_15_Pre-Op

description:
p23097-s015_Patient-15-Pre-Op-TotalRNA_S36
human_ev_counts.txt


title: Triple Negative Breast Cancer Tumor [CM22]

description: Gene expression data from triple negative breast cancer


title: Siglec-11 transgenic mouse 8, 24 months old, Sequencing Run 2


title: line 26C rep 1 short-read

description: Library name: 26C_4


title: line 26A rep 3 short-read

description: Library name: 26A_3


title: Wildtype mouse 6, 24 months old, Sequencing Run 2


title: Luminal Breast Cancer Tumor [CM13]


title: EV_Patient_12_Pre-Op

description:
p23097-s012_Patient-12-Pre-Op-TotalRNA_S33
human_ev_counts.txt


title: Triple Negative Breast Cancer Tumor [CM18]


title: Luminal Breast Cancer Tumor [CM14]


title: Triple Negative Breast Cancer Tumor [CM28]

value: not available


title: line 26A rep 2 short-read

description: Library name: 26A_14


title: Wildtype mouse 5, 24 months old, Sequencing Run 2


title: Luminal Breast Cancer Tumor [CM12]


title: EV_Patient_11_Pre-Op

description:
p23097-s011_Patient-11-Pre-Op-TotalRNA_S32
human_ev_counts.txt


title: Siglec-11 transgenic mouse 5, 6 months old, Sequencing Run 1


title: line 26A rep 1 short-read

description: Library name: 26A_10


title: EV_Patient_10_Pre-Op

description:
p23097-s010_Patient-10-Pre-Op-TotalRNA_S31
human_ev_counts.txt


title: Siglec-11 transgenic mouse 4, 6 months old, Sequencing Run 1


title: line 24C rep 1 short-read

description: Library name: 24C_12


title: EV_Patient_9_Pre-Op

description:
p23097-s009_Patient-9-Pre-Op-TotalRNA_S30
human_ev_counts.txt


title: Luminal Breast Cancer Tumor [CM11]


title: line 24B rep 1 short-read

description: Library name: 24B_23


title: DMSO rep 3 short-read

description: Library name: 24A_9


title: Triple Negative Breast Cancer Tumor [CM24]


title: Siglec-11 transgenic mouse 2, 6 months old, Sequencing Run 1


title: EV_Patient_7_Pre-Op

description:
p23097-s007_Patient-7-Pre-Op-TotalRNA_S28
human_ev_counts.txt


title: EV_Patient_8_Pre-Op

description:
p23097-s008_Patient-8-Pre-Op-TotalRNA_S29
human_ev_counts.txt


title: Siglec-11 transgenic mouse 1, 6 months old, Sequencing Run 1


title: Luminal Breast Cancer Tumor [CM10]


title: DMSO rep 2 short-read

description: Library name: 23_19


title: EV_Patient_6_Pre-Op

description:
p23097-s006_Patient-6-Pre-Op-TotalRNA_S27
human_ev_counts.txt


title: Wildtype mouse 4, 6 months old, Sequencing Run 1


title: EV_Patient_5_Pre-Op

description:
p23097-s005_Patient-5-Pre-Op-TotalRNA_S26
human_ev_counts.txt


title: line 21B rep 1 short-read

description: Library name: 21B_24


title: Wildtype mouse 3, 6 months old, Sequencing Run 1


title: Siglec-11 transgenic mouse 3, 6 months old, Sequencing Run 1


title: line 21B rep 2 short-read

description: Library name: 21B_6


title: EV_Patient_4_Pre-Op

description:
p23097-s004_Patient-4-Pre-Op-TotalRNA_S25
human_ev_counts.txt


title: Luminal Breast Cancer Tumor [CM9]


title: Wildtype mouse 2, 6 months old, Sequencing Run 1


title: EV_Patient_3_Pre-Op

description:
p23097-s003_Patient-3-Pre-Op-TotalRNA_S24
human_ev_counts.txt


title: line 21A rep 2 short-read

description: Library name: 21A_6


title: Luminal Breast Cancer Tumor [CM7]


title: line 21A rep 1 short-read

description: Library name: 21A_11


title: EV_Patient_2_Pre-Op

description:
p23097-s002_Patient-2-Pre-Op-TotalRNA_S23
human_ev_counts.txt


title: Luminal Breast Cancer Tumor [CM5]


title: SLO D6

city: Minneapolis

first: Marc

middle: K

last: Jenkins

state: MN

address: 2101 6th St SE

department: Microbiology

institute: University of Minnesota

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1
Data analysis was performed using Seurat v4.1 pipeline. Low-quality cells were defined as those with less than 500 or more than 3000 unique genes, or those with >10% mitochondrial gene reads and were removed.
Assembly: mm10
Supplementary files format and content: h5 aggregate file

source_name: SLO, spleen

extract_protocol:
Lymphocytes were prepared by mechanical disruption (SLO, spleen), followed by staining with floursecent antibodies and tetramers, hashing with Totalseq-C antibodies against MHCI and CD45,  and flow sorting tetramer positive T cells into DMEM2%FCS
Libraries were prepared according to 10x5'v2 protocols

