title: D60_ASD

description: 10x Genomics

data_processing:
Fastp 0.17.0 with default parameter to filter for the adaptor sequence and removed low-quality reads to obtain qualified clean data
UMI-tools 1.0.0 was used for Single-Cell Transcriptome Analysis to identify the cell barcode whitelist
The UMI-based clean data were mapped to the human genome (GRCh38) utilizing STAR 2.7 mapping with the customized parameter from the UMI-tools standard pipeline to obtain UMI counts for each sample
Cells containing more than 200 expressed genes with a mitochondrial rate of less than 30% passed the cell quality filter, which was followed by the deletion of mitochondrial genes from the expression table.
Assembly: GRCh38
Supplementary files format and content: gzip of 10x format gene expression matrix

source_name: scRNA-seq of human brain organoids: day60 in vitro

growth_protocol: ASD iPSC lines (ASD 3-28, ASD 1-4, ASD 2-3) were reprogrammed from 3 early-onset ASD patients without significant changes in head circumference using CytoTune™-iPS 2.0 Sendai Reprogramming Kit (Invitrogen), and then differentiated into organoids.

extract_protocol:
The single cell organoid cell suspension was resuspended in PBS with 0.05% BSA. Dissociated single cells for Single-cell RNA Sequencing were stained for viability assessment using Calcein-AM (Thermo Fisher Scientific, Waltham, MA, USA) and Draq7 (BD Biosciences, New Jersey, USA).
Cells (2000-10,000) were loaded on a 10x Genomics Chromium instrument to generate single-cell GEMs. scRNA-Seq libraries were prepared according to the manufacturer’s instructions.

tag: growth

value: day60 in vitro


title: scRNA-seq of human brain organoids: day30  in vitro [D30_NC3_1]

status: Public on Jan 22 2025

type: SRA

city: Nanjing

first: Yuanlin

last: He

address: 101Longmian Avenue, Jiangning District

country: China

institute: Nanjing medical university

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: brain organoids

extract_protocol:
The organoids were dissociated by trypLE (Life technology) into single cells. The cell debris and other aggregates were removed by an additional low-speed centrifugation. About 12,000 cells were captured and the released RNA were barcoded through reverse transcription in individual GEMs.
scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit V3 (10x Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 50000 reads per cell with a paired-end 150 bp (PE150) reading strategy

tag: tissue

value: brain organoids

tag: cell line

tag: cell type


title: saline_rep1

city: Chongqing

first: Wen

last: Zeng

address: Gaotanyan street

department: Department of Cell Biology

institute: Army Medical University

library_source: transcriptomic

data_processing:
reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: mRatBN7
Supplementary files format and content: total_count.csv file includes raw counts for each Sample

organism: Rattus norvegicus

source_name: brain tissue

extract_protocol:
RNA was harvested using Trizol reagent kit, Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities.  After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

treatment_protocol: Inject the corresponding drug (saline, rt-PA, Nano-patrol+NIR) 4.5 hours after modeling, and take brain tissue for testing three days later

value: brain tissue

tag: treatment

value: saline


title: Asxl1-MT2/T618I_3

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

country: USA

institute: Oregon Health and Science University

data_processing:
Reads were trimmed using Trimmomatic.
Adapter-trimmed reads were aligned to the mm10 genome using STAR.
Protein-coding genes were used to build the feature counts table, and differential expression analysis was performed using DESeq2 with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

growth_protocol: These cells are maintained in RPMI (11875119, Gibco) supplemented with 10% heat inactivated fetal bovine serum (FBS, HyClone), 2mM GlutaMAX (35050061, Gibco), 100units/mL Penicillin and 100 ug/mL Streptomycin (15140122, Gibco), 2% SCF from CHO,  conditioned media, and 0.6µM of Estrogen (E-2758, Sigma), cultured at 5% CO2 and 37°C.

extract_protocol:
RNeasy Plus Micro Kit (74004, Qiagen)
Libraries were prepared by BGI

treatment_protocol: Estrogen removal for 24h

value: Bone marrow immortelized

tag: genotype


title: Asxl1-MT2/Empty_2


title: HFuR_6

city: Grand Forks

first: Shanon

last: Casperson

state: ND

address: 2420 2nd Ave North

institute: USDA/ARS Grand Forks Human Nutrition Research Center

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and bgene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: mm10
Supplementary files format and content: Raw counts of sequencing reads (before normalization) is provided in the matrix file (named gene_count.xls  Column 1 provides the gene ID, Column B- AK provides the raw counts for each sample, columns AL - AT provides gene description (name, chromosomes, location, etc)

source_name: Skeletal Muscle

extract_protocol:
Total RNA from gastrocnemius muscles  tissues were extracted using the RNeasy Mini QIAcube Kit (Qiagen, Valencia, CA, USA). RNA quality was determined using the Fragment Analyzer RNA Kit (DNF-471, Agilent, Santa Clara, CA, USA) on the 5200 Fragment Analyzer System (Agilent, Santa Clara, CA, USA).  Samples were sent off to Novogene USA for the complete analysis.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: Skeletal Muscle

tag: diet

value: HFD

tag: strain

value: WT

value: HFD-U


title: Asxl1-MT2/T618I_2


title: Asxl1-MT2/Empty_1


title: D100_ASD

description: 10x Genomics

source_name: scRNA-seq of human brain organoids: day100 in vitro

value: day100 in vitro


title: IP48_692E_H

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

description: HPCs

library_source: genomic

data_processing:
Sequencing reads were aligned to the hg19 reference genome using bowtie2 following adapter trimming using Cutadapt. Duplicates and reads falling within blacklisted regions (ENCODE) were removed using Picards and bedtools, respectively. For visualization, bigwig files were created using the bamCoverage tool from deepTools, with the options of normalization using Bins Per Million, smoothLength 60, and binSize 20. Peak calling was performed using Homer. All figures were displayed using IGV.
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: human iPSC derived CD45+CD34+ hematopoietic progenitor cells (HPCs)

extract_protocol:
ChIP-seq experiments were conducted using feeder-free iPSCs, CD45+CD34+ HPCs, and K562 cells. A Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) was used to eliminate dead cells from feeder-free iPSCs and HPCs. Cells were fixed in PBS with 1% formaldehyde (Thermo Fisher Scientific) with gentle mixing for 10 minutes at room temperature. The reaction was stopped by adding a glycine solution (10x; Cell Signaling Technology) and incubating for 5 minutes at room temperature, followed by two rounds of cold PBS washing. The cells were processed using the SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol. The chromatin was sonicated with Covaris E220 (Covaris) using a microTUBE AFA Fiber Pre-Slit Crimp-Cap (130 µL). Immunoprecipitation of the cross-linked chromatin was performed using antibodies directed against histone H3 lysine 27 acetylation (H3K27ac) (Cell Signaling Technology).
ChIP-seq libraries were constructed using a ThruPLEX DNA-Seq Kit (Takara) according to the manufacturer’s protocol and sequenced using NextSeq 500 or NovaSeq 6000 (Illumina)

value: Control


title: saline_rep2


title: rt-PA_rep1

value: rt-PA


title: Asxl1-MT2/Empty_3


title: D100_IMR

description: 10x Genomics


title: IP77_3_8_JQ1_input_2

description: cell lines

source_name: cell lines

value: cell lines

value: Leukemia with t(3;8)


