title: SW48, Active-seq, Rep3

city: Birmingham

first: Robert

last: Neely

address: 97 Vincent Drive

institute: Tagomics LTD

description:
Library name: Active-Seq_SW48_Rep-3
Active-seq

data_processing:
Adapter and quality trimming: BBTools
Alignment: BWA-MEM2
Filtering of reads MAPQ<40: Samtools
Duplicate removal: Sambamba
Coverage bigWig generation: deepTools, bamCoverage tool
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Colon

extract_protocol:
Genomic DNA was obtained from the ATCC (https://www.atcc.org/)
Genomic DNA was sheared to an average of 180 bp in 8 microTube-50 AFA Fiber V2 Strips using a Covaris E220 evolution sonicator. 10 ng of input DNA was tagged using the Tagomics Active-Seq reaction kit and according to the manufacturer’s instructions. DNA was mixed with the methyltransferase enzyme and tagging compound and incubated at 37 °C for 1 hour. The reaction was stopped using the reaction termination buffer, with an incubation at 55°C for 15 mins. Without purification, the sample was cooled to 10°C. To this, was added 9 µL of End Repair & A-Tailing Master Mix (3.5 µL KAPA End Repair & A-Tailing Buffer, 1.5 µL KAPA End Repair & A-Tailing Enzyme and 4 µL water). The mixture was mixed thoroughly by pipette aspiration and incubated at 20°C for 30 mins followed by a 65°C incubation for a further 30 mins. The sample was cooled to 10°C, and to it were added IDT xGen Stubby Adapters (2.5 µL of 15µM Stocks) and 22.5 µL of Ligation Master Mix were added (15 µL KAPA Ligation Buffer, 5 µL KAPA DNA Ligase and 2.5 µL water). The mixture was thoroughly mixed by aspiration then incubated at 20 °C for 30 minutes.Without purification, DNA mixed with Tagomics Active-seq capture compound and the mixture was incubated at 37 °C for 1 hour with shaking at 500 rpm. The DNA was purified from the reaction mixture using AMPure Beads (Beckman Coulter) (washing with 150 µL 80% Ethanol) with final elution in 30 µL PBST (10mM Phosphate Buffer, 1M NaCl, pH 7.5, 0.005 % Tween-20). 5 µL Dynabeads MyOne Streptavidin C1 beads (ThermoFisher) were washed with 150 µL of PBST. Capture-ready DNA was added to the beads (29 µL - 1 µL was taken for QC) and mixed with by aspiration until a homogenous mixture was achieved. The mixture was further incubated at 23 °C for 15 minutes, with shaking at 1000 rpm. Once completed, the beads were washed twice with 150 µL of PBST. Finally, the beads were resuspended in 20 µL of Tagomics Active-seq Release Buffer and incubated at 50 °C for 30 minutes at 1000 rpm. After release of the DNA, the beads were placed on the magnet and left for 3 minutes. The supernatant containing the unmodified DNA fraction was transferred to a sterile tube and can be stored at this point or used directly for amplification. A mixture of KAPA HiFi HotStart ReadyMix (2x, 25 µL), IDT Unique Dual Index Primer Pairs (5 µL of 10 µM Stock) and the enriched DNA library (20 µL) was prepared and subjected to amplification by PCR (up to 13 cycles). The amplified library was purified using 1X AMPure XP Beads (washed with 150 µL 80% ethanol) and eluted in 10mM Tris-HCl (pH 8.5), 0.01% Tween-20.

value: Colon

value: Epithelial


title: HepG2, Active-seq, Rep3

status: Public on Aug 13 2025

type: SRA

country: United Kingdom

description:
Library name: Active-Seq_HepG2-Rep-3
Active-seq

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver

tag: tissue

value: Liver

tag: cell line

tag: cell type

value: Epithelial-like


title: MCF7, Active-seq, Rep2

description:
Library name: Active-Seq_MCF7-Rep-2
Active-seq

source_name: Breast

value: Breast


title: MCF7, Active-seq, Rep3

description:
Library name: Active-Seq_MCF7-Rep-3
Active-seq


title: SW48, Active-seq, Rep1

description:
Library name: Active-Seq_SW48_Rep-1
Active-seq


title: PacBio_KmgKD_rep1

city: Stanford

first: Neuza

last: Reis Matias

state: CA

address: 279 Campus Drive

department: Developmental Biology

country: USA

institute: Stanford University

description:
Library name: PacBio_KmgKD_rep1
(24hr run time) at the Chan Zuckerberg Biohub SF Genomics Platform

library_source: transcriptomic

data_processing:
Circular consensus sequencing (CCS) and Iso-Seq analysis were performed in SMRT Link v11.0
Data was mapped to Drosophila genome assembly: BDGP6.32 (GCA_000001215.4) using pbmm2 (1.12.0)
Tama (b0.0.0) collapse was used to collapse redundant transcript models (Kuo et al. 2020); -x capped (although our libraries are not 5' capped, this avoids over collapsing), -a 78 (78bp interquantile width that includes 90% of CAGE clusters, from parallel analysis), -z 80 (80bp interquantile width that includes 90% of 3?end clusters, from parallel analysis)
Transcriptome models from each PacBio library were merged into one single transcriptome with Tama (b0.0.0) merge (Kuo et al. 2020); -a 78 (78bp interquantile width that includes 90% of CAGE clusters, from parallel analysis), -z 80 (80bp interquantile width that includes 90% of 3?end clusters, from parallel analysis)
Analysis scripts are available at https://github.com/NeuzaRM/Kmg_FullerPaper2025
Assembly: dm6
Supplementary files format and content: gtf file of the merged transcriptome (control + KmgKD), after quality control and filters. Please see publication for details.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Testes

extract_protocol:
RNA was extracted from 150 pairs of testes using the RNeasy Plus Mini Kit from QIAGEN (74104)
Iso-Seq SMRTbell® libraries were made following the “Procedure & Checklist – Iso-Seq™ Express Template Preparation for Sequel® and Sequel II Systems”, protocol from PacBio.

value: Testes

tag: genotype

value: bamGAL4/ KmgRNAi

tag: treatment

value: Fly crosses were kept for 3 days at 25°C. Adults were then flipped to a new bottle, while the eggs and early larvae were shifted to 29°C. Testes were dissected from 0–2 day old males in 1xPBS.


title: HepG2, Active-seq, Rep2

description:
Library name: Active-Seq_HepG2-Rep-2
Active-seq


title: HepG2, Active-seq, Rep1

description:
Library name: Active-Seq_HepG2-Rep-1
Active-seq


title: MCF7, Active-seq, Rep1

description:
Library name: Active-Seq_MCF7-Rep-1
Active-seq


title: HT29, Active-seq, Rep3

description:
Library name: Active-Seq_HT29-Rep-3
Active-seq

value: Enterocyte


title: Participant7_Month_6_Fast

type: RNA

city: Banjul

first: Ismaila

middle: L.

last: Manneh

address: Atlantic Blvd

department: VIT

country: Gambia

institute: MRCG at LSHTM

description: SAMPLE 120

hyb_protocol: 65°C overnight

scan_protocol: Nanostring reader

data_processing: nSolver and Rosalind

molecule: total RNA

source_name: Blood

growth_protocol: Whole blood preserved in PAXgene tube and stored in -80 until needed

extract_protocol: RNA extraction

treatment_protocol: Left at Room temperature overnight

value: Blood

tag: paticipant

tag: timepoint

tag: response

value: Fast

tag: outcome

value: Cure


title: PacBio_Control_rep2

description:
Library name: PacBio_Control_rep2
(24hr run time) at the Chan Zuckerberg Biohub SF Genomics Platform


title: SW48, Active-seq, Rep2

description:
Library name: Active-Seq_SW48_Rep-2
Active-seq


title: HT29, Active-seq, Rep1

description:
Library name: Active-Seq_HT29-Rep-1
Active-seq


title: HT29, Active-seq, Rep2

description:
Library name: Active-Seq_HT29-Rep-2
Active-seq


title: HCC1937, Active-seq, Rep3

description:
Library name: Active-Seq_HCC1937_Rep-3
Active-seq


title: Participant7_Month_2_Fast

description: SAMPLE 118


title: PacBio_Control_rep1

description:
Library name: PacBio_Control_rep1
(24hr run time) at the Chan Zuckerberg Biohub SF Genomics Platform


title: HCC1937, Active-seq, Rep2

description:
Library name: Active-Seq_HCC1937_Rep-2
Active-seq


title: HCC1937, Active-seq, Rep1

description:
Library name: Active-Seq_HCC1937_Rep-1
Active-seq


title: Participant7_Baseline_Fast

description: SAMPLE 117

value: Baseline


title: MM.1S-p3-1-3

city: suzhou

first: Koukou

last: Tang

address: xietang

country: China

institute: Soochow universiy

description:
Library name: sample 6
MM.1S-p3-1-3

data_processing:
FastQC software was used to filter the raw data and then got the clean data.
Hisat2 was used to map the clean data to the refernce genome sequences.
Stringtie software was used to the assembly the reads that mapped the genome.
Stringtie software was used to caculate the expression amount readcount. Then caculate the FPKM of the gene and transcript.
Assembly: GRCh38.p14 Primary Assembly
Supplementary files format and content: ab-delimited text files include p-value for each Sample

extract_protocol:
The total RNA was extrated for libraries construction by the Triozol kit according the standard protocol.
Libraries were prepared for sequencing using standard lllumina protocols

value: Myeloma cells

value: PRKCN knockdown

value: PRKCN shRNA infection


title: MM.1S-p3-1-2

description:
Library name: sample 5
MM.1S-p3-1-2


title: Black_Hg3_Z173

city: Bethesda

first: Christian

last: Wake

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
Samples whose sex could not be determined by phenotype (Sex = 'UNK') were left out of this analysis.
Clipping - trimmomaticv 0.39 was used for adapter clipping and quality trimming. It was used in paired-end mode, converting to Phred quality 33, speicifying a minimum trailing and leading base quality of 3, sliding window of size 4 and required quiality of 20, and minimum read length of 50 (-phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50)
Alignment - star v 2.7.9 was used for alignment to genome, specifying maximum multimap per read of 20, max fraction of read length to mismatch as 0.04, and maximum number of junction to be inserted to the genome on the fly at the mapping stage as 1,200,000 (--outFilterMultimapNmax 20 --outFilterMismatchNoverReadLmax 0.04 --limitSjdbInsertNsj 1200000)
Counting - featureCounts from the Subreads package was used for quantification of read abundances per gene/sample. Only primary alignment were counted (--primary) and when relevant assigning a read to the feature with the largest overlap (--largestOverlap).
Genes filtering - genes were then removed if they were present in fewer than 30% of samples, had variance across samples below 100, or were ribosomal genes.
Downsampling - Three samples were above a read depth threshold chosen as 2.75 standard deviations from the mean, and so were randomly down-sampled to have depth just under the threshold while maintaining the same sample order. One sample (Z22) was removed for falling below the equivalent lower threshold.
Normalization - Counts were then normalized with the median of ratios method from DESeq2 v. 1.30.1 (Love, Huber & Anders 2014) implemented in R v 4.0.2
Sample filtering - Principle Component Analysis was conducted on normalized counts with the stats R package, from which 4 samples were flagged as outliers (more than 2.75 standard deviations from the mean of PC1, PC2 or PC3) and removed from the analysis.
Differential expression - comparisons were conducted with DESeq2, using sex, age of euthanasia and library plate as covariates in the statistical models.
Gene Set Enrichment Analysis - GSEA was conducted with R package fgsea and gene sets from canonical pathways (C2CP) in the Molecular Signature Database, MSigDB
Assembly: Taeniopygia guttata genome v1.p.111 from Ensembl, bTaeGut1_v1.p
Supplementary files format and content: Comma-delimited text file with normalized counts per gene (rows) and sample (columns).Row names match ensembl ID format and column names match the Sample "Description" field.

organism: Taeniopygia guttata

source_name: Bone marrow

extract_protocol:
Bulk bone marrow RNA was isolated using cold RNAzol RT (Molecular Research Center). mRNA was purified with Dynabeads Olgio(dt)25 (Invitrogen).
Libraries were constructed with NEBNext Ultra II RNA Prep reagents following manufacturer's protocols (New England Biolabs).