value: SLO, spleen

value: T cells

value: Female

value: None, Listeria monocytogenes


title: line 1B rep 1 short-read

description: Library name: 1B_9


title: EV_Patient_1_Pre-Op

city: Atlanta

description:
p23097-s001_Patient-1-Pre-Op-TotalRNA_S22
human_ev_counts.txt

value: Pre-Op


title: BR-like dwarf relative without phenotype rep 1 short-read

description: Library name: 1A_4_5

value: leaf


title: AID-cre tdTomato lymphocytes, AID+ MHV68+, 16 dpi M2.Stop 73.Bla MHV68, Rep. 3

city: Little Rock

first: Mark

last: Manzano

state: AR

address: 4301 W Markham St

department: Microbiology & Immunology

institute: University of Arkansas for Medical Sciences

description: Library name: M2-4-AB

data_processing:
Raw sequence reads were checked for their quality using FastQC and then trimmed based on quality (PHRED >30). After trimming, reads less than 30 bp were discarded.
Trimmed sequence reads were mapped to reference genome mm10 with STAR aligner with default parameters.
The gene count tables were extracted from the alignment results using bedtool2 software.
The read counts were normalized using voom method.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include cpm for each smple.

source_name: draining lymph nodes

extract_protocol:
RNA was harvested using trizol.
Library was constructed by GeneWiz by the ultra-low input RNA seq protocol - using Illumina RNA prep with enrichment for full length transcripts.  Polyadenylated transcripts were reverse transcribed using SMART-Seq® v4 Ultra® Low Input RNA Kit (Clontech), followed by second-strand synthesis of full-length cDNA and amplification of the product. Illumina RNA prep with enrichment for full length transcripts.  Polyadenylated transcripts were reverse transcribed using SMART-Seq® v4 Ultra® Low Input RNA Kit (Clontech), followed by second-strand synthesis of full-length cDNA and amplification of the product. Illumina®-compatible sequencing libraries were constructed and then validated for sufficient concentration and appropriate fragment sizes. Samples were  sequenced on the Illumina HiSeq® 2500 with a 1x100 bp single-end configuration.

treatment_protocol: At 16 dpi, draining lymph nodes were isolated and homogenized. Staining for beta-lactamase activity was performed with CCF4-AM. Cells were sorted on a FACS Aria for AID+MHV68- or AID+MHV68+ populations from animals infected with either WT or M2.Stop 73.Bla MHV68.

value: draining lymph nodes

value: AID+ MHV68+

value: AID-cre tdTomato

value: 16 dpi with M2.Stop 73.Bla MHV68


title: SLO D21


title: AID-cre tdTomato lymphocytes, AID+ MHV68-, 16 dpi M2.Stop 73.Bla MHV68, Rep. 3

description: Library name: M2-4-A

value: AID+ MHV68-


title: Luminal Breast Cancer Tumor [CM3]


title: Luminal Breast Cancer Tumor [CM8]


title: 22Rv1 CPSF1 sh2 BR3

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

institute: Masonic Cancer Center, University of Minnesota

data_processing:
Fastq files containing 150 bp paired-end reads were aligned to the GRCh37 reference genome using HiSat2 (v. 2.1.0). Subread (v. 2.0.3) was used to quantify gene expression using the version 87 GRCh37 annotation from Ensembl. Count data were filtered to include only genes that had a cpm (counts per million) value greater than 2 cpm across all experimental conditions per cell line.
Assembly: GRCh37
Supplementary files format and content: Read counts as tab separated values

source_name: Cell Line

extract_protocol:
Total RNA was extracted from cells using the ReliaPrep RNA miniprep system (Promega).
RNA was submitted to the University of Minnesota Genomics Center for RNA-seq library synthesis using a TruSeq Stranded mRNA kit (Illumina) according to manufacturer’s instructions.

value: Cell Line

value: Prostate Cancer

value: shRNA targeting CPSF1 (2)


title: AID-cre tdTomato lymphocytes, AID+ MHV68+, 16 dpi M2.Stop 73.Bla MHV68, Rep. 2

description: Library name: M2-2-AB


title: SLO D60


title: 22Rv1 CPSF1 sh1 BR3

value: shRNA targeting CPSF1 (1)


title: AID-cre tdTomato lymphocytes, AID+ MHV68-, 16 dpi M2.Stop 73.Bla MHV68, Rep. 2

description: Library name: M2-2-A


title: Luminal Breast Cancer Tumor [CM6]

value: Formalin-fixed paraffin-embedded tissue sections

value: Mexican Patient


title: Wildtype mouse 1, 6 months old, Sequencing Run 1

value: Brain

value: WT


title: ROSAmT

city: Columbia

first: Sathesh

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

data_processing:
Read were aligned using CellRanger v7.0.6
Assembly: Mus musculus GRCm39
Supplementary files format and content: Raw count matrix (matrix.mtx), cell barcodes (barcode.tsv) & gene feature table (feature.tsv) files in gun zipped format