title: IP79_MDS25J1_iPSC_input_2

description: iPSC

source_name: iPSC

value: iPSC

value: MDS


title: D60_IMR

description: 10x Genomics


title: HFuR_4


title: Empty/T618I_2


title: IP76_3_8_JQ1_H3K27ac_2

description: cell lines


title: IP75_3_8_DMSO_input_2

description: cell lines

value: DMSO


title: D12_IMR

description: 10x Genomics

source_name: scRNA-seq of human brain organoids: day12 in vitro

value: day12 in vitro


title: Empty/T618I_3


title: IP78_MDS25J1_iPSC_H3K27ac_2

description: iPSC


title: HFuR_5


title: Empty/Empty_3


title: HFuR_3


title: Empty/T618I_1


title: D6_ASD

description: 10x Genomics

source_name: scRNA-seq of human brain organoids: day6 in vitro

value: brain organoids

value: day6 in vitro


title: HFuR_1


title: IP74_3_8_DMSO_H3K27ac_2

description: cell lines


title: HFuR_2


title: Empty/Empty_2

value: pMIG-Empty/pMICH-Empty


title: HFS_6

value: HFD-C


title: D6_IMR

description: 10x Genomics


title: D12_ASD

description: 10x Genomics


title: Empty/Empty_1

value: Bone marrow immortelized


title: IP72_MDS25_PBMC_H3K27ac_2

description: PBMC

source_name: Peripheral Blood Mononuclear Cells CD45+34+ cells from MDS patient


title: neutrophils,H3K27ac,R848,HD3,ChIP

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
To avoid effects derived from different reads lengths, reads were truncated to 51bp using fastx_trimmer from the FASTX-toolkit. Trimmed reads were mapped to the human genome using Bowtie2 v2.3.5.1 with default parameters, and deduplication was performed with markdup of Sambamba v0.6.7. Only reads mapping to the nuclear genome were kept for downstream analyses.
H3K27Ac-enriched regions were identified by MACS3 with parameters –gsize hs  --broad –broad-cutoff 0.1 –nomodel –extsize 146. Peaks overlapping ENCODE blacklist regions were removed and biological replicates were combined by MSPC to construct consensus peaks. Consensus H3K27Ac coordinates were re-centered to the best nucleosome free regions (NFR) within a 200 bp window, using the command “getPeakTags –nfr”, and then resized to 2 kb
Differential H3K27ac occupancy and TFs binding (|log2[fold change]|>1)  and false discovery rare < 0.01 was performed using Bioconductor/R DiffBind v2.14.
Assembly: Genome Reference Consortium GRCh38, Dec/2013
Supplementary files format and content: bigWig

source_name: human neutrophil

growth_protocol: Granulocytes were isolated from buffy coats of healthy donors and manipulated under endotoxin-free conditions. After Ficoll-Plaque gradient centrifugation, followed by dextran sedimentation and hypotonic lysis of erythrocytes, neutrophils were isolated to reach 99.7 ± 0.2 % purity, by positively removing any eventual contaminating cells using the EasySep neutrophil enrichment kit (StemCell Technology, Vancouver, Canada). Neutrophils were then suspend at 5x106/ml in RPMI 1640 medium supplemented with 10 % low endotoxin FBS (< 0.5 EU/ml; from Sigma, Saint Louis, MO, USA). Human CD14+-monocytes were isolated from PBMCs by anti-CD14 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) to reach > 98% purity.

extract_protocol:
Protein-DNA cross-linking was achieved by incubating 2.5x106 cells with 1 % formaldehyde for 10 min at room T, under gentle agitation. Cross-linking reaction was stopped by adding glycine to a final concentration of 125 mM, and incubating cells at room T for five more minutes. After fixation, cells were washed with ice-cold PBS, collected by scraping, and finally pelleted by centrifugation (5 min, 300xg, 4°C). Pellets were suspended in 900 µl L1 lysis buffer (50 mM Tris, pH 8.0, 2 mM EDTA, 0.1 % IGEPAL, 10 % glycerol) containing protease inhibitors. Nuclei were pelleted at 1000xg at 4°C and resuspended in 300 µl L2 lysis buffer (50 mM Tris, pH 8.0, 1 % SDS, 5 mM EDTA) including protease inhibitors. Chromatin was sheared to an average DNA size of 300-400 bp by sonication on wet ice [6 pulses of 15 seconds at the 50 % maximum potency, with 15 second pauses, using a BANDELIN SONOPLUS ultrasonic homogenizers HD 2070 (Bandelin, Berlin, Germany)]. Lysates were then cleared by centrifugation to remove debris (10 min, 13000xg, 12°C), and diluted 10x in dilution buffer (50 mM Tris, 5 mM EDTA, 200 mM, 0.5 % IGEPAL). Immunoprecipitations were carried out overnight at 4°C using 5 µg/ml antibodies. Immune complexes were then collected by adding 15 µl of protein A sepharose-coupled magnetics beads (GE Healthcare, Piscataway, NJ, USA) for 1 h at 4°C under gentle rotation. Beads were then immobilized on a magnetic support and washed three times in washing buffer (20 mM Tris, pH 8.0, 0.1 % SDS, 2 mM EDTA, 1% IGEPAL, 500 mM NaCl) and once in TE. The resulting protein complexes were then eluted in TE containing 2 % SDS, and reversed crosslinked by an overnight incubation at 65°C. The DNA was purified by QiaQuick PCR purification kit (Qiagen) according to the manufacturer’s instructions, and eluted in 50-100 µl.
ChIP DNA was prepared for NextSeq 500 sequencing following TruSeq DNA sample preparation guide (Illumina, Cambridge, UK). In brief, 10-50 ng purified DNA from chromatin immunoprecipitation were adapter-ligated and PCR-amplified according to the manufacturer’s protocol (Illumina). Sequencing libraries were multiplexed and ran on NextSeq 500 sequencer (Illumina).

treatment_protocol: Neutrophils and monocytes were processed immediately after isolation, or treated with  5 µM R848, seated in 24-well tissue culture plates (Greiner Bio-One, Kremsmüster, Austria), and cultured at 37°, 5 % CO2 atmosphere, for 20 h.

tag: chip-antibody

value: Anti-H3K27Ac (Abcam # ab4729)

tag: donor

value: donor 3

tag: time

value: neutrophil


title: D0_IMR

description: 10x Genomics

source_name: scRNA-seq of human brain organoids: day0 in vitro

value: day0 in vitro


title: HFS_5

value: Skeletal Muscle

value: HFD

value: WT


title: BSF_C,biol rep 2,ATAC_seq

city: Hangzhou

first: Jian

last: Zhang

address: Yuhangtang Road, Xihu District, Hangzhou, Zhejiang Province

institute: Zhejiang University

data_processing:
Quality control: FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for initial quality control assessment of the data
Adapter trimming: The adapter (CTGTCTCTTATACACATCT) was trimmed using cutadapt v2.982
Alignment: STAR v2.7.2e83 was used for aligning the reads to the Mus musculus reference genome GRCm38.97. Splice junctions were neglected by creating a STAR index without a general feature format file and without allowing intron length
PCR duplicate removal: PCR duplicates were removed using the Samtools v1.984 rmdup function;Bigwig track generation: Bigwig tracks were created using bamCoverage v3.3.185, normalizing to RPKM using a bin size of 10 bp;Signal plotting: ATAC-seq signals over genomic regions were visualized using deeptools v3.3.1;Peak calling: ATAC-seq peaks were defined using MACS2 v2.2.7.187 with default parameters;  Motif analysis: Transcription factor (TF) motif files were obtained from Homer v4.788. Motif positions in the GRCm38 genome were calculated using the Homer scanMotifGenomeWide.pl function; Region-associated DEG analysis: The RAD website application89 (https://labw.org/rad) was used. Upregulated and downregulated DEGs were input as DEG lists, and the bed file of peak regions was used as the Genomic Regions of Interest (gROI) file.
GO term analysis: Genes within a range of ±50 kb from the peaks were selected. ClusterProfiler v4.8.1 was applied for GO term analysis with the parameters (OrgDb = org.Mm.eg.db, ont = ’BP’, pAdjustMethod = ’BH’, pvalueCutoff = 0.01, qvalueCutoff = 0.05); Peak visualization: Peaks were visualized using igv v2.16.290.
Assembly: mm10
Supplementary files format and content: Tab-delimited dw file includes raw counts for each sample

source_name: Jejunum

extract_protocol:
Mice were treated with Control, BSF, DSF and LSF for 2 weeks, and jejunal epithelial cells were collected by flow sorting.
The nuclei were collected by adding lysis solution [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween 20, 0.01% Digitonin] on ice for 5 min and centrifuged at 500 g for 5 min. Fragmentation was performed according to the recommended conditions of the kit (Novoprotein Chromation Profile Kit for Illumina, #N245). PCR enrichment was applied using the kit (Novoprotein NovoNGS Index Kit for Illumina, #N239) with the PCR amplification cycle number set to 11. PCR products were purified according to the recommended procedure of the kit (Novoprotein DNA Clean Beads, #N240), and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System used the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 150-bp paired-end reads were generated. ATAC sequencing was provided by Tianjin Novogene Bioinformatic Technology Co., Ltd.