value: Bone marrow

value: Hg

tag: Sex

value: F

tag: euth age

tag: cohort

tag: plate

value: H

tag: rna extraction_batch

tag: rin score

tag: library preparation_method

value: Adapted NEBNext Ultra II RNA library prep


title: MM.1S-p3-1-1

description:
Library name: sample 4
MM.1S-p3-1-1


title: MM.1S-PSG-3

description:
Library name: sample 3
MM.1S-PSG-3

value: WT

value: shscramble infection


title: Yellow_C11_Z170

value: C


title: Participant54_Month_2_Slow

description: SAMPLE 116

value: Slow


title: MM.1S-PSG-2

description:
Library name: sample 2
MM.1S-PSG-2


title: Black_2_Hg3_Z58

value: M

value: K


title: Orange_C13_Z59


title: MM.1S-PSG-1

description:
Library name: sample 1
MM.1S-PSG-1


title: Purple_C19_Z57


title: scRNAseq

city: New Haven

first: Jeffrey

last: Ishizuka

state: CT

address: 300 George Street

institute: Yale University

description: Library name: MCC1, scRNAseq

library_source: transcriptomic single cell

data_processing:
Cell Ranger software v7.0.0 was used to align the 5’ single cell sequencing reads in FASTQ files to reference GRCh38-2020-A, count gene expression, capture antibody hashtags and assemble V(D)J transcript sequences.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcode.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output files: filtered_contig_annotations.csv

source_name: PBMC

extract_protocol:
Cultured cells were collected stained with TotalSeq anti-human hashtags C0251- C0258 (Biolegend), viability dye (zombie red, Biolegend 423109) and anti-human CD45-FITC (clone HI30, Biolegend 304038) and enriched for live cells and up to 50% immune cells using BD FACS Aria II. Sorted cells were then resuspended to 700-1200 cells per ul and barcoded for multiplexed single cell sequencing using 10x Genomics 5’v2 chemistry (10x Genomics, PN-1000263).
Sorted cells were immediately loaded into a 10x Chromium reaction. Chromium Next GEM Single-Cell 5′ kits v.2 were used to generate GEX, VDJ and Cite-seq libraries according to the manufacturer’s protocol.

value: PBMC


title: TCRseq

description: Library name: MCC1, TCRseq

data_processing:
Cell Ranger software v7.0.0 was used to align the 5’ single cell sequencing reads in FASTQ files to reference GRCh38-2020-A, count gene expression, capture antibody hashtags and assemble V(D)J transcript sequences.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcode.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output files: filtered_contig_annotations.csv
Library strategy: TCR-Seq


title: CITEseq, HTO

description: Library name: MCC1, CITEseq

data_processing:
Cell Ranger software v7.0.0 was used to align the 5’ single cell sequencing reads in FASTQ files to reference GRCh38-2020-A, count gene expression, capture antibody hashtags and assemble V(D)J transcript sequences.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcode.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output files: filtered_contig_annotations.csv
Library strategy: CITE-seq


title: Monocyte derived Naive Macrophages without K21, ADT

city: Rīga

first: Bhupesh

last: Prusty

address: Rātsupītes iela 5

country: Latvia

institute: Rīga Stradiņš University

description:
Library name: 240036SC_22_ADT
10X Genomics

data_processing:
The sequencing data was processed using the CellRanger (v8.0.0 ) GEX+ADT pipeline, which conducts QC, cell filtration, read alignment, and generation of feature-barcode matrices. The reads were aligned to the human (GRCh38) reference genome. To obtain higher numbers of usable cells, we set the parameter ‘--expect-cells=10000’ within CellRanger. Seurat (v4.1, https://satijalab.org/seurat/) R packages were used to calculate QC matrices and to filter cells and features. For filtering of cells (https://github.com/satijalab/seurat/issues/3396), we first removed empty droplets. Subsequently, we removed low-quality cells with unique feature counts greater than 8000 or less than 200. Furthermore, low-quality or dying cells that exhibited extensive mitochondrial contamination were removed. Genes with expression for at least three cells are retained for filtering. (Hao Y ,  Hao S ,  Andersen-Nissen E , et al. Integrated analysis of multimodal single-cell data[J].  2021). Quality control (QC) was based on (1) nFeature_RNA: number of unique genes detected in each cell; (2) nCount_RNA: total number of molecules detected within a cell; (3) percent.mt: percentage of reads that map to the mitochondrial genome. Mitochondrial QC metrics were generated, calculating the percentage of counts originating from a set of features (the set of all genes starting with “MT-” mitochondrial genes).
Assembly: GRCh38
Supplementary files format and content: Separate folders for each individual sample

source_name: PBMC derived cells

growth_protocol: For single-cell RNA-seq (scRNA-seq) work, heterogeneous donor-derived PBMCs were used. PBMCs were prepared from healthy blood donors as a byproduct of platelet concentrates obtained using leukoreduction system chambers, kindly provided anonymously by the Department of Transfusion Medicine at the University Hospital Würzburg, under the guidelines of the Ethics Committee of the Medical Faculty of the University of Würzburg. PMBCs were isolated using a density gradient (Histopaque-1077, Sigma-Aldrich, #1077-100ml), washed twice with PBS, and resuspended in Monocyte Attachment Medium (PromoCell #C-28051). The frequency of mononuclear cells was analyzed by Flow cytometry (Attune Nxt Flow Cytometer). 1.5 × 10^6 cells/sq cm were seeded into 6-well plates (1.4 × 10^7 per well) and incubated for 1-2 hours at 5% CO2 and 37 °C in the incubator to facilitate cell attachment. Adherent cells were washed thrice intensively with warm Monocyte Attachment media to loosen non-adherent cells.

extract_protocol:
Incubation at 37 °C for 6 days yielded immature macrophages. On day 6, M1 immature macrophages were activated into classical M1 macrophages by adding 50 ng/ml IFN-γ (Immunotools rh-IFNγ #11343534) and 10 ng/ml LPS (Sigma-Aldrich, Lipopolysaccharides from Escherichia coli O111:B4 #L5293), or they remained without an activation stimulus. M2 immature macrophages were activated into M2a macrophages by adding 20 ng/ml IL-4 (rh IL-4 Sigma-Aldrich #SRP3093) or into M2c macrophages by adding 20 ng/ml TGFβ (R&D rhTGFβ #7754-BH/CF), respectively. The cells were further incubated until day 10 in the presence of K21 or without it as a control. On day 10, macrophages were washed with PBS and detached in the presence of 1 ml Accumax solution (Sigma-Aldrich #SLCR6580) for 5-10 min at 37 °C.
For single-cell RNA-seq analysis, 1 million macrophages per condition were washed with PBS on day 10 of the experiment and then detached in the presence of 1 mL Accumax solution (Sigma-Aldrich #SLCR6580) for 5-10 min at 37 °C. Cells were washed once again with PBS, fixed in PBS: methanol mix (ratio of 1:4), and stored in a -80 freezer until subsequent use. On the day of the experiment, methanol-fixed cells were thawed on ice and rehydrated in 1X PBS for 30 minutes on ice, filtered with a 40 μm cell strainer. Cells were barcoded using MULTI-seq Lipid Modified Oligos (Sigma-Aldrich #LMO001). After cell counting, single-cell suspension samples were pooled into four separate groups (Activated macrophages, -K21; Activated macrophages, +K21; naïve macrophages, -K21; and naïve macrophages, +K21). Ten thousand cells per sample were loaded on a Chromium Controller (10× Genomics). The scRNA-seq libraries were constructed using the Chromium Single Cell 3’ v3.1 Reagent Kit according to the manufacturer‘s guidelines (10× Genomics). cDNA libraries were uniquely sample-indexed and pooled for sequencing. A HiSeq (Illumina) sequencing run was used to sample balance on a NovaSeq 6000 SP flowcell (Illumina) targeting > 25,000 reads/cell.

treatment_protocol: M1 or M2 Macrophages were generated using M1 or M2 Generation Medium XF, respectively (PromoCell M1 #C-28055 containing GM-CSF or M2 #C-28056 containing M-CSF). One group was treated with 0.2 mM K21, and the control group received vehicle control.

value: PBMC derived cells

value: Immune cells

value: Naive Macrophages

tag: library type

value: ADT


title: Participant54_Baseline_Slow

description: SAMPLE 114

tag: tissue

value: Blood

value: Baseline

value: Cure


title: Blue_2_Hg6_Z56

value: Bone marrow

value: Hg

value: F


title: Monocyte derived Naive Macrophages with K21, mRNA

description:
Library name: 240036SC_23_mRNA
10X Genomics

value: WT

value: Naive Macrophages + K21

value: mRNA


title: Monocyte derived Naive Macrophages with K21, ADT

description:
Library name: 240036SC_23_ADT
10X Genomics


title: Participant54_Week_2_Slow

description: SAMPLE 115

value: Slow


title: Participant51_Week_2_Fast

description: SAMPLE 113

value: Fast


title: Participant55_Month_2_Slow

description: SAMPLE 111


title: Participant56_Month_2_Slow

description: SAMPLE 112


title: Monocyte derived Naive Macrophages without K21, mRNA

description:
Library name: 240036SC_22_mRNA
10X Genomics


title: Monocyte derived Activated Macrophages with K21, ADT

description:
Library name: 240036SC_21_ADT
10X Genomics

value: Activated Macrophages + K21


title: Monocyte derived Activated Macrophages with K21, mRNA

description:
Library name: 240036SC_21_mRNA
10X Genomics


title: Participant56_Week_2_Slow

description: SAMPLE 110


title: Blue_C9_Z55

value: C

value: K

value: Adapted NEBNext Ultra II RNA library prep


title: Red_Hg18_Z54


title: Monocyte derived Activated Macrophages without K21, ADT

description:
Library name: 240036SC_20_ADT
10X Genomics

value: PBMC derived cells

value: Immune cells

value: Activated Macrophages


title: Red_C19_Z53


title: Monocyte derived Activated Macrophages without K21, mRNA

description:
Library name: 240036SC_20_mRNA
10X Genomics


title: ribodeplete - Vector3B

city: Chicago

first: Katherine

last: Borden

address: 675 N St Claire Street

department: Pharmacology/ Cancer Center

institute: Northwestern University

description: Library name: Vector3B

data_processing:
Samples were sequenced at the Genome Quebec sequencing facility and obtained as FASTQ files.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 37 (based on Ensembl 103)
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

growth_protocol: U2-OS cells was grown in DMEM sumplemented with 10% fetal bovine serum (FBS) and penicilin/streptavidin in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Extraction with direct-zol mini prep Kit from Zymo research
KAPA RNA Hyperprep Ribodepletion

tag: cell line


title: Participant55_Week_2_Slow

description: SAMPLE 109

value: Blood


title: Blue_Hg1_Z52

value: M


title: ribodeplete - Vector2A

description: Library name: Vector2A


title: Participant7_Month_4_Fast

description: SAMPLE 119

value: Cure


title: Participant56_Baseline_Slow

description: SAMPLE 108

value: Baseline


title: ribodeplete - Vector1C

description: Library name: Vector1C


title: ribodeplete - CbcA4B

description: Library name: CbcA4B


title: ribodeplete - CbcA4A

description: Library name: CbcA4A


title: ribodeplete - CbcA1C

description: Library name: CbcA1C


title: ribodeplete - CbcA1B

description: Library name: CbcA1B


title: ribodeplete - CbcA4C

description: Library name: CbcA4C


title: Participant55_Baseline_Slow

description: SAMPLE 107


title: Orange_Hg1_Z48

value: Bone marrow

value: Hg

value: F


title: Participant40_Month_2_Slow

description: SAMPLE 106


title: Purple_Hg18_Z50


title: Participant49_Week_2_Slow

description: SAMPLE 105


title: Participant40_Baseline_Slow

description: SAMPLE 104


title: Green_Hg13_Z46


title: Yellow_C19_Z47


title: CAF107 KO MCL-1

city: Nantes

first: jennifer

last: Derrien

address: 8 quai moncousu

country: France

institute: INSERM

description: Library name: CAF-107-SG-20221109-MCL1

data_processing:
The demultiplexing, barcode processing, and gene counting were performed using Cell Ranger software v.7.0.1.
Assembly: GRCh38-3.0.0
Supplementary files format and content: The processed data files include tab-separated values (.tsv) files and matrix files (.mtx

source_name: Cancer-associated fibroblast

extract_protocol:
Cancer-associated fibroblasts were recovered from breast tumor exeresis of treatment-naive patients. Fibroblasts were selected for their ability to adhere to plastic culture dishes.
Libraries were prepared according to the manufacturer’s instructions using the Chromium Single Cell 3’ v3.1 protocol (10x Genomics). Sequencing was performed on a NovaSeq 6000 platform as paired-end reads: 28 bp for Read 1 and 90 bp for Read 2 (GenoA, UMS Biocore, SFR Bonamy, Nantes).

tag: cell type

value: Cancer-associated fibroblast


title: CAF65 KO MCL-1

description: Library name: CAF-65-SG-20221109-MCL1


title: CAF107 KO CTRL

description: Library name: CAF-107-SG-20221109-NT


title: CAF51 KO MCL-1

description: Library name: CAF-51-SG-20221121-MCL1


title: CAF51 KO CTRL

description: Library name: CAF-51-SG-20221121-NT


title: Red_C12_Z45


title: Participant27_Month_2_Fast

description: SAMPLE 103


title: Participant27_Week_2_Fast

description: SAMPLE 102


title: Red_Hg15_Z44


title: 2-Month S2P2 hKPA transplant, Replicate 2 d59, GEX Library

city: Los Angeles

first: Zhongwei

last: Li

address: 1425 San Pablo St

department: Keck medicine

institute: University of Southern California

description:
library name: GEX_2_Month_S2P2_hKPA_transplant_2
10X GEM-X 3’ kit

data_processing:
Sequencing reads were aligned to the human genome (GRCh38.p14) and mouse genome (GRCm39) with the Cell Ranger software (version 9.0.0) using STAR aligner on the University of Southern California High Performance Cluster.
Assembly: GRCh38_and_GRCm39-2024-A
Supplementary files format and content: filtered_feature_bc_matrix

source_name: Human kidney progenitor assembloid (KPA) in vivo

growth_protocol: D5-D7 hKPA were transplanted in NSG mice under kidney capsule for 1-2 months.