source_name: Inguinal Axillary Lymphatic Vessels

extract_protocol:
Full length IALVs from both the left and right side of each mouse ROSA26mTmG were isolated and cleaned of excessive matrix and adipose tissue. Isolated vessels were digested into single cell suspensions as described above and the cells were kept on ice following single cell suspension until all the tissues had been processed. Cells from all vessels were combined and sorted for tdTomato expression to remove debris and concentrate the cells for downstream single cell 3’ RNA-Seq libraries creation with 10x Genomics Chromium Chip.
Chromium Next GEM Single Cell 3’ RNA-Seq reagents. Samples were sequenced with the NovaSeq 6000 S4-PE100 flow cell.

value: Inguinal Axillary Lymphatic Vessels

value: lymphatic vessel cells

value: Normal


title: BR-like dwarf rep 1 short-read

description: Library name: 1A_14_18

value: leaf

value: etoposide


title: line 17B rep 2 short-read

description: Library name: 17B_6


title: PR8 immune P14 replicate B, HTO

first: David

last: Masopust

department: Microbiology and Immunology

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

data_processing:
RNA, ADT, and HTO libraires were sequenced with an Illumina NovaSeq 6000 S4 flow cell at the University of Minnesota’s Genomics Core. Reads were processed with 10X Genomics Cell Ranger v.7.0.0 with feature barcoding, where RNA reads were mapped to the mouse mm10–2.1.0 mouse reference and antibody reads mapped to known barcodes
Assembly: mm10-2.1.0
Supplementary files format and content: CellRanger output files
Library strategy: CITE-seq

molecule: protein

source_name: Blood, female reproductive tract, lung, medLN, salivary gland, and spleen

growth_protocol: 5 x 104 naïve CD45.1+ P14 TCR transgenic CD8 T cells, specific for the H-2Db-restricted LCMV gp33-41 epitope, were adoptively transferred to adult naïve female C57BL/6J mice followed by i.p. infection with 2x105 PFU LCMV Armstrong (Arm) or i.n. infection with 500 PFU PR8-gp33 1 day later. Memory mice immune to LCMV Armstrong (56 days post-infection) or PR8-gp33 (47 days post-infection) were sacrificed. Tissues were excised and digested, lymphocytes enriched, and P14 cells were purified using FACS.

extract_protocol:
After enzymatic and mechanical tissue diggestions, enriched lymphocyte cell suspensions were stained with Live/Dead dye (Ghost-Dye 510, Tonbo), fluorescent-conjugated antibodies (CD8b (RPA-T8), Thy1.1 (HIS51), CD45.1 (A20), Thy1.2 (30-H12)), and oligonucleotide-conjugated Biolegend TotalSeq-A antibodies (30 min at 4ºC ). P14 (Live, CD8a+, Thy1.1+ and CD45.1+) P14 T cells were sorted using a FACS Aria II (BD Biosciences).
We followed the 10X Genomics Chromium Single Cell 3’ v3 protocol to prepare RNA, antibody-derived-tag (ADT), and hashtag oligos (HTO) libraries.

treatment_protocol: After removing tissues, cells were released from the spleen, lymph nodes, and liver by mechanically disrupting them, followed by filtration through a 70-µm filter and washing in RPMI 1640 containing 5% fetal bovine serum (FBS). Spleen and Liver RBCs were lysed with ACK buffer and washed once. Blood RBCs were lysed with ACK buffer twice and and washed twice. Cells were enzymatically released from the lung, salivary gland, female reproductive tract (FRT), from the epithelial and lamina propria compartments of small intestine (SI). After enzymatic digestion, lymphocytes from single-cell suspensions of the lung and SI were enriched using a Percoll gradient.

value: CD8+ T cell

tag: library type

value: HTO

tag: hto


title: AID-cre tdTomato lymphocytes, AID+ MHV68+, 16 dpi M2.Stop 73.Bla MHV68, Rep. 1

description: Library name: M2-1-AB

tag: tissue

value: draining lymph nodes

value: AID+ MHV68+

value: AID-cre tdTomato

tag: treatment

value: 16 dpi with M2.Stop 73.Bla MHV68


title: PR8 immune P14 replicate B, ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: Blood, female reproductive tract, lung, medLN, salivary gland, and spleen

value: ADT

tag: adt


title: AID-cre tdTomato lymphocytes, AID+ MHV68-, 16 dpi M2.Stop 73.Bla MHV68, Rep. 1

description: Library name: M2-1-A

value: AID+ MHV68-

tag: genotype


title: line 17B rep 1 short-read

description: Library name: 17B_15


title: AID-cre tdTomato lymphocytes, AID+ MHV68+, 16 dpi WT 73.Bla MHV68, Rep. 3

description: Library name: WT-4-AB

value: 16 dpi with WT 73.Bla MHV68