value: Jejunum

value: Enterocytes


title: HFS_4


title: D30_IMR

description: 10x Genomics

source_name: scRNA-seq of human brain organoids: day30 in vitro

value: day30 in vitro


title: D0_ASD

description: 10x Genomics


title: BSF_C,biol rep 1,ATAC_seq


title: DMSO; GFP control transfection; 72h; 3

city: Berkeley

first: Joshua

last: Tworig

state: CA

address: Weill Hall, Frank Schlessinger Way

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Reads were aligned to the human genome via Hisat2 with default parameters.
Genomic features were counted using Subread featurecounts with default parameters.
Assembly: GRCh38.110
Supplementary files format and content: Comma-separated values file contains raw counts for all samples.

molecule: polyA RNA

growth_protocol: HEK293 cells were maintained in suspension in BalanCD expression medium with 4mM L-glutamine on an orbital shaker (125 rpm,19 mm orbital throw) in a 37°C, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from cell pellets before and during AAV production. RNA was extracted using Direct-zol-96 RNA Kit.
mRNA libraries were constructed by SeqMatic using the Illumina Stranded mRNA prep kit.

treatment_protocol: HEK293 cells were resuspended in fresh BalanCD + 4mM glutamine expression medium at a density of 2.5M/ml and triple-transfected with TransIT-VirusGEN and a pHelper plasmid, a RepCap9 plasmid and an ITR containing reporter plasmid. Controls contained 0.1% DMSO in media, and experimental condition contained 1uM small molecule inhibitor.

value: DMSO, GFP transfection

tag: time point


title: neutrophils,H3K27ac,R848,HD2,ChIP

value: donor 2


title: LSF,biol rep 2,ATAC_seq

value: LSF


title: DMSO; GFP control transfection; 24h; 3


title: HFS_3


title: HFS_2


title: neutrophils,H3K27ac,R848,HD1,ChIP

value: donor 1


title: LSF,biol rep 1,ATAC_seq


title: neutrophils,H3K27ac,NT,HD3,ChIP

value: no treatment

value: freshly isolated cells


title: IP73_MDS25_PBMC_input_2

description: PBMC

value: Peripheral Blood Mononuclear Cells CD45+34+ cells from MDS patient

value: MDS


title: HFS_1

value: HFD-C


title: neutrophils,H3K27ac,NT,HD2,ChIP

value: Anti-H3K27Ac (Abcam # ab4729)

value: neutrophil


title: DMSO; GFP control transfection; 72h; 2


title: DSF,biol rep 2,ATAC_seq

value: DSF


title: DMSO; GFP control transfection; 24h; 2


title: neutrophils,H3K27ac,NT,HD1,ChIP


title: DSF,biol rep 1,ATAC_seq


title: DMSO; GFP control transfection; 72h; 1


title: HF75_5

value: Skeletal Muscle

value: HFD


title: Control,biol rep 2,ATAC_seq

value: Jejunum

value: Control


title: monocytes,H3K27ac,R848,HD3,ChIP

source_name: human CD14+ monocytes

value: donor 3

value: monocyte


title: DMSO; GFP control transfection; 24h; 1

value: WT

value: DMSO, GFP transfection


title: HF75_4


title: HF75_3


title: DMSO; GFP control transfection; 0h

value: pre-treatment, GFP transfection


title: monocytes,H3K27ac,R848,HD2,ChIP

value: donor 2


title: BSF,biol rep 2,ATAC_seq

value: Enterocytes

value: BSF


title: monocytes,H3K27ac,R848,HD1,ChIP

value: donor 1


title: HF75_2


title: D30_ASD

description: 10x Genomics

value: brain organoids

value: day30 in vitro


title: monocytes,H3K27ac,NT,HD3,ChIP

value: Anti-H3K27Ac (Abcam # ab4729)

value: no treatment

value: freshly isolated cells


title: DMSO; triple transfection; 24h; 3

value: DMSO, triple transfection


title: HF75_1

value: Skeletal Muscle

value: HFD


title: Remdesivir + virus_3

city: Los Angeles

first: Chandani

last: Sen

state: California

address: 650 Charles Young Drive South Laboratory of Dr. Brigitte Gomperts, CHS 64-200

department: Pediatrics

institute: University of California, Los Angeles

data_processing:
The reads were mapped by STAR 2.7.9a
Read counts per gene were quantified using the human  genome GRCh38.104.
In Partek Flow, read counts were normalized by CPM +1.0E-4.
Differential expression of genes was measured with  Partek’s gene-specific analysis (GSA).
Assembly: GRCh38.104.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: airway

growth_protocol: Primary human airway basal stem cells were expanded  (PneumaCult Ex media) and differentiated  (PneumaCult ALI media) in 96-well Air Liquid Interface  model.

extract_protocol:
Zymo Direct-zol RNA Miniprep kit  according to manufacturer’s instructions
KAPA RNA Hyper + RiboErase HMR Kit  according to manufacturer’s instructions

treatment_protocol: After differentiation, the cells were treated or not with  Remdesivir, MKGaA#49 and were exposed to SARS-CoV-2 virus or not

value: airway

value: Primary human airway basal stem cells

tag: drug treatment

value: Remdesivir

tag: infected with

value: SARS-CoV-2 (Wuhan)


title: monocytes,H3K27ac,NT,HD2,ChIP

value: monocyte


title: Control,biol rep 1,ATAC_seq

value: Jejunum

value: Control


title: DMSO; triple transfection; 72h; 2

value: WT


title: Remdesivir + virus_2


title: HF75_6


title: HF50_6


title: HF50_5


title: DMSO; triple transfection; 24h; 2


title: monocytes,H3K27ac,NT,HD1,ChIP

value: donor 1


title: Remdesivir + virus_1


title: MM-8-196

city: Brno

first: Monika

last: Vlachová

address: Kamenice 753/5

country: Czech Republic

institute: Masaryk University

data_processing:
Adaptor trimming, alignment and read count performed using Chimira tool (http://wwwdev.ebi.ac.uk/enright-dev/chimira/)
Supplementary_files_format_and_content: counts
Assembly: GRCh38-p10

source_name: bone marrow plasma (extracellular vesicles)

extract_protocol:
Izon qEV columns + miRNeasy Micro Kit (Qiagen)
CleanTag Small RNA Library Prep Kit by Trilink

tag: disease state

value: plasma cell leukemia


title: DMSO; triple transfection; 72h; 1


title: HF50_4


title: MM-12-228

value: bone marrow plasma (extracellular vesicles)


title: DMSO; triple transfection; 72h; 3


title: DMSO; triple transfection; 24h; 1


title: Mock_2

value: no infection


title: DMSO; triple transfection; 0h

value: pre-treatment, triple transfection


title: MM-13-77


title: HF50_2


title: Mock_1


title: HF50_3


title: MM-10-120


title: BSF,biol rep 1,ATAC_seq

value: Enterocytes

value: BSF


title: MM-9-253


title: Virus Only_3


title: small molecule; triple transfection; 72h; 3

value: small molecule, triple transfection


title: HF25_6

value: Skeletal Muscle

value: HFD


title: small molecule; triple transfection; 24h; 3


title: Virus Only_2

value: airway

value: Primary human airway basal stem cells


title: HF25_5


title: MM-17-138

value: extramedullary disease


title: MM-17-129


title: HF25_4


title: Mock_3


title: small molecule; triple transfection; 24h; 2


title: MKGaA#49 + virus_3

value: SARS-CoV-2 (Wuhan)