extract_protocol:
Transplanted hKPA were dissected out from surgical NSG mice and digested in CAP digestion solution (10mg/ml Cold Active Protease+ 2.5 mg/ml Collagenase type 4 + 0.125U/ul Dnase1)  at 12°C for 30 mins. Cells were then spun down at 350G for 5 mins and resuspended in cold autoMACS Running Buffer. Cell viablity was accessed (99% Live) and cells spun down again. 10X genomics Demonstarated Proocol CG000365 (REV C) was then used to isolate nuclei with 5 min lysis time. The single nuclei suspension was than transposed and run through a microfuidic chip (Chip J) for barcoding.
10X Chromium Single Cell Multiome + Gene Expression protocol (CG000338 Rev E) or 10X GEM-X 3’ kit.

value: Kidney cells

tag: genotype

value: SIX2-GFP; PAX2-RFP

value: S2P2 hKPA were transplanted in NSG mice under kidney capsule for 59 days


title: 1-Month S2P2 hKPA transplant, Replicate 2 d32, GEX Library

description:
library name: GEX_1_Month_S2P2_hKPA_transplant_2
10X Chromium multiome ATAC + gene expression kit

treatment_protocol: D5-D7 hKPA were transplanted in NSG mice under kidney capsule for 1-2 months.

value: Human kidney progenitor assembloid (KPA) in vivo

tag: treatment

value: S2P2 hKPA were transplanted in NSG mice under kidney capsule for 32 days


title: Red_C11_Z43

value: C

value: K

value: Adapted NEBNext Ultra II RNA library prep


title: 2-Month S2P2 hKPA transplant, Replicate 1 d59, GEX Library

description:
library name: GEX_2_Month_S2P2_hKPA_transplant_1
10X GEM-X 3’ kit


title: Participant27_Baseline_Fast

description: SAMPLE 101

tag: paticipant

value: Fast


title: Blue_2_C14_Z51


title: 2-Month PKD2 hKPA transplant, Replicate 1 d66, GEX Library

description:
library name: GEX_2_Month_PKD2_hKPA_transplant_1
10X GEM-X 3’ kit

value: SIX2-GFP; PKD2-/-

value: PKD2-/- hKPA were transplanted in NSG mice under kidney capsule for 66 days


title: Yellow_Hg13_Z42

value: M


title: Participant70_Month_2_Slow

description: SAMPLE 100

value: Blood

tag: timepoint

value: Slow

value: Cure


title: 1-Month S2P2 hKPA transplant, Replicate 1 d32, GEX Library

description:
library name: GEX_1_Month_S2P2_hKPA_transplant_1
10X Chromium multiome ATAC + gene expression kit


title: hKPA, TT removal medium, Replicate 1 d5, GEX Library

description:
library name: GEX_hKPA_TT_Removal_1
10X GEM-X 3’ kit

data_processing:
Sequencing reads were aligned to the human genome (GRCh38.p14) with the Cell Ranger software (version 9.0.0) using STAR aligner on the University of Southern California High Performance Cluster.
Assembly: GRCh38-2024-A
Supplementary files format and content: filtered_feature_bc_matrix

molecule: nuclear RNA

source_name: Human kidney progenitor assembloid (hKPA) in vitro

growth_protocol: hKPA were cultured with complete Stage I medium or TT removal medium, 37C, 5% CO2.

extract_protocol:
Human kidney progenitor assembloid (hKPA) were miccrodissected and digested with AccuMax solution at 37°C for 10 mins. Cells were then spun down at 350G for 5 mins and resuspended in cold autoMACS Running Buffer. Cell viablity was accessed (99% Live) and cells spun down again. 10X genomics Demonstarated Proocol CG000365 (REV C) was then used to isolate nuclei with 5 min lysis time. The single nuclei suspension was than transposed and run through a microfuidic chip (Chip J) for barcoding.
10X GEM-X 3’ kit

value: hKPA were cultured with TT removal medium


title: hKPA, TT removal medium, Replicate 2 d5, GEX Library

description:
library name: GEX_hKPA_TT_Removal_2
10X GEM-X 3’ kit

treatment_protocol: hKPA were cultured with complete Stage I medium or TT removal medium, 37C, 5% CO2.

value: Human kidney progenitor assembloid (hKPA) in vitro


title: Red_2_C4_Z41

value: Bone marrow


title: Participant69_Month_2_Fast

description: SAMPLE 99

tag: response


title: Participant66_Month_2_Slow

description: SAMPLE 97

tag: outcome


title: hKPA, Complete Stage I medium, Replicate 2 d5, GEX Library

description:
library name: GEX_hKPA_Stage_I_2
10X GEM-X 3’ kit

value: Kidney cells

value: SIX2-GFP; PAX2-RFP

value: KPA were cultured with complete Stage I medium


title: ribodeplete - CbcA1A

description: Library name: CbcA1A


title: hKPA, Complete Stage I medium, Replicate 1 d5, GEX Library

description:
library name: GEX_hKPA_Stage_I_1
10X GEM-X 3’ kit


title: N8, AD, iPSC-Neuron derived EV

city: Baltimore

first: Vasiliki

last: Machairaki

state: Maryland

address: 733 N. Broadway, Edward D. Miller Research Building

department: Department of Genetic Medicine

institute: Johns Hopkins University

description: Library name: N8

library_source: other

data_processing:
Adapters and poly‑A tails were removed with cutadapt 3.4.
Reads longer than 15 nt were aligned to custom-curated hg38 reference transcriptomes using bowtie 1.2.2.
The quantification data was normalized and log2 transformed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes normalized and log2 transformed counts for each Sample.

molecule: other

source_name: iPSC-derived excitatory glutamatergic neuron

growth_protocol: Peripheral blood mononuclear cells or skin fibroblasts were reprogrammed into iPSCs, expanded on Matrigel‑coated plates, and differentiated for 21 days into excitatory glutamatergic neurons.

extract_protocol:
Conditioned medium was centrifuged to remove debris, concentrated with a 100 kDa ultrafilter, and passed through 70 nm qEV SEC columns to collect EV‑enriched fractions. Small RNA was extracted from EVs by using the Qiagen miRNeasy Mini Kit.
Small RNA libraries were generated with the BioLiqX Small RNA‑seq Kit and were assessed for size and yield by analysis on a Fragment Bioanalyzer. Multiplexed libraries were pooled together and sequenced on a NovaSeq 6000 using the S4 Reagent Kit v1.5.

tag: Sex

value: Male

tag: age

tag: subject status

value: diagnosed with sporadic Alzheimer’s disease (sAD)


title: N7, AD, iPSC-Neuron derived EV

description: Library name: N7

value: iPSC-derived excitatory glutamatergic neuron


title: Blue_Hg1_Z167

value: Hg

tag: euth age

tag: cohort

tag: plate

value: K

value: Adapted NEBNext Ultra II RNA library prep


title: N6, AD, iPSC-Neuron derived EV

description: Library name: N6

value: Female


title: Participant70_Week_2_Slow

description: SAMPLE 96


title: N5, AD, iPSC-Neuron derived EV

description: Library name: N5


title: CAF65 KO CTRL

description: Library name: CAF-65-SG-20221109-NT

value: Cancer-associated fibroblast


title: Blue_2_Hg18_Z168

value: F

tag: rna extraction_batch

tag: rin score

tag: library preparation_method


title: Purple_C18_Z166

tag: tissue

value: C

value: M


title: N3, AD, iPSC-Neuron derived EV

description: Library name: N3

tag: cell type


title: Orange_Hg7_Z165


title: N2, AD, iPSC-Neuron derived EV

description: Library name: N2


title: N1, AD, iPSC-Neuron derived EV

description: Library name: N1


title: Orange_Hg17_Z164


title: Participant67_Month_2_Fast

description: SAMPLE 98

value: Blood

value: Fast

value: Cure


title: Yellow_2_C19_Z163

value: Bone marrow


title: CTRL5, control, iPSC-Neuron derived EV

description: Library name: CTRL5

value: healthy control


title: Participant69_Baseline_Fast

description: SAMPLE 93

value: Baseline


title: CTRL4, control, iPSC-Neuron derived EV

description: Library name: CTRL4


title: Participant67_Week_2_Fast

description: SAMPLE 92


title: CTRL3, control, iPSC-Neuron derived EV

description: Library name: CTRL3


title: Participant66_Week_2_Slow

description: SAMPLE 91

value: Slow


title: CTRL1, control, iPSC-Neuron derived EV

description: Library name: CTRL1


title: Participant69_Week_2_Fast

description: SAMPLE 95


title: N4, AD, iPSC-Neuron derived EV

description: Library name: N4

value: diagnosed with sporadic Alzheimer’s disease (sAD)


title: Participant67_Baseline_Fast

description: SAMPLE 90


title: CTRL8, control, iPSC-Neuron derived EV

description: Library name: CTRL8

value: iPSC-derived excitatory glutamatergic neuron


title: Black_C4_Z161


title: ALSP6_FC

city: Saint Louis

first: Siling

last: Du

address: 4515 Mckinley Ave

institute: Washington University in St. Louis

description:
Library name: ALSP6_FC
10x Genomics

data_processing:
Sample demultiplexing, barcode processing and single-cell counting was performed using the Cell Ranger Single-Cell Software Suite (5.0.0, 10x Genomics). Cellranger count was used to align samples to the reference genome provided by 10X Genomics (GRCh38-2020-A for human) with “include introns = TRUE”.
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated values files and count matrix of processed Seurat object

source_name: frontal cortex

extract_protocol:
Post-mortem frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice for 15 min. The suspension was filtered through a 30-μm filter to remove debris and pelleted at 500g for 5 min at 4 oC. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U μl–1 RNasin (Promega)). Nuclei pellets were resuspended in 500 μl nuclei wash and 900 µl 1.8 M sucrose. This 1,400 μl mixture was carefully layered on top of 500 μl 1.8 M sucrose and centrifuged at 13,000g for 45 min at 4 oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in nuclei wash at 1,000 nuclei μl–1 and filtered through a 40-μm FlowMi Cell Strainer.
Chromium Single Cell 5′ Reagent Kits (v2)