title: small molecule; triple transfection; 72h; 1


title: MKGaA#49 + virus_2


title: MM-17-56

value: not included


title: small molecule; triple transfection; 24h; 1


title: MKGaA#49 + virus_1


title: HF25_2


title: MM-17-49


title: small molecule; triple transfection; 0h


title: HF50_1


title: small molecule; triple transfection; 72h; 2


title: MM-17-85


title: DMSO; no transfection; 72h; 3

value: DMSO; no transfection


title: HF25_1

value: WT


title: MM-17-34


title: HF25_3


title: Virus Only_1


title: Dd2

city: Bamenda

first: Ines

last: Ngoh

state: North west region

address: Bambili

department: Microbiology & Parasitology

country: Cameroon

institute: University of Bamenda

data_processing:
Initial processing and quality assessment of raw paired-end fastQ files involved base quality check and de-multiplexing of indexed reads using FastQC v11.9 from Babraham Bioinformatics (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
This was followed by trimming of adapter sequences and filtering of low-quality reads (<36 base pairs) using TrimGalore v0.4.1 tools with the parameter-illumina from Babraham Bioinformatics (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
The filtered reads were assembled by alignment to the P. falciparum 3D7 v3 reference genome using the Division based Alignment for RNA-Seq Transcripts (DART) algorithm. Reads originating from PCR duplication in the 3D7-aligned reads were removed using Picard version 2.9.1 “MarkDuplicates” function (https://broadinstitute.github.io/picard/).
Mapped reads were then converted to bam files using SAM tools.
Raw read counts of each gene (transcript abundance) was estimated with the Rsubread package in R using a P. falciparum 3D7 reference genome annotation file that had masked out extremely polymorphic gene regions, duplicated genes, and the var, rifin and stevor large sub-telomeric gene families.
Assembly: P. falciparum 3D7 v3 reference genome
Supplementary files format and content: csv file of raw counts of each sample

organism: Plasmodium falciparum

source_name: Plasmodium falciparum

growth_protocol: Cryopreserved clinical isolates and laboratory adapted Plasmodium falciparum 3D7 and Dd2 strains (serving as controls) were thawed and cultured at 37oC in complete RPMI-1640 medium (supplemented with 0.5% albumax II (Gibco) for laboratory strains and with 20% heat-inactivated human AB serum for clinical isolates). Cultures were maintained at 2% haematocrit (HCT) in 10mL culture flasks using human group O+ RBCs from a single donor and incubated in a gas mixture of 1% O2, 5% CO2, and 94% N2.

extract_protocol:
Frozen schizont concentrate mixed with trizol (of clinical isolates + 3D7 and Dd2 controls) were thawed at room temperature and the total RNA of each schizont concentrate was extracted with RNeasy mini columns (Qiagen) according to manufacturer’s protocol. DNA was removed by DNase I digestion on RNeasy mini columns (Qiagen). The total RNA was eluted in 50μL RNase-free H2O and stored at − 80°C until library preparation.
Sequencing library preparation proceeded with an initial input of 150ng total RNA per sample with RNA Integrity Number (RIN) score of at least 7. Messenger RNA libraries were prepared using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770, E7775) as per manufacturer’s protocols.

treatment_protocol: Schizont stage enrichment proceeded with maintaining parasites in cultures for up to 48 hours with close monitoring every 6 hours for parasite stage development using light microscopy of Giemsa-stained thin smears. When most infected erythrocytes were segmented with 8 or more visible merozoites, parasite cultures were harvested. Approximately 500µL of the harvested parasite culture was aliquoted for use in setting up invasion-inhibition assays. The remaining culture volume was centrifuged and the recovered pellet was layered on 3mL of 70% percoll (Sigma –Aldrich)/phosphate buffered saline (PBS) density (v/v) solution and centrifuged at 800g for 10 minutes. After which, the supernatant containing the schizont-concentrate was washed twice in complete RPMI, mixed with a 4x volume of TRIzol® reagent (Ambion) and stored at −80°C until RNA extraction.

tag: sample origin

value: SA-dependent Control

value: schizont stage enriched

value: Plasmodium falciparum


title: 14A

value: NWR


title: CS_6

value: NFD

value: NFD-C


title: DMSO; no transfection; 72h; 2


title: CS_5


title: MM-17-5

value: bone marrow plasma (extracellular vesicles)


title: MM-17-9


title: 3D7

value: SA-independent Control


title: CS_4

value: Skeletal Muscle


title: 24A


title: MM-17-37

value: multiple myeloma


title: DMSO; no transfection; 24h; 2


title: 07A

value: SWR


title: MM-17-19


title: DMSO; no transfection; 72h; 1


title: CS_2


title: MM-16-140


title: 73A


title: 19A


title: CS_1


title: DMSO; no transfection; 24h; 1


title: HCC_M1_LIL, scTCRseq

city: Gangnam-gu

first: Hong-Hee

last: Won

address: 81, Irwon-ro

country: South Korea

institute: SungKyunKwan University

description: 10x Genomics v7.0.0

data_processing:
The scTCR-seq data were assembled using the Cell Ranger VDJ pipeline (10x Genomics).
For demultiplexing for HCC_M1_LIL sample, we used Demuxlet software in scRNA-seq data.
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
Supplementary files format and content: Comma-separated matrix files
Library strategy: TCR-Seq

source_name: adjacent normal liver from tumor

extract_protocol:
The library preparation was performed using either the Chromium Next GEM Single cell 5’kit v2 (10x Genomics) with a cell recovery target of 5,000 per patient, following the manufacturer’s instruction.
The libraries were processed according to manufacturer’s recommendation (10x Genomics), and sequenced on a HiSeq 2500, MGI seq, and Novaseq systems.

treatment_protocol: Tissues were minced and mechanically dissociated using gentleMACS (Miltenyi biotec), and then enzymatically dissociated using a tumor dissociation kit (Miltenyi biotec, 130-095-929) at 37°C for 20 minutes.

value: adjacent normal liver from tumor

value: T cell receptors


title: TRM_132_LIL, scTCRseq

description: 10x Genomics v7.0.0


title: small molecule; no transfection; 72h; 3

value: small molecule; no transfection


title: 32A


title: DMSO; no transfection; 24h; 3


title: 13A


title: small molecule; no transfection; 72h; 2


title: MM-13-78

value: plasma cell leukemia


title: 42A


title: small molecule; no transfection; 24h; 3


title: 20A


title: MM-9-256


title: N2 control, replicate 4

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

institute: University of Pittsburgh

description: P2 100 Flow Cell

data_processing:
Stranded reads were checked for quality using FastQC (v0.11.5) and they were trimmed for quality and adapters using Cutadapt (v2.1).
Each sample was mapped to the Ensembl's version of C. elegans reference fasta (WBcel235 v110), using the fast alignment tool STAR 2.7.9a with default settings
Genes in WBcel235.110 were quantified used HTSeq v0.11.2 using default settings.
edgeR version 4.0.16, an R Bioconductor package, with R version 4.3, was used for differential gene analysis comparing various sample groups
Assembly: WBcel235 v110
Supplementary files format and content: HT-Seq Raw Counts in tab-delimited text file

organism: Caenorhabditis elegans

source_name: germ line (mitotic region to bend)

growth_protocol: Worms were grown unstarved on MyoB plates for >5 generations prior to collection of L4 larvae.

extract_protocol:
Germ lines were dissected and collected with a finely pulled pipette to collect pre-diplotene germ cell nuclei. Germ lines were immediately transferred directly into RNAzol on ice.  50 germ lines were collected per sample and then samples were immediately frozen at -80°C until preparation of the RNA.  PolyA+ RNA was isolated using NEBNext PolyA+ magnetic isolation module.
Libraries were constructs according to the manufacturers instructions using NEBNext® Ultra™ II RNA Library Prep Kit

treatment_protocol: L4 larvae were transferred to MyoB plates with 1mM auxin for 24 hours

value: germ line (mitotic region to bend)


title: DMSO; no transfection; 0h

value: WT

value: pre-treatment, no transfection


title: MM-11-182


title: small molecule; no transfection; 24h; 2


title: N2 control, replicate 2

description: P2 100 Flow Cell


title: 10A

value: schizont stage enriched


title: MM-12-106


title: small molecule; no transfection; 72h; 1


title: MM-12-140


title: 31A

value: Plasmodium falciparum


title: MM-17-150


title: 11A


title: N2, +auxin, replicate 4

description: P2 100 Flow Cell

value: Auxin


title: small molecule; no transfection; 24h; 1


title: MM-17-46


title: small molecule; no transfection; 0h


title: N2, +auxin, replicate 3

description: P2 100 Flow Cell


title: 09A

value: NWR


title: N2 control, replicate 3

description: P2 100 Flow Cell


title: IP41_25J1iPS_INP

description: iPSC

value: iPSC

value: MDS


title: MM-17-158

value: bone marrow plasma (extracellular vesicles)