value: frontal cortex

tag: disease state

value: ALSP

tag: genotype

tag: sample identifier


title: Participant66_Baseline_Slow

description: SAMPLE 89

tag: paticipant

tag: timepoint


title: ALSP6_SC

description:
Library name: ALSP6_SC
10x Genomics

source_name: subcortical

value: subcortical


title: ALSP6_OC

description:
Library name: ALSP6_OC
10x Genomics

source_name: occipital cortex

value: occipital cortex


title: CTRL7, control, iPSC-Neuron derived EV

description: Library name: CTRL7

value: Female


title: Black_C9_Z159

tag: treatment

value: F

value: Adapted NEBNext Ultra II RNA library prep


title: Participant65_Month_2_Slow

description: SAMPLE 88

tag: response

tag: outcome


title: ALSP5_OC

description:
Library name: ALSP5_OC
10x Genomics

tag: Sex

tag: age


title: Orange_Hg19_Z162

value: Hg

value: M

tag: euth age

tag: cohort


title: Participant70_Baseline_Slow

description: SAMPLE 94

value: Blood


title: ALSP4_FC

description:
Library name: ALSP4_FC
10x Genomics


title: Purple_Hg11_Z158

tag: plate

tag: rna extraction_batch


title: ALSP6_WM

description:
Library name: ALSP6_WM
10x Genomics

source_name: white matter

value: white matter


title: Green_2_C19_Z157

value: Bone marrow

value: C

tag: rin score

tag: library preparation_method


title: Blue_Hg13_Z160

tag: tissue


title: ALSP3_BG

description:
Library name: ALSP3_BG
10x Genomics

source_name: basal ganglia

value: basal ganglia

tag: disease state


title: Black_2_Hg8_Z146


title: ALSP3_parietal

description:
Library name: ALSP3_parietal
10x Genomics

source_name: parietal cortex

value: parietal cortex

tag: genotype


title: ALSP3_temporal

description:
Library name: ALSP3_temporal
10x Genomics

source_name: temporal cortex

value: temporal cortex

tag: sample identifier


title: ALSP3_FC

description:
Library name: ALSP3_FC
10x Genomics


title: ALSP5_WM

description:
Library name: ALSP5_WM
10x Genomics


title: Red_C16_Z145


title: ALSP5_SC

description:
Library name: ALSP5_SC
10x Genomics


title: Participant65_Baseline_Slow

description: SAMPLE 82

tag: paticipant

value: Baseline

value: Slow

value: Cure


title: Control13_OC

description:
Library name: Control13_OC
10x Genomics

value: Control

value: WT


title: Participant64_Month_2_Slow

description: SAMPLE 87

tag: timepoint


title: ALSP2_OC

description:
Library name: ALSP2_OC
10x Genomics

value: occipital cortex

value: ALSP


title: Participant61_Month_2_Slow

description: SAMPLE 83


title: Blue_C6_Z141

tag: treatment

value: F

value: Adapted NEBNext Ultra II RNA library prep


title: ALSP5_FC

description:
Library name: ALSP5_FC
10x Genomics

value: frontal cortex


title: Black_Hg13_Z114

value: Hg

value: J


title: ALSP2_WM

description:
Library name: ALSP2_WM
10x Genomics

value: white matter

value: M


title: ALSP2_FC

description:
Library name: ALSP2_FC
10x Genomics


title: Participant62_Week_2_Fast

description: SAMPLE 81

value: Blood

tag: response

value: Fast


title: ALSP1_FC

description:
Library name: ALSP1_FC
10x Genomics


title: Participant62_Month_2_Fast

description: SAMPLE 86

tag: outcome


title: Purple_Hg6_Z140

value: Bone marrow

tag: Sex


title: Participant65_Week_2_Slow

description: SAMPLE 85


title: Black_C1_Z139

value: C


title: ALSP1_CB

description:
Library name: ALSP1_CB
10x Genomics

source_name: cerebellum

value: cerebellum

tag: age


title: Participant64_Week_2_Slow

description: SAMPLE 84

value: Slow

value: Cure


title: ALSP1_WM

description:
Library name: ALSP1_WM
10x Genomics


title: ALSP1_OC

description:
Library name: ALSP1_OC
10x Genomics


title: Control3_FC

description:
Library name: Control3_FC
10x Genomics

value: Control

value: WT


title: Blue_2_Hg1_Z112

value: UNK

tag: euth age


title: Control3_CB

description:
Library name: Control3_CB
10x Genomics


title: Participant62_Baseline_Fast

description: SAMPLE 79

value: Baseline


title: Control2_WM

description:
Library name: Control2_WM
10x Genomics


title: Participant64_Baseline_Slow

description: SAMPLE 80


title: Participant61_Week_2_Slow

description: SAMPLE 78


title: Control2_FC

description:
Library name: Control2_FC
10x Genomics


title: Green_2_Hg1_Z110

tag: cohort

value: Adapted NEBNext Ultra II RNA library prep


title: Control1_OC

description:
Library name: Control1_OC
10x Genomics

value: occipital cortex

value: F


title: ALSP2_CB

description:
Library name: ALSP2_CB
10x Genomics

value: ALSP


title: Participant61_Baseline_Slow

description: SAMPLE 77


title: Control2_CB

description:
Library name: Control2_CB
10x Genomics


title: Yellow_C13_Z109

tag: plate

value: J


title: Blue_3_C10_Z111

value: M

tag: rna extraction_batch


title: Participant60_Month_2_Fast

description: SAMPLE 76

value: Blood


title: Control3_WM

description:
Library name: Control3_WM
10x Genomics

value: white matter


title: Participant58_Month_2_Slow

description: SAMPLE 74


title: TOV21G parental, untreated, Rep 1

city: London

first: Karen

last: Lane

address: 237 Fulham Road

institute: Institute of Cancer Research

description:
Library name: TOV_UT_1
column name on processed data file: TOV_PS_1.x

data_processing:
Fastq reads were trimmed using TrimGalore --trim-n --paired (fastqc0.11.9).
Residual ribosomal RNA reads were removed using Ribodetector with -e norRNA setting (v0.2.7) and strandedness was detected using RSeQC (v4.0.0).
Reads were aligned to the T2T-CHM13v2.0 genome using STAR alignment software (v2.7.6a) --outFilterMultimapNmax 10
Reads mapping to genes were quantified using HTSeqCount (v0.12.4) --stranded=reverse --nonunique=none
Differential analysis of gene expression was calculated in R using DESeq2 (v1.38.3).
Assembly: T2T-CHM13v2.0
Supplementary files format and content: .csv file showing normalised reads calculated using DESeq2 (v1.38.3).

source_name: ovary

growth_protocol: TOV21G cells were maintained in a 1:1 mixture of MCDB 105 medium with 1.5 g/L sodium bicarbonate and Medium 199 with 2.2 g/L sodium bicarbonate, + 1% pen/strep + 15% FBS

extract_protocol:
Pellets were resuspended in 500µL TRIzol reagent (Invitrogen) and total RNA was extracted using a Direct-zol RNA miniprep kit (Zymo Research) according to the manufacturer’s protocol.
Library preparation was performed by Novogene Corporation Ltd, using the Novogene NGS Stranded RNA Library Prep Set (PT044) and an in-house protocol for 250~300 bp insert strand specific library preparation. 50 million 150bp paired-end stranded reads were sequenced on an Illumina NovaSeq 6000 using an S4 flow cell.

treatment_protocol: Cells were treated with 10µM PDS (dissolved in UF H2O) and harvested by scraping in ice-cold PBS after 4hr. Untreated cells were harvested concurrently.

value: ovary

tag: cell line

tag: cell type

value: adenocarcinoma


title: Red_Hg1_Z108

tag: tissue

value: Bone marrow

value: Hg

tag: rin score

tag: library preparation_method


title: TOV21G parental, untreated, Rep 2

description:
Library name: TOV_UT_2
column name on processed data file: TOV_PS_2.x

tag: genotype


title: Blue_C11_Z107

value: C


title: Black_C19_Z113


title: TOV21G parental, PDS-treated, Rep 3

description:
Library name: TOV_PS_3
column name on processed data file: TOV_18_PS_2.x

value: 10µM PDS, 4hr


title: TOV21G parental, PDS-treated, Rep 1

description:
Library name: TOV_PS_1
column name on processed data file: TOV_8_PS_2.x

value: WT


title: TOV21G parental, PDS-treated, Rep 2

description:
Library name: TOV_PS_2
column name on processed data file: TOV_18_PS_1.x


title: Participant57_Month_2_Fast

description: SAMPLE 73

source_name: Blood

tag: paticipant

value: Fast

value: Cure


title: TOV21G + ARID1A, clone 2 (TOV18), untreated, Rep 2

description:
Library name: TOV18_UT_2
column name on processed data file: TOV_8_PS_1.x

value: WT+exogenous ARID1A


title: Participant60_Week_2_Fast

description: SAMPLE 72

tag: timepoint


title: TOV21G + ARID1A, clone 2 (TOV18), untreated, Rep 1

description:
Library name: TOV18_UT_1
column name on processed data file: TOV_UT_3.x

tag: treatment


title: Red_Hg15_Z106

source_name: Bone marrow

value: Adapted NEBNext Ultra II RNA library prep


title: TOV21G + ARID1A, clone 1 (TOV8), untreated, Rep 2

description:
Library name: TOV8_UT_2
column name on processed data file: TOV_18_UT_2


title: TOV21G + ARID1A, clone 2 (TOV18), PDS-treated, Rep 2

description:
Library name: TOV18_PS_2
column name on processed data file: TOV_UT_2.x


title: TOV21G parental, untreated, Rep 3

description:
Library name: TOV_UT_3
column name on processed data file: TOV_PS_3.x


title: Participant58_Week_2_Slow

description: SAMPLE 70

tag: response

value: Slow


title: TOV21G + ARID1A, clone 2 (TOV18), PDS-treated, Rep 1

description:
Library name: TOV18_PS_1
column name on processed data file: TOV_UT_1.x


title: Participant59_Week_2_Fast

description: SAMPLE 71

tag: outcome


title: Participant59_Month_2_Fast

description: SAMPLE 75


title: TOV21G + ARID1A, clone 1 (TOV8), untreated, Rep 1

description:
Library name: TOV8_UT_1
column name on processed data file: TOV_18_UT_1.x


title: Black_C16_Z105

tag: Sex

value: UNK


title: TOV21G +ARID1A, clone 1 (TOV8), PDS-treated, Rep 2

description:
Library name: TOV8_PS_2
column name on processed data file: TOV_8_UT_2


title: Green_Hg19_Z104

value: F

value: J


title: TOV21G +ARID1A, clone 1 (TOV8), PDS-treated, Rep 1

description:
Library name: TOV8_PS_1
column name on processed data file: TOV_8_UT_1.x


title: Participant60_Baseline_Fast

description: SAMPLE 69

value: Blood

value: Baseline


title: Purple_C7_Z103

value: M


title: Vector3B

description: Library name: Vector3B

growth_protocol: U2-OS cells were grown in DMEM sumplemented with 10% fetal bovine serum (FBS), penicilin/streptavidin and G418 (1mg/ml) in humidified atmosphere with 5% CO2 at 37°C .

extract_protocol:
Cells were harvested at ~80% confluency and RNAs were extracted using Trizol and Direct-zol mini prep Kit from Zymo research
Libraries were prepared using KAPA RNA HyperPrep with PolyA selection at IRIC's genomic platform (University of Montreal)

value: osteosarcoma


title: Vector2A

description: Library name: Vector2A


title: Vector1C

description: Library name: Vector1C


title: Participant57_Week_2_Fast

description: SAMPLE 68


title: Yellow_C10_Z101

value: Bone marrow


title: CbcA4C

description: Library name: CbcA4C


title: CbcA4B

description: Library name: CbcA4B


title: Participant59_Baseline_Fast

description: SAMPLE 67


title: Green_Hg8_Z100

value: Hg


title: Black_C6_Z99

value: C


title: Participant58_Baseline_Slow

description: SAMPLE 66


title: CbcA4A

description: Library name: CbcA4A


title: CbcA1C

description: Library name: CbcA1C


title: CbcA1B

description: Library name: CbcA1B


title: Participant57_Baseline_Fast

description: SAMPLE 65


title: Blue_Hg3_Z98


title: Blue_Hg8_Z102


title: Blue_Hg7_Z96


title: CbcA1A

description: Library name: CbcA1A


title: Participant52_Month_2_Fast

description: SAMPLE 64


title: Green_C16_Z97


title: hb_cell_913613_rk33

city: Montreal

first: Tarik

last: Moroy

state: QC

address: 110, West Pine Avenue, 597

country: Canada

institute: Institut de recherches cliniques de Montréal

description: Library name: hb_cell_913613_rk33

data_processing:
The quality of the raw reads was assessed with FASTQC v0.12.1. After examining the quality of the raw reads, no trimming was deemed necessary. The reads were aligned to the GRCh38 reference genome with STAR v2.7.11b with mean of 87 % of reads uniquely mapped. The raw counts were calculated with FeatureCounts v2.0.6 based on the GRCh38 reference genome (release 110). Differential expression was performed using DESeq2 R package. DEGs heatmap was drawn based on z-score of normalized count. Functional enrichment analysis of DEGs (gene ontology and pathway enrichment) was performed with the gprofiler2 R package.
Assembly: GRCh38
Supplementary files format and content: csv delimited file including raw count for all samples: gene_matrix_count.csv

growth_protocol:
Raji and CA46 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
Primary B cells were resuspended in RPMI supplemented with 10% charcoal-stripped FBS and a total of 1 × 10⁶ purified B cells were seeded into 12-well plates pre-coated with an irradiated feeder cell layer (YK6-CD40L-IL21) that express CD40 ligand and secrete Il-21 to support B cell activation and proliferation.

extract_protocol:
RNA was extracted using the RNeasy® Mini Kit. RNA integrity and quality were verified using the RNA 6000 Pico Kit on an Agilent Bioanalyzer system.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit, following the manufacturer's protocol.

treatment_protocol:
Raji and CA46 cells were treated with either RK-33 (50 μM for Raji and 10 μM for CA46) or DMSO for 24 hours.
Primary B cells were with either 5 µM RK-33 or 0.4% DMSO (vehicle control) for 24 hours and were carefully collected to prevent feeder cell contamination.
Raji and CA46 cells were electroporated with 10 pmol of either the scrambled control, DDX3X, DDX3Y, or a combination of DDX3X and DDX3Y siRNAs using the Neon Transfection System.

value: B lymphocytes


title: hb_cell_913614_dmso

description: Library name: hb_cell_913614_dmso

value: DMSO


title: hb_cell_913615_rk33

description: Library name: hb_cell_913615_rk33


title: hb_cell_913614_rk33

description: Library name: hb_cell_913614_rk33


title: Participant51_Month_2_Fast

description: SAMPLE 63

value: Fast


title: hb_cell_913615_dmso

description: Library name: hb_cell_913615_dmso


title: hb_cell_913613_dmso

description: Library name: hb_cell_913613_dmso


title: Participant50_Month_2_Fast

description: SAMPLE 62

value: Cure


title: raji_siddx3y_1

description: Library name: raji_siddx3y_1

source_name: Raji

value: Raji

value: Burkitt lymphoma

value: DDX3Y siRNA


title: Orange_C8_Z95

value: Adapted NEBNext Ultra II RNA library prep


title: raji_siddx3x_2

description: Library name: raji_siddx3x_2

value: DDX3X siRNA


title: Participant52_Week_2_Fast

description: SAMPLE 61


title: raji_siddx3y_2

description: Library name: raji_siddx3y_2


title: Participant52_Baseline_Fast

description: SAMPLE 60


title: Green_Hg17_Z94

value: F

value: J


title: raji_siddx3x_1

description: Library name: raji_siddx3x_1


title: Black_C16_Z93


title: raji_siddx3xy_2

description: Library name: raji_siddx3xy_2

value: DDX3X + DDX3Y siRNA


title: raji_siddx3xy_1

description: Library name: raji_siddx3xy_1


title: Participant50_Week_2_Fast

description: SAMPLE 59

value: Blood


title: Participant51_Baseline_Fast

description: SAMPLE 58

value: Baseline


title: Yellow_2_Hg3_Z92

value: Bone marrow

value: M


title: raji_scrbl_1

description: Library name: raji_scrbl_1

value: scramble siRNA


title: raji_scrbl_2

description: Library name: raji_scrbl_2


title: raji_rk33_2

description: Library name: raji_rk33_2


title: raji_rk33_1

description: Library name: raji_rk33_1


title: Green_C4_Z91

value: C


title: Participant50_Baseline_Fast

description: SAMPLE 57


title: Red_C6_Z137

value: I


title: Green_2_Hg6_Z138

value: Hg


title: ca46_siddx3y_3

description: Library name: ca46_siddx3y_3


title: raji_dmso_2

description: Library name: raji_dmso_2

value: DMSO


title: Participant48_Month_2_Fast

description: SAMPLE 55

value: Fast

value: Cure


title: raji_dmso_1

description: Library name: raji_dmso_1

value: Raji

value: Burkitt lymphoma


title: Black_Hg11_Z135

value: Adapted NEBNext Ultra II RNA library prep


title: ca46_siddx3xy_2

description: Library name: ca46_siddx3xy_2


title: Purple_C4_Z136

value: D


title: ca46_siddx3y_2

description: Library name: ca46_siddx3y_2

value: DDX3Y siRNA


title: Participant47_Month_2_Fast

description: SAMPLE 54


title: Blue_Hg9_Z133

value: F


title: Participant49_Baseline_Slow

description: SAMPLE 51

value: Blood

value: Slow


title: ca46_siddx3x_1

description: Library name: ca46_siddx3x_1

value: DDX3X siRNA


title: Participant46_Month_2_Fast

description: SAMPLE 53


title: ca46_siddx3xy_1

description: Library name: ca46_siddx3xy_1

value: DDX3X + DDX3Y siRNA


title: Participant47_Week_2_Fast

description: SAMPLE 50


title: ca46_dmso_2

description: Library name: ca46_dmso_2


title: Participant48_Week_2_Fast

description: SAMPLE 52


title: Red_C7_Z131

value: Bone marrow

value: M


title: ca46_scrbl_1

description: Library name: ca46_scrbl_1

value: scramble siRNA


title: ca46_scrbl_2

description: Library name: ca46_scrbl_2


title: Purple_C17_Z134

value: C

value: I


title: ca46_rk33_2

description: Library name: ca46_rk33_2


title: ca46_siddx3x_2

description: Library name: ca46_siddx3x_2


title: ca46_rk33_1

description: Library name: ca46_rk33_1


title: Participant49_Month_2_Slow

description: SAMPLE 56


title: ca46_dmso_1

description: Library name: ca46_dmso_1

value: DMSO


title: Healthy control plasma sample #9

city: Tianjin

first: Shuo

last: Wang

address: No.13 Liu Lin Road

institute: Tianjin Anding Hospital

description:
Library name: CTRL_9
HCW-009

data_processing:
Adapter Trimming and Quality Control: Software: Cutadapt (version 2.7) was used to remove adapter sequences. Filtering: Reads shorter than 16 bp, reads with excessive “N” characters, or low-quality reads were removed. Quality Metrics: Q30 scores and GC content were calculated to assess overall read quality. UMI Processing: Software: A custom Perl script (perl5, version 26) was employed to filter out reads with UMIs shorter than 12 bp or lacking UMIs entirely, and to extract UMI sequences for downstream analysis. Alignment: Clean reads were aligned using Bowtie (version 1.3.0) to reference databases: miRBase (v22.1) for known mature miRNAs and hairpin precursors. piRNAbank for piRNA identification. Rfam (v14.1) for other non-coding RNAs (e.g., snoRNA, tRNA, rRNA). Quantification: The UMI counts for each small RNA species were tabulated. Normalization was performed by calculating counts per million (CPM) using the edgeR package in R.
Assembly: Small RNA libraries were prepared using the QIAseq miRNA Library Kit (Cat#331505, Qiagen), which incorporates unique molecular indices (UMIs) during reverse transcription. Briefly, 3′ and 5′ adapters were ligated to the RNA, followed by reverse transcription with UMI-containing primers. The resulting cDNA was amplified using universal forward and reverse primers. Final library quality and concentration were checked prior to sequencing on an Illumina NovaSeq platform (single-end reads).
Supplementary files format and content: read counts

source_name: Exosome-derived small RNA from plasma of a healthy control

extract_protocol:
Exosomes were isolated from human plasma samples using an ultracentrifugation protocol. Total RNA, including small RNAs, was then extracted using the Qiagen miRNeasy Micro Kit (Cat#217084, Qiagen). RNA quality was assessed with the Agilent 4200 TapeStation (Agilent Technologies) following the manufacturer’s guidelines.
Small RNA libraries were prepared using the QIAseq miRNA Library Kit (Cat#331505, Qiagen), which incorporates unique molecular indices (UMIs) during reverse transcription. Briefly, 3′ and 5′ adapters were ligated to the RNA, followed by reverse transcription with UMI-containing primers. The resulting cDNA was amplified using universal forward and reverse primers. Final library quality and concentration were checked prior to sequencing on an Illumina NovaSeq platform (single-end reads).

value: Plasma

value: blood plasma

tag: condition

value: healthy control

tag: batch


title: Healthy control plasma sample #7

description:
Library name: CTRL_7
HCW-007


title: Green_Hg7_Z132

value: Hg

tag: euth age

tag: cohort

value: Adapted NEBNext Ultra II RNA library prep


title: Participant46_Week_2_Fast

description: SAMPLE 48

value: Fast

value: Cure


title: Orange_C10_Z129

tag: plate

tag: rna extraction_batch


title: Yellow_Hg13_Z128


title: Healthy control plasma sample #10

description:
Library name: CTRL_10
HCW-010

tag: cell type


title: DSP-G9, Ribbon, Layer 3

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

state: New York

address: 140 Old Orangeburg Rd

department: Center for Dementia Research

institute: Research Foundation for Mental Hygiene

description: Library name: DSP-G9

data_processing:
GeoMxNGS Pipeline 3.1.1.6 was used to convert fastq files to DCC files. FastQ files were aligned to hg38 genome build.
DCC files were uploaded to GeoMx DSP Control Center 3.1.0.222 for further analysis.
Probe filtration, and normalization steps were conducted using default settings on GeoMx DSP Control Center.
Assembly: GRCh38
Supplementary files format and content: DSP.dcc: gene expression count data for each well
Supplementary files format and content: DSP.stats: quality metrics data for each fastq
Library strategy: Spatial Transcriptomics

source_name: Frontal Cortex Brain Tissue

extract_protocol:
Samples were processed with xylenes and ethanol washes and embedded in paraffin blocks.
Sequencing libraries of spatial transcriptome data were prepared using the GeoMx Manual Slide Preparation User Manual (Bruker Spatial Biology; MAN-10150-04) with adjustments in antigen retrieval steps.

treatment_protocol: Human postmortem brain tissues were obtained from the National Disease Research Interchange (NDRI). Tissues were fixed and stored at room temperature (RT) in 10% formalin from time of acquisition until dissection for the GeoMx protocol. Brodmann Area 9 (BA9) frontal cortex was dissected from n = 7 samples

tag: tissue

value: Frontal Cortex Brain Tissue

tag: segment type

value: Ribbon

tag: layer

value: Layer 3


title: Participant47_Baseline_Fast

description: SAMPLE 47

data_processing: nSolver and Rosalind

value: Blood

value: Baseline


title: Healthy control plasma sample #2

description:
Library name: CTRL_2
HCW-002


title: Participant48_Baseline_Fast

description: SAMPLE 49


title: Blue_2_C13_Z126

value: Bone marrow

value: F

tag: rin score

tag: library preparation_method


title: Healthy control plasma sample #5

description:
Library name: CTRL_5
HCW-005


title: Healthy control plasma sample #4

description:
Library name: CTRL_4
HCW-004


title: Healthy control plasma sample #8

description:
Library name: CTRL_8
HCW-008


title: Participant44_Month_2_Fast

description: SAMPLE 45

tag: paticipant

tag: timepoint


title: Healthy control plasma sample #3

description:
Library name: CTRL_3
HCW-003


title: Black_C2_Z127

tag: treatment

value: C

value: M

value: G


title: Yellow_C12_Z124

value: I


title: Schizophrenia plasma sample #8

description:
Library name: SCZ_8
FESW-008

source_name: Exosome-derived small RNA from plasma of a schizophrenia patient

value: Plasma

value: blood plasma

value: schizophrenia


title: Black_2_Hg13_Z130

value: Hg

value: Adapted NEBNext Ultra II RNA library prep


title: Purple_Hg8_Z125


title: Schizophrenia plasma sample #11

description:
Library name: SCZ_11
FESW-011


title: Healthy control plasma sample #1

description:
Library name: CTRL_1
HCW-001

value: healthy control


title: Participant45_Month_2_Slow

description: SAMPLE 44

tag: response

value: Slow

tag: outcome

value: Cure


title: Schizophrenia plasma sample #10

description:
Library name: SCZ_10
FESW-010

tag: condition


title: Schizophrenia plasma sample #6

description:
Library name: SCZ_6
FESW-006

tag: batch


title: Schizophrenia plasma sample #7

description:
Library name: SCZ_7
FESW-007


title: Schizophrenia plasma sample #9

description:
Library name: SCZ_9
FESW-009


title: Schizophrenia plasma sample #5

description:
Library name: SCZ_5
FESW-005


title: Participant42_Week_2_Slow

description: SAMPLE 40


title: Participant45_Week_2_Slow

description: SAMPLE 42


title: Blue_Hg17_Z123

tag: Sex

tag: euth age


title: Participant44_Week_2_Fast

description: SAMPLE 41

value: Fast


title: Participant46_Baseline_Fast

description: SAMPLE 46

value: Blood


title: Green_2_C2_Z122

tag: cohort

tag: plate


title: Participant44_Baseline_Fast

description: SAMPLE 38

value: Baseline


title: Patient6T,Single Cell V(D)J,Tumor

city: Suzhou

first: Tengfei

last: Jia

address: 199 Renai Road

department: Institutes of Biology and Medical Sciences

institute: Soochow University

description:
Library name: Patient6_T_5_20200422N
10x Genomics

data_processing:
Sequencing reads were aligned to the human reference genome GRCh38 using the CellRanger software package. All libraries are then aggregated for batch effect correction and sequencing depth normalization. An expression matrix was generated, with each row representing one gene and each column representing one cell, and then loaded into the R software package Seurat.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz:list of spatial barcodes
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: features.tsv.gz:list of spatial barcodes

source_name: Colon cancer tissue

extract_protocol:
Use the gentleMACS™ Dissociators for cell dissociation. Prepare enzyme mix (4.7 mL DMEM ,200 µL Enzyme H , 100 µL Enzyme R, 25 µL Enzyme A). Remove fat, fibrous and necrotic areas from the tumor sample. Cut the tumor into small pieces of 2–4 mm. Transfer the tissue pieces into the gentleMACS C Tube containing the enzyme mix.Tightly close C Tube and attach it upside down onto the sleeve of the gentleMACS Dissociator. Start the dissociation of  medium tumors by running the gentleMACS program h_tumor_01. After termination of the program, detach C Tube from the gentleMACS Dissociator. Incubate sample for 30 minutes at 37 °C under continuous rotation using the MACSmix™ Tube Rotator. Attach C Tube upside down onto the sleeve of the gentleMACS Dissociator. Run the next gentleMACS Program. After termination of the program, detach C Tube from the gentleMACS Dissociator. Incubate sample for 30 minutes at 37 °C under continuous rotation using the MACSmix Tube Rotator.  Attach C Tube upside down onto the sleeve of the gentleMACS Dissociator. After termination of the program, detach C Tube from the gentleMACS Dissociator. Resuspend sample and apply the cell suspension to a MACS SmartStrainer (30 µm or 70 µm) placed on a 50 mL tube.  Wash cell MACS SmartStrainer (30 µm or 70 µm) with 20 mL of RPMI 1640 or DMEM. Centrifuge cell suspension at 300×g for 7 minutes. Aspirate supernatant completely. Resuspend cells as required for further applications.
The Chromium Single Cell V(D)J workflow with Feature Barcode technology provides a comprehensive, scalable method to examine cell surface proteins as well as gene expression and immunorepertoire information from the same single cell. This is achieved by labeling cell surface proteins with antibodies conjugated to Feature Barcode oligonucleotides and then directly capturing Feature Barcode with gel bead primers. To analyze the immune repertoire of cells, 100-10,000 individual cells in each sample can be evaluated for full-length (5' UTR to the constant region), paired T-cell receptor (TCR), and/or B-cell immunoglobulin (Ig) transcripts. Approximately 750,000 barcode pools were sampled separately to index the transcriptome and cell surface proteins of each cell. This is done by dividing thousands of cells into nanoliter gel bead emulsions (GEMs), where all generated cDNA shares a common 10x barcode. Generate and sort libraries and use 10x barcodes to associate individual readings with individual zones.The Chromium Single Cell V(D)J Enrichment Library, 5' Gene Expression Library, and Cell Surface Protein Library contain standard Illumina double-ended constructs that start with P5 and end with P7. These libraries include a 16 bp 10x barcode encoded at the beginning of TruSeq Read 1. Sample index sequences were merged as i7 index reads for V(D)J enrichment and 5' gene expression libraries; As an i7 index read N merge for cell surface protein libraries. TruSeq Read 1, TruSeq Read 2, and Nextera Read 2 (Read 2N) are all standard Illumina sequencing primer sites. TruSeq Read 1 and TruSeq Read 2 are used for paired-end sequencing of V(D)J enrichment and 5' gene expression libraries. TruSeq Read 1 and Nextera Read 2 (Read 2N) are used for paired-end sequencing of cell surface protein libraries. Sorting these libraries results in a standard Illumina BCL data output folder.