title: N2, +auxin, replicate 12

description: P2 100 Flow Cell


title: CS_3

source_name: Skeletal Muscle

value: Skeletal Muscle

value: NFD

value: NFD-C


title: 37A

value: SWR


title: RfxCas13d + g1 Chemically Synthesized (si:dkey-93m18.4), rep4

city: Kansas City

first: Gabriel

last: da Silva Pescador

state: MO

institute: Stowers Institute for Medical Research

description: Library name: T_pRfxCas13d_g1Syn_R4

data_processing:
Following sequencing, Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.
Assembly: danrer11
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA then was extracted using Direct-zol RNA Miniprep Kit (#R2050, Zymo Research) following manufacturer’s instructions.
Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high-quality total RNA, as assessed using the Bioanalyzer (Agilent), with the Watchmaker mRNA Library Prep Kit (Watchmaker, Cat. No. 7BK0001) at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification, 2 µL of IDT indexed primers (using xGen™ Stubby Adapter-UDI Primers, 96 reactions, Cat No. 10005921) was added to 3 µL of library, and 5 µL of Equinox Amplification Master Mix (2x). These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect (Beckman Coulter, Cat. No. B23318) bead ratio was used during the Post-Amplification Cleanup, and post amplification libraries were eluted in 10 µL of Qiagen EB (Qiagen, Cat. No. 19086). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer (Life Technologies). Equal molar libraries were pooled, quantified, and converted to process on the Element AVITI.

value: whole embryo

tag: age

value: 4 hpf

value: Knockdown - Chemically Synthesized gRNA


title: IP40_25J1iPS_Ac_2

description: iPSC


title: RfxCas13d + g1 Chemically Synthesized (si:dkey-93m18.4), rep3

description: Library name: T_pRfxCas13d_g1Syn_R3


title: 05A


title: N2, +auxin, replicate 1

description: P2 100 Flow Cell

value: germ line (mitotic region to bend)


title: MDS_25G1_3

data_processing:
For the computational analyses, we trimmed adapter sequences by using cutadapt, remove the reads mapped to ribosomal RNA by using bowtie2 and samtools.
The STAR index was constructed from the genome index, and RNA-seq single-end reads were aligned to the genome using STAR
Using the bam files produced by the alignment tool, use the modules in RseQC to evaluate the quality of the RNA-seq data with the reference files.
HTSeq was used to count reads mapping to individual genes by processing the sorted bam files with accepted read quality.
Counts generated by HTSeq-count were normalized using DESeq2. This normalization utilized the size factor derived from the count data of all samples.
Assembly: Hg38 (GRCh38)
Supplementary files format and content: tab-delimited text files includes raw counts values for each sample
Supplementary files format and content: tab-delimited text files includes normalized counts for each sample

source_name: human iPSC derived CD45+CD34+ hematopoietic progenitor cells (HPCs)

growth_protocol: iPSCs were dissociated into single cells and seeded on a low-binding plate to form embryoid bodies, which were subsequently differentiated in suspension. Human iPSC-derived CD45+CD34+ hematopoietic progenitor cells (HPCs) were sorted using FACS.

extract_protocol:
Sample homogenization was performed using 700 μL of QIAZOL (QIAGEN) by manual crushing with a pestle. After homogenization, two supernatants were collected in new 1.5 mL RNase-free microcentrifuge tubes. RNA extraction was carried out using the miRNeasy Micro Kit with a Rnase-Free Dnase Set (QIAGEN).
The cDNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit and protocol from Illumina (Illumina Inc., San Diego, CA).

value: MDS 25G1


title: 12A


title: N2 control, replicate 1

description: P2 100 Flow Cell


title: RfxCas13d + g3 Chemically Synthesized (si:dkey-93m18.4), rep4

description: Library name: T_pRfxCas13d_g3Syn_R4


title: MDS_25G1_2

value: human iPSC derived CD45+CD34+ hematopoietic progenitor cells (HPCs)


title: RfxCas13d + g3 Chemically Synthesized (si:dkey-93m18.4), rep3

description: Library name: T_pRfxCas13d_g3Syn_R3


title: arsenic 5 -2nd exp

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

institute: National Institute for Environmental Studies

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Adapter-and quality-trimmed sequencing reads were mapped to the mouse reference genomes (mm10) using the Bismark
The methylation level of each CpG was calculated using a methylKit package
Assembly: mm10
Supplementary files format and content: txt

source_name: embryos

extract_protocol:
DNA was prepared from the homogenate of each embryo using an AllPrep DNA Mini spin column (Qiagen) according to the manufacturer’s protocol.
RRBS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina following manufacturer's protocols.

value: embryos


title: TIR1 driver, +auxin, replicate 3

description: P2 100 Flow Cell

value: ieSi38[sun-1p::TIR1::mRuby::sun-1 3'UTR + Cbr-unc-119(+)] IV


title: RfxCas13d control, rep6

description: Library name: T_pRfxCas13d_R6

value: RfxCas13d control


title: MDS_25G1_1


title: arsenic 4 -2nd exp


title: TIR1 driver, +auxin, replicate 1

description: P2 100 Flow Cell

value: Auxin


title: TIR1 driver control, replicate 4

description: P2 100 Flow Cell


title: KM25_T_A1_3

value: KM25 T-A1

value: Normal


title: arsenic 3 -2nd exp


title: TIR1 driver control, replicate 3

description: P2 100 Flow Cell


title: KM25_T_A1_2


title: arsenic 2 -2nd exp


title: RfxCas13d + g1 Chemically Synthesized (si:dkey-93m18.4), rep1

description: Library name: T_pRfxCas13d_g1Syn_R1


title: KM25_T_A1_1


title: TIR1 driver control, replicate 2

description: P2 100 Flow Cell


title: RfxCas13d + g3 Chemically Synthesized (si:dkey-93m18.4), rep2

description: Library name: T_pRfxCas13d_g3Syn_R2


title: TIR1 driver control, replicate 1

description: P2 100 Flow Cell


title: RfxCas13d + g3 Chemically Synthesized (si:dkey-93m18.4), rep1

description: Library name: T_pRfxCas13d_g3Syn_R1


title: arsenic 1 -2nd exp


title: TIR1 driver, +auxin, replicate 2

description: P2 100 Flow Cell


title: bra-2 KD, replicate 4

description: P2 100 Flow Cell

value: HA::AID::bra-2; ieSi38[sun-1p::TIR1::mRuby::sun-1 3'UTR + Cbr-unc-119(+)] IV


title: IP63_38_J500_I_1hr

description: cell lines

source_name: cell lines

value: cell lines

value: Leukemia with t(3;8)


title: control 4 -2nd exp


title: RfxCas13d + g3 IVTed (si:dkey-93m18.4), rep3

description: Library name: T_pRfxCas13d_g3_R3

value: Knockdown - IVTed gRNA


title: IP61_38_D_I_1hr

description: cell lines

value: DMSO


title: bra-2 KD, replicate 3

description: P2 100 Flow Cell


title: RfxCas13d control, rep5

description: Library name: T_pRfxCas13d_R5

value: whole embryo


title: IP60_38_D_H_1hr

description: cell lines


title: RfxCas13d + g1 Chemically Synthesized (si:dkey-93m18.4), rep2

description: Library name: T_pRfxCas13d_g1Syn_R2

value: 4 hpf


title: IP62_38_J_H_1hr

description: cell lines


title: control 3 -2nd exp


title: control 2 -2nd exp


title: bra-2 KD, replicate 2

description: P2 100 Flow Cell


title: IP53_PBMC_W

description: PBMC

value: Peripheral Blood Mononuclear Cells CD45+34+ cells from MDS patient

value: MDS


title: bra-2 KD, replicate 1

description: P2 100 Flow Cell

value: germ line (mitotic region to bend)


title: RfxCas13d control, rep4

description: Library name: T_pRfxCas13d_R4


title: IP52_PBMC_H

description: PBMC


title: control 1 -2nd exp


title: RfxCas13d + g3 IVTed (si:dkey-93m18.4), rep1

description: Library name: T_pRfxCas13d_g3_R1


title: bra-2 control, replicate 4

description: P2 100 Flow Cell


title: IP47_25E_W

description: HPCs

source_name: human iPSC-derived CD45+CD34+ hematopoietic progenitor cells (HPCs)

value: Hematopoietic differentiation


title: control 5 -2nd exp

value: embryos


title: IP46_25E_H

description: HPCs

value: human iPSC-derived CD45+CD34+ hematopoietic progenitor cells (HPCs)


title: RfxCas13d control, rep3

description: Library name: T_pRfxCas13d_R3

value: RfxCas13d control


title: bra-2 control, replicate 3

description: P2 100 Flow Cell


title: arsenic 4

extract_protocol:
Embryos DNA was extracted with a phenol-chloroform mixture, precipitated with ethanol, dried and dissolved in TE buffer. Sperm DNA was purified using Allprep DNA/RNA mini kit (Qiagen) and was used for the construction of RRBS libraries.
RRBS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina following manufacturer's protocols.