value: Colon cancer tissue


title: Green_C19_Z119

data_processing:
Samples whose sex could not be determined by phenotype (Sex = 'UNK') were left out of this analysis.
Clipping - trimmomaticv 0.39 was used for adapter clipping and quality trimming. It was used in paired-end mode, converting to Phred quality 33, speicifying a minimum trailing and leading base quality of 3, sliding window of size 4 and required quiality of 20, and minimum read length of 50 (-phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50)
Alignment - star v 2.7.9 was used for alignment to genome, specifying maximum multimap per read of 20, max fraction of read length to mismatch as 0.04, and maximum number of junction to be inserted to the genome on the fly at the mapping stage as 1,200,000 (--outFilterMultimapNmax 20 --outFilterMismatchNoverReadLmax 0.04 --limitSjdbInsertNsj 1200000)
Counting - featureCounts from the Subreads package was used for quantification of read abundances per gene/sample. Only primary alignment were counted (--primary) and when relevant assigning a read to the feature with the largest overlap (--largestOverlap).
Genes filtering - genes were then removed if they were present in fewer than 30% of samples, had variance across samples below 100, or were ribosomal genes.
Downsampling - Three samples were above a read depth threshold chosen as 2.75 standard deviations from the mean, and so were randomly down-sampled to have depth just under the threshold while maintaining the same sample order. One sample (Z22) was removed for falling below the equivalent lower threshold.
Normalization - Counts were then normalized with the median of ratios method from DESeq2 v. 1.30.1 (Love, Huber & Anders 2014) implemented in R v 4.0.2
Sample filtering - Principle Component Analysis was conducted on normalized counts with the stats R package, from which 4 samples were flagged as outliers (more than 2.75 standard deviations from the mean of PC1, PC2 or PC3) and removed from the analysis.
Differential expression - comparisons were conducted with DESeq2, using sex, age of euthanasia and library plate as covariates in the statistical models.
Gene Set Enrichment Analysis - GSEA was conducted with R package fgsea and gene sets from canonical pathways (C2CP) in the Molecular Signature Database, MSigDB
Assembly: Taeniopygia guttata genome v1.p.111 from Ensembl, bTaeGut1_v1.p
Supplementary files format and content: Comma-delimited text file with normalized counts per gene (rows) and sample (columns).Row names match ensembl ID format and column names match the Sample "Description" field.

value: Bone marrow

value: F

tag: rna extraction_batch


title: Schizophrenia plasma sample #2

description:
Library name: SCZ_2
FESW-002

tag: tissue

tag: cell type


title: Schizophrenia plasma sample #1

description:
Library name: SCZ_1
FESW-001


title: Blue_Hg13_Z121


title: Participant45_Baseline_Slow

description: SAMPLE 39

extract_protocol: RNA extraction


title: Patient5LiverM,Single Cell V(D)J,Tumor

description:
Library name: ganT_5_20201211NB
10x Genomics


title: Patient4T,Single Cell V(D)J,Tumor

description:
Library name: Patient4_T_5_20200918NB
10x Genomics


title: Patient5P,Single Cell V(D)J,Paracancerous

description:
Library name: changN_5_20201211NB
10x Genomics

source_name: Colon cancer paracancerous tissue

value: Colon cancer paracancerous tissue


title: Healthy control plasma sample #6

description:
Library name: CTRL_6
HCW-006


title: Schizophrenia plasma sample #3

description:
Library name: SCZ_3
FESW-003


title: Patient5T,Single Cell V(D)J,Tumor

description:
Library name: changT_5_20201211NB
10x Genomics


title: Patient5LiverP,Single Cell V(D)J,Paracancerous

description:
Library name: ganN_5_20201211NB
10x Genomics


title: Patient6P,Single Cell V(D)J,Paracancerous

description:
Library name: Patient6_N_5_20200422N
10x Genomics


title: Black_Hg14_Z118

value: M


title: Participant41_Month_2_Fast

description: SAMPLE 36


title: Participant42_Baseline_Slow

description: SAMPLE 37


title: Participant37_Month_2_Fast

description: SAMPLE 34


title: Participant39_Month_2_Slow

description: SAMPLE 33


title: Participant42_Month_2_Slow

description: SAMPLE 43


title: Patient4P,Single Cell V(D)J,Paracancerous

description:
Library name: Patient4_N_5_20200918NB
10x Genomics


title: Purple_C5_Z120

value: C

value: I


title: Participant38_Month_2_Slow

description: SAMPLE 35


title: Yellow_C4_Z115


title: Red_2_C19_Z117


title: Patient3P,Single Cell V(D)J,Paracancerous

description:
Library name: CRC_2_N_5_20200515N
10x Genomics


title: Patient3T,Single Cell V(D)J,Tumor

description:
Library name: CRC_2_T_5__20200515N
10x Genomics


title: Orange_Hg11_Z116


title: Patient2P,Single Cell V(D)J,Paracancerous

description:
Library name: N_5_20200908NB
10x Genomics


title: 9L_152R

city: Camden

first: Samera

middle: P.

last: Hamad

state: NJ

address: 401 South Broadway

institute: Cooper Medical School of Rowan University

description: Library name: H596_Tumor_NO-DOX_Rep5

data_processing:
Align fastqs with STAR to GRCh38/h838 using default parameters
QC performed using FastQC (fastqs) and Picard CollectRnaSeqMetrics (aligned bams)
Transcript read counts were quantified with Salmon
Gene counts were generated by summing Salmon transcript counts by gene
Assembly: GRCh38/hg38
Supplementary files format and content: A tsv format file of raw gene x sample expression, from aggregated salmon transcript counts

source_name: xenograft

growth_protocol: Xenograph tumors were obtained by inoculating mice with ~5M cells sub-cutaneously and collected 8 weeks after achieving a size of ~150 mm^3 or at signs of distress.

extract_protocol:
Total RNA was extracted from harvested from flash frozen samples-as described in Escobar MD, Hunt JL. A cost-effective RNA extraction technique from animal cells and tissue using silica columns. J Biol Methods 2017; 4--using TRIZOL (Invitrogen, 15596026) following the manufacturer’s protocol
polyA enrichment performed by Novogene

treatment_protocol: To activate NRF2 signaling, "DOX" condition mice were fed DOX in water  (2 mg/ml +1% Sucrose) upon xenograph tumors achieving a size of ~150 mm^3.

value: xenograft

tag: cell line

value: NRF2 inducible mutant

value: NO-DOX


title: Purple_Hg1_Z171

extract_protocol:
Bulk bone marrow RNA was isolated using cold RNAzol RT (Molecular Research Center). mRNA was purified with Dynabeads Olgio(dt)25 (Invitrogen).
Libraries were constructed with NEBNext Ultra II RNA Prep reagents following manufacturer's protocols (New England Biolabs).

value: Hg

value: H

tag: rin score

value: Adapted NEBNext Ultra II RNA library prep


title: 9L_151R

description: Library name: H596_Tumor_NO-DOX_Rep4


title: 7L_133R

description: Library name: H596_Tumor_NO-DOX_Rep3


title: Patient1T,Single Cell V(D)J,Tumor

description:
Library name: CRC_1_T_5_20200515N
10x Genomics


title: Red_Hg17_Z172

tag: library preparation_method


title: Purple_C10_Z169


title: Patient2T,Single Cell V(D)J,Tumor

description:
Library name: CA_5_20200908NB
10x Genomics


title: Purple_2_Hg19_Z16

value: G


title: Participant41_Week_2_Fast

description: SAMPLE 32

tag: paticipant

value: Fast

value: Cure


title: Patient1P,Single Cell V(D)J,Paracancerous

description:
Library name: CRC_1_N_5_20200515N
10x Genomics


title: 7L_131L

description: Library name: H596_Tumor_NO-DOX_Rep1


title: Participant37_Week_2_Fast

description: SAMPLE 31

value: Blood

tag: timepoint


title: 9L_157RD

description: Library name: H596_Tumor_DOX_Rep5

tag: treatment

value: DOX


title: 7L_132L

description: Library name: H596_Tumor_NO-DOX_Rep2


title: Participant39_Week_2_Slow

description: SAMPLE 29

tag: response

value: Slow


title: 9L_156RD

description: Library name: H596_Tumor_DOX_Rep4


title: Participant38_Week_2_Slow

description: SAMPLE 30

tag: outcome


title: 9L_158RD

description: Library name: H596_Tumor_DOX_Rep6


title: Yellow_Hg11_Z74

value: Bone marrow

value: F


title: Participant41_Baseline_Fast

description: SAMPLE 28

value: Baseline


title: Green_2_C19_Z73

value: C

value: M


title: 7L_138RD

description: Library name: H596_Tumor_DOX_Rep3

value: xenograft


title: Participant38_Baseline_Slow

description: SAMPLE 27


title: 7L_137LD

description: Library name: H596_Tumor_DOX_Rep2

value: NRF2 inducible mutant


title: Orange_Hg15_Z72


title: 9H_165L

description: Library name: H358_Tumor_NO-DOX_Rep6

value: NO-DOX


title: Participant37_Baseline_Fast

description: SAMPLE 26


title: 7L_136RD

description: Library name: H596_Tumor_DOX_Rep1


title: Participant39_Baseline_Slow

description: SAMPLE 25


title: 9H_163R

description: Library name: H358_Tumor_NO-DOX_Rep4


title: 9H_164R

description: Library name: H358_Tumor_NO-DOX_Rep5


title: Red_C10_Z71


title: 7H_125L

description: Library name: H358_Tumor_NO-DOX_Rep3


title: Yellow_Hg8_Z14

value: Hg


title: 9H_169RD

description: Library name: H358_Tumor_DOX_Rep6


title: 7H_122R

description: Library name: H358_Tumor_NO-DOX_Rep1


title: Green_Hg13_Z10


title: 9H_166RD

description: Library name: H358_Tumor_DOX_Rep4


title: 7H_124L

description: Library name: H358_Tumor_NO-DOX_Rep2


title: Participant29_Month_2_Fast

description: SAMPLE 24


title: Participant24_Month_2_Slow

description: SAMPLE 21


title: 7H_129LD

description: Library name: H358_Tumor_DOX_Rep3


title: Participant28_Month_2_Slow

description: SAMPLE 23


title: 7H_127RD

description: Library name: H358_Tumor_DOX_Rep2


title: Purple_Hg3_Z36


title: Black_C19_Z35


title: Participant29_Week_2_Fast

description: SAMPLE 20


title: Participant26_Month_2_Fast

description: SAMPLE 22


title: 7H_126LD

description: Library name: H358_Tumor_DOX_Rep1


title: DSP-B7, outlined, Layer 3

description: Library name: DSP-B7

value: Frontal Cortex Brain Tissue

tag: segment type

value: outlined

tag: layer

value: Layer 3


title: Red_Hg11_Z34

tag: Sex

value: G

value: Adapted NEBNext Ultra II RNA library prep


title: Participant28_Week_2_Slow

description: SAMPLE 19

value: Blood

value: Cure


title: DSP-B3, outlined, Layer 3

description: Library name: DSP-B3


title: Participant26_Week_2_Fast

description: SAMPLE 18

value: Fast


title: DSP-B4, outlined, Layer 3

description: Library name: DSP-B4


title: DSP-B5, outlined, Layer 3

description: Library name: DSP-B5


title: Yellow_2_Hg17_Z78

value: Bone marrow

tag: euth age


title: DSP-B2, outlined, Layer 3

description: Library name: DSP-B2


title: Red_C20_Z13

tag: cohort


title: DSP-A11, outlined, Layer 5

description: Library name: DSP-A11

value: Layer 5


title: 9H_168RD

description: Library name: H358_Tumor_DOX_Rep5

value: DOX


title: Purple_C2_Z75

value: C

tag: plate


title: DSP-B1, outlined, Layer 3

description: Library name: DSP-B1


title: DSP-A12, outlined, Layer 3

description: Library name: DSP-A12


title: Participant24_Week_2_Slow

description: SAMPLE 15

value: Slow


title: DSP-B6, outlined, Layer 3

description: Library name: DSP-B6


title: Black_Hg18_Z32

value: F

tag: rna extraction_batch


title: DSP-A8, outlined, Layer 5

description: Library name: DSP-A8

tag: tissue


title: DSP-A10, outlined, Layer 5

description: Library name: DSP-A10


title: DSP-A9, outlined, Layer 5

description: Library name: DSP-A9


title: DSP-A7, outlined, Layer 5

description: Library name: DSP-A7


title: Yellow_Hg19_Z70

value: M


title: Participant26_Baseline_Fast

description: SAMPLE 14

value: Baseline


title: DSP-A6, outlined, Layer 5

description: Library name: DSP-A6


title: DSP-A5, outlined, Layer 5

description: Library name: DSP-A5


title: Participant24_Baseline_Slow

description: SAMPLE 13


title: Participant29_Baseline_Fast

description: SAMPLE 17


title: Purple_Hg17_Z76

value: Hg


title: Participant28_Baseline_Slow

description: SAMPLE 16


title: DSP-A3, outlined, Layer 3

description: Library name: DSP-A3

value: Frontal Cortex Brain Tissue


title: Yellow_2_C19_Z69


title: Participant33_Month_2_Slow

description: SAMPLE 12


title: DSP-A2, outlined, Layer 3

description: Library name: DSP-A2

value: outlined


title: Purple_Hg15_Z68


title: Participant33_Week_2_Slow

description: SAMPLE 10


title: DSP-D8, ribbon, Layer 5

description: Library name: DSP-D8

value: ribbon


title: DSP-H11, segmented, Layer 3

description: Library name: DSP-H11

value: segmented

value: Layer 3


title: DSP-D7, ribbon, Layer 5

description: Library name: DSP-D7


title: Black_C17_Z67

value: G

value: Adapted NEBNext Ultra II RNA library prep


title: DSP-D6, ribbon, Layer 5

description: Library name: DSP-D6


title: DSP-D11, ribbon, Layer 5

description: Library name: DSP-D11


title: Black_2_C10_Z81


title: DSP-D5, ribbon, Layer 5

description: Library name: DSP-D5


title: Orange_2_Hg13_Z66


title: Participant31_Month_2_Fast

description: SAMPLE 9

value: Blood

value: Fast

value: Cure


title: Red_C2_Z23

value: Bone marrow


title: DSP-D3, ribbon, Layer 3

description: Library name: DSP-D3


title: DSP-H8, outlined, Layer 3

description: Library name: DSP-H8


title: DSP-A4, outlined, Layer 3

description: Library name: DSP-A4


title: Blue_C19_Z65

value: C


title: DSP-D2, ribbon, Layer 3

description: Library name: DSP-D2


title: DSP-D4, ribbon, Layer 5

description: Library name: DSP-D4

value: Layer 5


title: Participant33_Baseline_Slow

description: SAMPLE 7

value: Slow


title: Participant32_Month_2_Fast

description: SAMPLE 11


title: Purple_Hg11_Z64

value: M


title: Purple_C16_Z77


title: Participant32_Week_2_Fast

description: SAMPLE 6


title: Participant31_Week_2_Fast

description: SAMPLE 5


title: DSP-C12, ribbon, Layer 3

description: Library name: DSP-C12


title: Yellow_Hg3_Z62


title: DSP-C7, ribbon, Layer 5

description: Library name: DSP-C7


title: DSP-C11, ribbon, Layer 3

description: Library name: DSP-C11


title: Participant31_Baseline_Fast

description: SAMPLE 2

value: Baseline


title: Participant30_Month_2_Slow

description: SAMPLE 8


title: Participant30_Week_2_Slow

description: SAMPLE 4


title: DSP-C9, ribbon, Layer 5

description: Library name: DSP-C9


title: DSP-D10, ribbon, Layer 3

description: Library name: DSP-D10


title: Black_2_C16_Z63

value: F


title: DSP-D1, ribbon, Layer 3

description: Library name: DSP-D1

value: Frontal Cortex Brain Tissue


title: Healthy_dentin

city: Rio de Janeiro

first: Rodrigo

last: Jardim

state: RJ

address: Av. Brasil 4365

department: Oswaldo Cruz Institute

country: Brazil

institute: Oswaldo Cruz Foundation

data_processing:
Gene expression and differential transcript analysis were conducted using R software (R Core Team 2021), incorporating DESeq2 package (Love et al. 2014), adhering to criteria of FDR < 0.05 and |log2FC| ≥ 1
Assembly: CHR38
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: dentin

extract_protocol:
The RNAlater™ solution was discarded and samples went through the lysis process. The pulp and predentin were lysed with a manual pestle and then homogenized with an 18G needle and syringe. The dentin samples were vigorously vortexed for 2 minutes with 20 glass beads and then centrifuged at 12,000 x g for 2 minutes. RNA extraction was performed using the PureLink™ RNA Mini Kit (Invitrogen, USA), according to the manufacturer's instructions. RNA concentration was measured using the Qubit™ RNA IQ Assay kit (Invitrogen, USA) and RNA integrity was assessed using the High Sensitivity RNA ScreenTape kit (Agilent 4200 TapeStation, USA)
Library construction was carried out using the Illumina® Stranded Total RNA Prep kit and the Ligation with Ribo-Zero Plus kit (Illumina, USA), which included cDNA synthesis and rRNA removal.

value: dentin


title: DSP-C5, ribbon, Layer 3

description: Library name: DSP-C5

value: ribbon


title: DSP-C4, ribbon, Layer 5

description: Library name: DSP-C4


title: DSP-B11, ribbon, Layer 3

description: Library name: DSP-B11


title: DSP-C3, ribbon, Layer 3

description: Library name: DSP-C3


title: Participant30_Baseline_Slow

city: Banjul

first: Ismaila

last: Manneh

address: Atlantic Blvd

institute: MRCG at LSHTM

description: SAMPLE 1


title: DSP-C8, ribbon, Layer 5

description: Library name: DSP-C8


title: DSP-C2, ribbon, Layer 3

description: Library name: DSP-C2


title: Blue_C5_Z156


title: DSP-B9, ribbon, Layer 3

description: Library name: DSP-B9


title: Healthy_predentin

source_name: predentin

value: predentin


title: DSP-B12, ribbon, Layer 5

description: Library name: DSP-B12


title: Orange_Hg11_Z155

value: Hg


title: DSP-B8, ribbon, Layer 3

description: Library name: DSP-B8

value: Layer 3


title: Healthy_pulp

source_name: pulp

value: pulp


title: Purple_Hg7_Z60

value: G

value: Adapted NEBNext Ultra II RNA library prep


title: DSP-H7, ribbon, Layer 5

description: Library name: DSP-H7


title: Black_Hg13_Z153


title: Yellow_C5_Z152


title: DSP-B10, ribbon, Layer 3

description: Library name: DSP-B10


title: Caries_predentin


title: DSP-H6, ribbon, Layer 5

description: Library name: DSP-H6


title: DSP-C6, ribbon, Layer 3

description: Library name: DSP-C6


title: Purple_2_Hg3_Z154


title: Caries_dentin


title: Caries_pulp


title: Green_C11_Z61


title: DSP-C1, ribbon, Layer 5

description: Library name: DSP-C1


title: late 2-cell, CTR, H3K27ac, rep2

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: Library name: BAP1_CTR_L2C_K27ac_rep2

data_processing:
Raw paired-end reads from CUT&RUN experiments were trimmed using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore) with the --paired option. For FGOs, trimmed reads were aligned to the mm10 mouse reference genome using Bowtie2 (v2.4.2)(Langmead and Salzberg, 2012) with the parameters:
--no-unal --no-mixed --no-discordant -I 0 -X 1000. Uniquely mapped reads were filtered using Sambamba (v0.6.8) (Tarasov et al., 2015) with the criteria: -F "mapping_quality >= 30 and not (unmapped or mate_is_unmapped)". PCR duplicates were removed using Picard (v2.18.22) (http://broadinstitute.github.io/picard/). BigWig coverage files were generated using deepTools (v2.0.0)(Ramirez et al., 2016) with the options:
--binSize 25 --normalizeUsing RPKM --scaleFactor 1.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Run

organism: Mus musculus

source_name: late 2-cell

growth_protocol: Embryos were cultured in KSOM (Millipore) at 37 °C under 5% CO2 with air

extract_protocol:
For CUT&RUN, oocytes and embryos were directly added to the binding buffer containing conA beads.
The CUT&RUN libraries were prepared as previously described (PMID: 40418442)

treatment_protocol: Conditional KO in oocytes was achieved using Gdf9-iCre mediated recombination of Bap1 flox/flox allele

value: late 2-cell

tag: genotype

value: Bap1flox/flox x PWK


title: DSP-H4, ribbon, Layer 5

description: Library name: DSP-H4


title: DSP-H5, ribbon, Layer 3

description: Library name: DSP-H5


title: late 2-cell, matKO, H3K27ac, rep2

description: Library name: BAP1_mKO_L2C_K27ac_rep2

value: Gdf9-iCre, Bap1flox/flox x PWK


title: SK-MEL-147,replicate 2

city: Barcelona

first: Neus

last: Mestre-Farràs

state: Barcelona

address: C/ Doctor AIguader 88

country: Spain

institute: CRG

description: Library name: SK2

data_processing:
Nanopore sequencing basecalling and demultiplexing of raw fast5 files was done using Guppy (version 3.6.1) through the “MasterOfPores” pipeline. Fastq files were then mapped to the GRCm38 mouse genome and the GRCh38 human genome, using minimap2 (version 2.14). Isoquant version 3.0 was used to quantify CSDE1 isoforms. Initial bam files were filtered so that only non-ambiguous CSDE1 reads were kept. The results were manually curated to correct for isoform mis-assignments.
Assembly: GRCh38, GRCm38
Supplementary files format and content: Tab-delimited text file with transcript per million (TPM) values for each detected CSDE1 isoform

growth_protocol: SK-Mel-147 cells were cultured in DMEM (high glucose, pyruvate and GlutaMax; Gibco #31966021), supplemented with 10% heat-inactivated fetal bovine serum (FBS; Gibco #10270106) and 1% penicillin-streptomycin (Gibco #15070063).  PMK were isolated from the skin of newborn C57BL/6J mice and growth in EMEM complete media (Lonza, Cat 06-174G) supplemented with 8% of chelated FBS (Fetal Bovine Serum, see below), 0.05 mM CaCl2, 10 ng/ml EGF (Sigma-Aldrich) and 1% penicillin/streptomycin (Life technologies). Cell lines were maintained at 37 ºC with 5% CO2 .

extract_protocol:
Maxwell kit (Promega #AS1280) was used to extract total RNA. 100 μg of total RNA were incubated with Turbo DNA-free kit components (Invitrogen # AM1907) for DNase digestion in the presence of 40U/20μL reaction of RNaseOUT (Invitrogen # 10777019). Total RNA was then cleaned-up with AMPure XP beads (Agencourt #082A63881) according to the manufacturer's specifications. Poly(A) selection was performed using 100 µl of Oligo (dT)25 Dynabeads (Invitrogen #61002) previously washed with binding buffer (20 mM Tris–HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8) and then resuspended in 100 µl of the same buffer. Poly(A)-containing RNA was eluted twice from beads with 10 mM Tris–HCl pH 7.5 by heating the mixture at 75ºC for 2 minutes.
One hundred ng of poly(A)-selected RNA was mixed with 2.5 µL of VNP (ONT cDNA sequencing kit), 1 µL of 10 mM dNTPs and filled to a total of 7.5 µL with RNase-free water. The mixture was incubated at 65 °C for 5 minutes and then snap cooled on ice. In a separate tube 4 µL of 5x RT buffer, 1 µL RNaseOUT, 1 µL of RNase-free water and 2 µL of Strand-Switching Primer (SSP, ONT cDNA sequencing kit) were mixed. The tubes were gently mixed and incubated at 65 °C for 2 minutes. One µL of Maxima H Minus Reverse Transcriptase (Life Technologies #EP0751) was added to the reaction mixture, and incubated for 90 minutes at 42 °C, followed by heat inactivation at 85 °C for 5 minutes. RNA was degraded by adding 1 µL of RNase Cocktail Enzyme Mix (ThermoFisher #AM2286) followed by incubation for 10 minutes at 37 °C. DNA was cleaned-up using AMPure XP beads and quantity and quality were assessed using Qubit and Tapestation. The second cDNA strand was synthesized by mixing 25 µL of 2X LongAmp Taq Master Mix (NEB #174M0287S), 2 µL PR2 primer (ONT cDNA sequencing kit), 20 µL reverse-transcribed sample and 3 µL RNase-free water. The reaction mixture was incubated at 94 °C for 1 minute, at 50 °C for 1 minute, at 65 °C for 15 minutes and then kept 4 °C. Another AMPure XP beads clean-up step was performed, proceeding to the end-prep step by mixing the following reagents: 20 µL cDNA sample, 30 µL RNase-free water, 7 µL Ultra II End-prep reaction buffer (NEB #E7647A), 3 µL Ultra II End-prep enzyme mix (NEB #E76468). The mixture was incubated at 20 °C for 5 minutes and 65 °C for 5 minutes. After another AMPure XP beads clean-up step, the samples were barcoded by mixing the following reagents: 22.5 µL End-prepped cDNA, 2.5 µL native barcode (NB01-NB12, ONT barcode extension kit #EXP-NBD104), 25 µL Blunt/TA ligase master mix. The reaction mixture was incubated for 10 minutes at room temperature, and the barcoded samples were cleaned up using AMPure XP beads. cDNA amount was measured using Qubit, and samples were pooled in equal ratios, not exceeding 120 ng (200 fmol) as the maximum total amount of barcoded cDNA. The adapter ligation was performed by mixing 65 µL of the pooled barcoded sample, 5 µL Adapter Mix II (AMII, ONT cDNA sequencing kit), 20 µL NEBNext Quick Ligation Reaction Buffer 5X (NEB #B6058S) and 10 µL Quick T4 DNA Ligase (NEB #M2200L). The reaction mixture was incubated for 10 minutes at room temperature, after which the cDNA was cleaned up using AMPure XP beads and eluted in 13 μL of Elution Buffer (EB, ONT cDNA sequencing kit). The final amount was ~50 ng of cDNA, which was mixed with 37.5 µL Sequencing Buffer (SQB) and 2.5 µL Loading Beads (LB, ONT cDNA sequencing kit) and loaded onto a previously primed MinION R9.4.1 flow cell.