title: RfxCas13d + g1 IVTed (si:dkey-93m18.4), rep3

description: Library name: T_pRfxCas13d_g1_R3


title: bra-2 control, replicate 2

description: P2 100 Flow Cell


title: arsenic 3


title: IP45_692i_W

description: iPSC

source_name: iPSC

value: iPSC

value: Control


title: RfxCas13d + g2 IVTed (si:dkey-93m18.4), rep3

description: Library name: T_pRfxCas13d_g2_R3


title: IP44_692i_H

description: iPSC


title: RfxCas13d + g3 IVTed (si:dkey-93m18.4), rep2

description: Library name: T_pRfxCas13d_g3_R2


title: bra-2 control, replicate 1

description: P2 100 Flow Cell


title: arsenic 2


title: RfxCas13d + g1 IVTed (si:dkey-93m18.4), rep2

description: Library name: T_pRfxCas13d_g1_R2


title: arsenic 1


title: Sample_6-3B-GC

city: Ås

first: Gabriela

last: Carril

address: Oluf Thesens vei 30

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
The raw files were processed using Orion High-Performance Computing Cluster at the Norwegian University of Life Sciences
RNA raw reads were trimmed using BBDuk (v34.56)
alignment to P. salmonis genome Psal-013 (ASM970875v1 - RefSeq GCF_009708755.1) or Psal-182 genome (ASM970941v1 – RefSeq GCF_009709415.1) using HISAT (v2.1.0)
The fragments mapped were counted with featureCounts (v1.4.6-1)
differentially expressed genes (DEGs) between groups were estimated using SARTools (v1.7.3) package in Rstudio (v4.2.0).
Assembly: ASM970875v1 - RefSeq GCF_009708755.1 and ASM970941v1 – RefSeq GCF_009709415.1
Supplementary files format and content: count files

organism: Piscirickettsia salmonis

source_name: Bacteria

extract_protocol:
Total RNA was extracted from each culture using Qiagen RNeasy Mini Kit (Qiagen), followed by rRNA depletion using QIAseq FastSelect 5S/16S/23S (Qiagen).
RNA libraries for RNA-seq were made using TruSeq Stranded mRNA library prep

value: Bacteria

value: Piscirickettsia salmonis LF89

value: Single culture Psal013


title: IP39_25G1iPSOld_INP

description: iPSC


title: Sample_5-3A-GC

value: Piscirickettsia salmonis EM90

value: Single culture Psal182


title: arsenic 5


title: RfxCas13d control, rep2

description: Library name: T_pRfxCas13d_R2


title: control 5


title: IP38_25G1iPSOld_Ac

description: iPSC


title: Sample_4-2B-GC


title: control 4


title: IP37_692D2EB_INP

description: HPCs


title: RfxCas13d + g1 IVTed (si:dkey-93m18.4), rep1

description: Library name: T_pRfxCas13d_g1_R1

value: Knockdown - IVTed gRNA


title: IP36_692D2EB_Ac

description: HPCs


title: RfxCas13d + g2 IVTed (si:dkey-93m18.4), rep1

description: Library name: T_pRfxCas13d_g2_R1

value: whole embryo


title: Sample_2-1B-GC


title: Sample_3-2A-GC


title: Sample_1-1A-GC


title: control 3


title: control 1


title: exp1_A498_sgCtrl_KDM5C

status: Public on Jan 21 2025

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Hospital Freiburg

description: Library name: exp1_A498_sgCtrl_KDM5C

data_processing:
Sequence reads were trimmed for adapter sequences and low-quality sequences using Trim Galore (v 0.6.6) with default settings.
Sequences were aligned to UCSC hg19 using Bowtie2 (v 2.4.5) (parameters: --dovetail, --local, --very-sensitive-local, --no-unal, --no-mixed, --no-discordant, -I 10, -X 700). Spike-in sequences were aligned to UCSC dm6 for exp1 and exp2 and to E. coli NCBI K12 MG1655 for exp3.
BigWig files were generated using bamCoverage from deepTools (v 3.5.0)
Tag directories were generated using makeTagDirectory with the option -totalReads from Homer (v 4.11)
Peaks were called using Homer's findPeaks with -style histone and -C 0 and experimental samples were compared to the corresponding IgG control. Peaks with 4-fold more tags in the experimental sample compared to the control and cumulative Poisson p-value ≤ 0.0001 were kept, while peaks within blacklisted regions from ENCODE were excluded using intersectBed from BEDTools.
Unique and overlapping peaks were determined using Homer's mergePeaks with -d given.
Assembly: hg19
Supplementary files format and content: bigWig of coverage, peaks (.Clean.bed) (except for IgG controls)
Library strategy: CUT&RUN

source_name: kidney

extract_protocol:
Samples were processed following the EpiCypher® CUTANATM CUT&RUN Protocol (for histone PTMs, transcription factors (TFs), and chromatin regulators).
RNA libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit and NEBNext® Multiplex Oligos Set (New England Biolabs).

value: kidney

value: sgCtrl

tag: antibody


title: IP34_K562_Ac

description: cell lines

tag: tissue

value: cell lines

value: Leukemia


title: DU145, HTO

city: South San Francisco

first: Tomasz

last: Włodarczyk

address: 1 DNA Way

institute: Genentech

description:
DNA-seq
LIB5463784_SAM24425416

data_processing:
scMultiome data processing of sequencing reads was performed using our Single Cell Multiome ATAC + Gene Expression (ARCSeq) - 10X Cellranger bioinformatics pipeline (martian v4.0.5)which implements the CellRanger ARC seq (cellranger-arc count ) workflow (cellranger-arc_2.0.0) using the GRCh38 genome reference. ATAC-seq (atac_fragments.tsv.gz) and scRNA-seq (raw_feature_bc_matrix.h5) matrices were generated from fastq files.
The cell hashing (hashed-tag oligonucleotide (HTO)) (*.hashing.tsv) feature count matrices were generated with  cumulus_feature_barcoding (https://github.com/lilab-bcb/cumulus_feature_barcoding) (v0.11.1). This  barcode count matrix was then used to demultiplex the scRNAseq data using a DropleUtils (v1.21.0)-based  workflow with the emptyDrops(test.ambient = TRUE, by.rank=30000) and hashedDrops(  doublet.nmads=3, doublet.min=2, confident.nmads=1, confident.min=1) key steps and parameters. ATAC-seq data was processed with ArchR v1.0.3. Briefly, low quality cells were removed (minTSS>=4 and  minFrags>=1000) and arrow files were generated followed by generation of Tile and Gene Score matrices  using a tile size of 500 bp. Doublets were identified and filtered out using ArchR’s addDoubletScores()  function with default parameters.  Filtered ATACSeq data was merged with the libary-size normalized scRNAseq using the function addGeneIntegrationMatrix. For both modalities we used addIterativeLSI to reduce dimensionality. The results were combined into single space in which cell clusters were identified. Peaks were generated using addReproduciblePeakSet() with macs2. Peaks were annotated with addPeakAnnotations()(using public cisBP database) followed by  addDeviationsMatrix().  The peaks.mtx.gz and gex.mtx.gz files contains processed peaks and normalized gene expression data.
Assembly: GRCh38-2020-A
Supplementary files format and content: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz - output of Cellranger
Supplementary files format and content: gex.mtx.gz, peaks.mtx.gz, gex_peaks_barcodes.tsv, peaks_features.tsv, gex_features.tsv - files representing ArchR GeneExpressionMatrix (normalized counts) and PeakMatrix assays, row names (genes or peaks) and column names (barcodes)
Supplementary files format and content: <library name>.hashing.csv cell hashing count matrix generated by cumulus_feature_barcoding with the first column storing HTO ID and other column names being barcodes
Library strategy: Single cell multiome (scMultiome)