tag: cell line

tag: cell type

value: Metastatic melanoma


title: Participant32_Baseline_Fast

description: SAMPLE 3

value: Blood

value: Fast

value: Cure


title: late 2-cell, matKO, H3K27me3, rep2

description: Library name: BAP1_mKO_L2C_K27me3_rep2


title: SK-MEL-147,replicate 1

description: Library name: SK1


title: Yellow_Hg17_Z148

city: Bethesda

first: Christian

last: Wake

address: 9000 Rockville Pike

institute: National Institutes of Health

value: Bone marrow

value: M

value: F

tag: rin score

tag: library preparation_method


title: JCP_1525, YNB with 0.2% oleic acid, anerobic, 30C, 24h, biological replicate 3

city: Houston

first: Jose

middle: Christian

last: Perez

state: TX

address: 6431 Fannin

institute: UTHealth Houston

description: Library name: sokOA3

data_processing:
Sequenced reads were trimmed for adaptors using Galaxy Trim Galore (Galaxy v. 0.6.7+galaxy0). Read quality cutoff was set to 20.
The reads were mapped to C. albicans Build 21 genome using RNA STAR (Galaxy Version v2.7.10b+galaxy4) with modification of these selected paramaters: with-gtf,  --sjdbOverhang '100' --genomeSAindexNbases 12 --outSAMtype BAM --alignIntronMin 21 --alignIntronMax 5000
Counting of aligned reads was executed with htseq-count (Galaxy version 0.9.1+galaxy1) with --stranded=reverse, --minaqual=10, --type='exon'
Differentially expressed genes from count files were determined using DESeq2(Galaxy Version 2.11.40.8+galaxy0).
Assembly: Candida albicans Build 21
Supplementary files format and content: TABULAR file includes counts (after htseq-count) for each sample

organism: Candida albicans

source_name: liquid culture

growth_protocol: YNB with 0.2% oleic acid, anerobic, 30 degrees C, 24h

extract_protocol:
RiboPure™ RNA purification kit for yeast (Ambion, Life Technologies)
Directional mRNA library preparation (with poly A enrichment) according to standard operating procedures of Novogene Corporation Inc.

treatment_protocol: Cells from liquid culture

value: liquid culture

value: YNB, 0.2% oleic acid, anerobic, 30°C for 24h

tag: batch


title: Purple_C10_Z150

tag: treatment

value: C


title: DSP-H3, ribbon, Layer 5

description: Library name: DSP-H3

value: Frontal Cortex Brain Tissue

value: ribbon

value: Layer 5


title: DSP-H2, ribbon, Layer 3

description: Library name: DSP-H2

value: Layer 3


title: late 2-cell, CTR, H3K27me3, rep2

description: Library name: BAP1_CTR_L2C_K27me3_rep2

value: late 2-cell


title: Black_C8_Z147

value: UNK

value: Adapted NEBNext Ultra II RNA library prep


title: late 2-cell, CTR, H3K27me3, rep1

description: Library name: BAP1_CTR_L2C_K27me3_rep1

value: Bap1flox/flox x PWK


title: Red_Hg5_Z151

value: Hg


title: Blue_Hg19_Z143


title: JCP_1525, YNB with 0.2% oleic acid, anerobic, 30C, 24h, biological replicate 2

description: Library name: sokOA2


title: DSP-G12, ribbon, Layer 5

description: Library name: DSP-G12


title: Yellow_Hg6_Z142


title: late 2-cell, matKO, H3K27ac, rep1

description: Library name: BAP1_mKO_L2C_K27ac_rep1

value: Gdf9-iCre, Bap1flox/flox x PWK


title: late 2-cell, CTR, H3K27ac, rep1

description: Library name: BAP1_CTR_L2C_K27ac_rep1


title: DSP-H1, ribbon, Layer 3

description: Library name: DSP-H1


title: DSP-G11, ribbon, Layer 3

description: Library name: DSP-G11


title: SC5314, YNB with 0.2% oleic acid, anerobic, 30C, 24h, biological replicate 2

description: Library name: refOA2

value: wild-type


title: JCP_1525, YNB with 0.2% oleic acid, anerobic, 30C, 24h, biological replicate 1

description: Library name: sokOA1


title: FGO, CTR, H3K27me3, rep2

description: Library name: BAP1_CTR_GV_H3K27me3_rep2

source_name: Fully grown oocyte

value: Fully grown oocyte


title: Yellow_2_Hg1_Z90

value: Bone marrow

value: E


title: SC5314, YNB with 0.2% oleic acid, anerobic, 30C, 24h, biological replicate 1

description: Library name: refOA1

value: liquid culture


title: FGO, CTR, H3K27ac, rep2

description: Library name: BAP1_CTR_GV_H3K27ac_rep2


title: DSP-G10, ribbon, Layer 5

description: Library name: DSP-G10


title: Black_C4_Z89

value: M


title: DSP-G8, ribbon, Layer 3

description: Library name: DSP-G8


title: Black_Hg15_Z144

value: F


title: late 2-cell, matKO, H3K27me3, rep1

description: Library name: BAP1_mKO_L2C_K27me3_rep1


title: AHY940, YNB with 0.2% oleic acid, anerobic, 30C, 24h, biological replicate 3

description: Library name: refOA4

growth_protocol: YNB with 0.02% dextrose or 0.2% oleic acid, anerobic, 30C, 24h

tag: strain

value: YNB, 0.2% oleic acid, anerobic, 30°C for 24h


title: Purple_Hg13_Z88


title: FGO, CTR, H2AK119ub1, rep2

description: Library name: BAP1_CTR_GV_H2AK119ub_rep2


title: Orange_C12_Z87

value: C


title: DSP-G7, ribbon, Layer 3

description: Library name: DSP-G7

value: Frontal Cortex Brain Tissue

value: ribbon


title: DSP-G6, ribbon, Layer 5

description: Library name: DSP-G6

value: Layer 5


title: SC5314, YNB with 0.2% oleic acid, anerobic, 30C, 24h, biological replicate 3

description: Library name: refOA4


title: AHY940, YNB with 0.2% oleic acid, anerobic, 30C, 24h, biological replicate 2

description: Library name: refOA2


title: AHY940, YNB with 0.2% oleic acid, anerobic, 30C, 24h, biological replicate 1

description: Library name: refOA1


title: FGO, CTR, H3K27ac, rep1

description: Library name: BAP1_CTR_GV_H3K27ac_rep1


title: FGO, CKO, H3K27me3, rep2

description: Library name: BAP1_CKO_GV_H3K27me3_rep2

value: Gdf9-iCre, Bap1flox/flox


title: FGO, CKO, H3K27ac, rep2

description: Library name: BAP1_CKO_GV_H3K27ac_rep2


title: DSP-G1, ribbon, Layer 5

description: Library name: DSP-G1


title: Purple_Hg5_Z86

value: UNK

value: Adapted NEBNext Ultra II RNA library prep


title: DSP-F12, ribbon, Layer 5

description: Library name: DSP-F12


title: Green_Hg15_Z84

value: Hg


title: AHY940, YNB with 0.02% dextrose, anerobic, 30C, 24h, biological replicate 2

description: Library name: refDX2

value: YNB, 0.02% dextrose, anerobic, 30°C for 24h


title: DSP-G2, ribbon, Layer 5

description: Library name: DSP-G2


title: FGO, CKO, H2AK119ub1, rep2

description: Library name: BAP1_CKO_GV_H2AK119ub_rep2


title: AHY940, YNB with 0.02% dextrose, anerobic, 30C, 24h, biological replicate 3

description: Library name: refDX3


title: Blue_C19_Z85


title: AHY940, YNB with 0.02% dextrose, anerobic, 30C, 24h, biological replicate 1

description: Library name: refDX1


title: FGO, CKO, H3K27ac, rep1

description: Library name: BAP1_CKO_GV_H3K27ac_rep1


title: FGO, CTR, H3K27me3, rep1

description: Library name: BAP1_CTR_GV_H3K27me3_rep1


title: Blue_C12_Z83


title: DSP-F11, ribbon, Layer 5

description: Library name: DSP-F11


title: DSP-F10, ribbon, Layer 5

description: Library name: DSP-F10


title: Blue_Hg20_Z82


title: FGO, CTR, H2AK119ub1, rep1

description: Library name: BAP1_CTR_GV_H2AK119ub_rep1


title: E. coli K12 BW113, silver nitrate 7 µM, BT2

city: Calgary

first: Daniel Armando

last: Salazar-Alemán

state: Alberta

address: 2500 University Drive NW

department: Department of Biological Sciences

institute: University of Calgary

description:
Library name: Silver 2
Silver2

data_processing:
Initial FASTQ files were assessed and trimmed with the Bioconductor package rfastp (version 1.10).
Gene expression counts were obtained by aligning to the Escherichia coli K12 BW25113 RefSeq assembly annotation file GCF_000750555.1 using the Bioconductor package Rsubread (version 2.14.2), with counts assigned to the CDS meta-feature.
A counts matrix for the 4,378 identified features was imported into the Bioconductor package DESeq2 (version 1.40.2) for differentially expressed genes determination. The adjusted p-value (p-adj) for multiple test adjustment (Benjamini-Hochberg correction, FDR < 0.05) was set to 0.05.
Differentially expressed genes were defined as those with a p-adj value < 0.05 and whose expression had an absolute fold-change (FC) of at least 2 (|log2 FC| > 1) when contrasting the silver nitrate treatment versus the unchallenged control; those with a negative FC were deemed as down-regulated genes in the silver nitrate treatment, while a positive FC indicated up-regulation.
Assembly: Escherichia coli K12 BW25113 from NCBI RefSeq (GCF_000750555.1)
Supplementary files format and content: Tab-delimited text file specifies gene name (or its "BW25113_[…]" gene ID, if the gene name was not found), along with their respective raw counts for each sample.
Supplementary files format and content: Comma-delimited file with DESeq2 outputs including log2-fold change and p-values. Each gene is identified by its gene name, gene_id and uniprot entry ID.

organism: Escherichia coli

source_name: Bacterial cell

growth_protocol: Escherichia coli K12 BW25113 was cultured in 15mL of M9-glucose minimal media and incubated at 37 ºC 150 rpm for 10 hours in a shaker incubator.

extract_protocol:
2 mL of samples were centrifuged at 14,000 X g for 2 minutes to pellet the cells. Zirconia beads were used for cell lysis for 10 minutes using a bead beater instrument. Total RNA was then extracted with a RiboPure Bacteria RNA Isolation Kit AM1925 (Invitrogen, USA) according to the manufacturer's recommendations, including DNase treatment.
Ribosomal RNA depletion was performed using the NEB rRNA Depletion Bacterial Module (New England Biolabs, USA). The cDNA library preparation for Illumina sequencing was executed using the NEBNext Ultra II Directional RNA Library Prep Kit and NEB Indexing Kit (New England Biolabs, USA). After adaptor ligation and amplification, the average library fragment size was 373 bp.

treatment_protocol: Control treatments were grown for 10 hours in M9-glucose minimal media. Experimental treatments were grown for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of silver nitrate (39 µM, 6.22 µg/mL) prior to inoculation.

value: Bacterial cell

value: Wild type

value: Silver nitrate 7 µM sublethal concentration


title: E. coli K12 BW113, silver nitrate 7 µM, BT1

description:
Library name: Silver 1
Silver1


title: DSP-F9, ribbon, Layer 5

description: Library name: DSP-F9


title: FGO, CKO, H3K27me3, rep1

description: Library name: BAP1_CKO_GV_H3K27me3_rep1

value: Fully grown oocyte


title: Yellow_Hg7_Z80

value: Bone marrow

value: E


title: Red_C16_Z79

value: F


title: E. coli K12 BW113, silver nitrate 7 µM, BT3

description:
Library name: Silver 3
Silver3


title: E. coli K12 BW113, untreated, BT3..

description:
Library name: Control 3
AgUnch3

value: Control - no metal challenge


title: Red_Hg9_Z22

value: M

value: D