source_name: prostate adenocarcinoma

growth_protocol: LNCap Clone FGC, VCAP and DU145 cells were obtained from ATCC and cultured with RPMI-1640 media with 10% FBS and 2mM L-Glutamine; NCI-H660 cells were obtained from ATCC and cultured with DMEM/F12 with 0.005 mg/ml insulin,0.01 mg/ml Transferrin, 30nM Sodium selenite,10nM Hydrocortisone,10nM beta-estradiol, 4mM L-Glutamine. The cells were split every 4-5 days to maintain the appropriate density. For the drug response assay, cells were seeded in 6 well format.The cells were split every 4-5 days to maintain the appropriate density.

extract_protocol:
After 24 hours from treatment, the cells were harvested for the single-cell RNA-ATAC Co-assay.
The library construction was following the standard 10X protocol with the following modifications to the protocol:  1) 1µl of 10µM HTO additive primer was spiked in during the pre-AMP and cDNA PCR steps; 2) during the 0.6X cDNA cleanup, the supernatant was saved to amplify the HTO library. Along with the transcriptome library, the HTO library was amplified from the supernatant using the HTO-specific primer. The detailed protocol can be found on the cell hashing website (https://cite-seq.com/cell-hashing/).

treatment_protocol: 1.5E5 DU145 cells were seeded into each well of a 6 well plate and 5E3 DU145 cells were seeded into each well of a 96 well plate; 1.5-2E6 LNCAP or VCAP cells were seeded into T75 flasks; 5E5 cells NCI-H660 cells were seeded into each well of a 6 well plate. After 48 hours, the media was removed and cells were treated with DMSO, 1uM Enzalutamide, 0.1 uM SMARCA2.4_1 or 1 uM ARV-110 in complete media.

value: prostate adenocarcinoma

tag: cell line


title: TS161_Fujioka_KD-1_VPE_GGCTAC_GCTCCGGACGTGCGGTAC

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

country: United Kingdom

institute: Cancer Research UK

data_processing:
Sequencing data were deconvoluted using cutadapt version 1.18. Reads were mapped and analysis performed using 4Cseqpipe (van de Werken et al., 2012 and 4C-ker (Raviram et al., 2016) software.
Assembly: GRCh37
Supplementary files format and content: bedGraph
Library strategy: 4C-seq

source_name: Fujioka Cells

growth_protocol: Cryopreserved leukemic blast cells from bone marrow or blood of patients at presentation were thawed and co-cultured on MS5 stromal cells, as described (van Gosliga et al., 2007) in α-MEM medium (Life Technologies, Carlsbad, CA) supplemented with 12.5% heat-inactivated FBS (Life Technologies), 12.5% heat-inactivated horse serum (Life Technologies), 2 mM L-glutamine (Sigma-Aldrich, St. Louis, MO), 10U/ml penicillin and 10μg/ml streptomycin (Sigma-Aldrich), 57.2 μM β-mercaptoethanol (Sigma- Aldrich), 1 μM hydrocortisone (Sigma-Aldrich), 500nM StemRegenin1 and 500nM UM729 (Stem cell Technologies, Vancouver, BC) to prevent differentiation of acute myeloid leukemia (AML) cells in culture (Pabst et al., 2014) and IL-3, IL-6, SCF, Flt3-L, G-CSF, and TPO (all at 20 ng/ml; PeproTech, London, UK).

extract_protocol:
4C-seq libraries preparation for all samples was performed as previously described (Splinter et al., 2012). In brief, a total of 1x107cells was resuspended in 10ml of PBS/10%FBS and crosslinked with formaldehyde at a final concentration of 2%. The resuspended cells were incubated for 10 minutes at RT while tumbling and subsequently the formaldehyde activity was quenched using glycine at a final concentration of 0.125M. The quenched solution was then lysed in 1ml of lysis buffer (50mM Tris–HCl at pH 7.5, 150mM NaCl, 5mM EDTA, 0.5% NP-40, 1% TX-100), resuspended in 450µl of Milli-Q water and digested with the 4bp cutter restriction enzyme (DpnII) (Thermo Scientific). After first digestion step, samples were subjected to proximity ligation overnight using 50U of T4 DNA Ligase (Sigma-Aldrich). The ligated chromatin was then de-cross-linked overnight with 30µl of Prot K (10mg/ml) and DNA was purified using phenol-chloroform and subjected to a second digestion with the 4bp cutter restriction enzyme (NlaIII) (Thermo Scientific). Digested DNA was then subjected to a second step of proximity ligation overnight and eventually DNA was extracted using phenol-chloroform and further purified using the QIAquick PCR purification kit (QIAGEN).  The resulting 4C-seq libraries were amplified to generate fragments containing the viewpoint ligation partners. Each primer contained specific Illumina sequencing adaptors which allow the amplified DNA fragments to adhere to the flow-cell where the sequencing takes place. The set of primers was designed using the 4C-seq primer design tool of the University of Chicago (https://mnlab.uchicago.edu/4Cpd/).   PCR reactions were performed with the Expand Long Template polymerase (Roche) using 3.2μg of 4C template product using the following thermocycling conditions: 94°C for 2min, 30 cycles of (94°C for 10s, 55°C for 1min, 68°C for 3min), 68°C for 5min. Subsequently, the 16 reactions were pooled together and purified using the High Pure PCR Product Purification Kit (Roche). At this point, the libraries were quantified using the Nanodrop spectrophotometer and quality was assessed by running 300ng of each library on a 1.5% agarose gel. The obtained libraries were quality-check using the Agilent Bioanalyzer and subsequently sequenced with 10% phiX using a MiSeq desktop sequencing system (Illumina, San Diego, CA) with a setting of 76-bp single-end.
Samples were sequenced with 10% phiX using a MiSeq desktop sequencing system (Illumina, San Diego, CA) with a setting of 76-bp single-end. The sequencing generated around 1 million reads for Fujioka cells, primary samples and around 3 million reads for Fujioka cells after the FTO-ncAML KDs

tag: cell type

value: Fujioka Cells


title: TS161_Fujioka_NTC-1_VPE_TAGCTT_GCTCCGGACGTGCGGTAC


title: TS103_189T2M_E_IRX3_low_VE_TTAGGC_GAAGGTGGGCGCCCGATC

source_name: Primary AML

value: Primary AML


title: RfxCas13d control, rep1

description: Library name: T_pRfxCas13d_R1

value: 4 hpf

tag: treatment

value: RfxCas13d control


title: RfxCas13d + g2 IVTed (si:dkey-93m18.4), rep2

description: Library name: T_pRfxCas13d_g2_R2


title: TS161_Fujioka_NTC-2_VPE_CTTGTA_GCTCCGGACGTGCGGTAC


title: TS103_287T1M_A_IRX3_high_VE_TAGCTT_GAAGGTGGGCGCCCGATC


title: S103_352T1B_C_IRX3_high_VE_CTTGTA_GAAGGTGGGCGCCCGATC


title: smad6ab_DKO_5, biol rep 1, 5 dpf, 5 fish pooled

city: Ghent

first: Michiel

last: Vanhooydonck

address: Corneel Heymanslaan  10

department: Biomolecular medicine

country: Belgium

institute: Ghent University

description: Library name: quantseq_sample_30

data_processing:
Raw read QC: UMI and spacer were removed using UMI-tools (v1.1.4), resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC (v0.12.1) for their quality and length. Putative contaminations were checked using FastQ Screen (v0.15.3) and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross-mapping to other organisms is normal and caused by homology between organisms.
Adapter and quality trimming: Adaptor trimming was done using cutadapt (v4.9) with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC
Read mapping and feature counting: For each sample, trimmed reads were mapped on the zebrafish genome (GRCz11, ENSEMBL release 112) using the splice-aware STAR (v2.7.10a) mapper. UMI-based deduplication of mapped reads was done with UMI-tools (v1.1.4). Feature counting at the gene and transcript isoform level was done using rsem-calculate-expression (RSEM v1.3.3). Raw counts for all samples are available as an Excel file. We used the gene-level counts for all subsequent analyses.
Differential gene expression:
Assembly: GRCz11
Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all_samples_raw_feature_counts.xlsx

source_name: pool of 3 whole embryos

growth_protocol: Embryos were grown at 27°C in E3 medium with methylene blue until 5 days post fertilization (dpf). At 1 and 3 dpf, medium was refreshed. For adults, zebrafish  were housed at the zebrafish facility Ghent in semi-closed recirculating housing systems (ZebTEC and WTU systems, Tecniplast) at a constant temperature (27-28°C), pH (~7,5), conductivity (~550µS) and light dark cycle (14/10). Zebrafish were fed every day with dry food (Gemma Micro) and with artemia (Ocean Nutrition).

extract_protocol:
For RNA extraction, the Rneasy® minikit (Qiagen; Hilden, Germany) was used following manufacturers guidelines.
For each sample, a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) and the UMI Second Strand Synthesis Module for QuantSeq FWD (Illumina, Read 1). This incorporates a unique molecular identifier (UMI) in the first 6 nucleotides of each read, allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single-read 75 on an Aviti device (Element Biosciences).

value: pool of 3 whole embryos

tag: genotype

value: smad6a/b DKO


title: smad6ab_DKO_3, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_28


title: smad6ab_DKO_4, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_29


title: smad6ab_DKO_2, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_27


title: hPheo1 rep2

type: RNA

city: Linköping

first: Mouna

last: Tababi

state: Östergötland

country: Sweden

institute: Linköping University

hyb_protocol: Samples were hybridized with GeneChip HuGene-1_0-st-v1 Arrays (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G  according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with the Transcriptome Analysis Console Software (Affymetrix) for background correction, quality control, normalization and the calculation of log2 fold-changes between sample expression values.
RMA expression value derived from Transcriptome Analysis Console Software (Affymetrix)
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: Wild type hPheo1

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The cell line was maintained as adherent monolayer cultures in RPMI 1640 medium (Gibco), supplemented with 5% heat inactivated FBS (Gibco), 1% L-glutamine (Gibco) and 1% penicillin-streptomycin (Gibco). Cells were seeded at 2x105 /ml in T75 tissue culture flasks and the media was changed once a week

extract_protocol: Total cellular RNA was extracted using the RNeasy Plus Mini kit (Qiagen , Cat. 74134), according to the manufacturer’s instructions

value: human pheochromocytoma cell line


title: control 2

value: embryos


title: hPheo1 rep3

description: RMA expression value derived from Transcriptome Analysis Console Software (Affymetrix)


title: smad6ab_DKO_1, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_26


title: IP35_K562_INP

city: Kyoto

first: Yoshinori

last: Yoshida

institute: Kyoto University

description: cell lines

data_processing:
Sequencing reads were aligned to the hg19 reference genome using bowtie2 following adapter trimming using Cutadapt. Duplicates and reads falling within blacklisted regions (ENCODE) were removed using Picards and bedtools, respectively. For visualization, bigwig files were created using the bamCoverage tool from deepTools, with the options of normalization using Bins Per Million, smoothLength 60, and binSize 20. Peak calling was performed using Homer. All figures were displayed using IGV.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
ChIP-seq experiments were conducted using feeder-free iPSCs, CD45+CD34+ HPCs, and K562 cells. A Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) was used to eliminate dead cells from feeder-free iPSCs and HPCs. Cells were fixed in PBS with 1% formaldehyde (Thermo Fisher Scientific) with gentle mixing for 10 minutes at room temperature. The reaction was stopped by adding a glycine solution (10x; Cell Signaling Technology) and incubating for 5 minutes at room temperature, followed by two rounds of cold PBS washing. The cells were processed using the SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol. The chromatin was sonicated with Covaris E220 (Covaris) using a microTUBE AFA Fiber Pre-Slit Crimp-Cap (130 µL). Immunoprecipitation of the cross-linked chromatin was performed using antibodies directed against histone H3 lysine 27 acetylation (H3K27ac) (Cell Signaling Technology).
ChIP-seq libraries were constructed using a ThruPLEX DNA-Seq Kit (Takara) according to the manufacturer’s protocol and sequenced using NextSeq 500 or NovaSeq 6000 (Illumina)


title: exp1_A498_sgCtrl_IgG

description: Library name: exp1_A498_sgCtrl_IgG


title: control 2_for_smad6abDKO, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_22

value: wt control


title: control 4_for_smad6abDKO, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_24


title: TS161_Fujioka_KD-2_VPE_ACAGTG_GCTCCGGACGTGCGGTAC


title: smad3ab_DKO_5, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_20

value: smad3a/b DKO


title: control 3_for_smad6abDKO, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_23


title: smad3ab_DKO_4, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_19


title: control 1_for_smad6abDKO, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_21


title: smad3ab_DKO_2, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_17


title: hPheo1 rep1


title: smad3ab_DKO_1, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_16


title: smad3ab_DKO_3, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_18


title: control 4_for_smad3abDKO, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_14


title: control 2_for_smad3abDKO, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_12


title: control 5_for_smad3abDKO, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_15


title: control 3_for_smad3abDKO, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_13


title: TS103_575T1M_F_IRX3_low_VE_TGACCA_GAAGGTGGGCGCCCGATC


title: control 1_for_smad3abDKO, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_11


title: qKO 4, biol rep 1, adult aorta, 3 aortas pooled

description: Library name: quantseq_sample_9

source_name: pool of 3 adult aortas and bulbus arteriosus

value: qKO


title: qKO 5, biol rep 1, adult aorta, 3 aortas pooled

description: Library name: quantseq_sample_10

value: pool of 3 adult aortas and bulbus arteriosus


title: qKO 1, biol rep 1, adult aorta, 3 aortas pooled

description: Library name: quantseq_sample_6


title: control 5, biol rep 1, adult aorta, 3 aortas pooled

description: Library name: quantseq_sample_5


title: control 5_for_smad6abDKO, biol rep 1, 5 dpf, 5 fish pooled

description: Library name: quantseq_sample_25


title: qKO 3, biol rep 1, adult aorta, 3 aortas pooled

description: Library name: quantseq_sample_8


title: control 4, biol rep 1, adult aorta, 3 aortas pooled

description: Library name: quantseq_sample_4


title: control 3, biol rep 1, adult aorta, 3 aortas pooled

description: Library name: quantseq_sample_3


title: control 1, biol rep 1, adult aorta, 3 aortas pooled

description: Library name: quantseq_sample_1


title: control 2, biol rep 1, adult aorta, 3 aortas pooled

description: Library name: quantseq_sample_2


title: CJFPSTA3

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

description: Library name: Sta3

data_processing:
The raw sequence data generated was converted into FASTQ files using Illumina CASSAVA 1.8.2
GALAXY (https://usegalaxy.org/). Low quality base pairs were trimmed from the ends and the sequence reads were mapped to the C. japonicus reference genome with RPKM values calculated for genes. Log2 transformation and quantile normalization was performed for the RPKM values and a Student’s T-test conducted to compare gene expression between various groups of samples. Additional analysis and visualization of the data was performed using ArrayStar.
Assembly: GCA_000019225.1
Supplementary files format and content: RPKM for every replicate for both the LOG and STA conditions

organism: Cellvibrio japonicus

source_name: bacterial cell

extract_protocol: RNA extraction used Rneasy kit (Qiagen)

value: bacterial cell

value: wild-type strain (Ueda107)

tag: growth phase

value: stationary phase


title: CJFPLOG3

description: Library name: Log3

value: exponential phase


title: CJFPLOG2

description: Library name: Log2


title: CJFPSTA1

description: Library name: Sta1


title: CJFPLOG1

description: Library name: Log1


title: CJFPSTA2

description: Library name: Sta2


title: N4

city: Kuala Lumpur

first: Retnagowri

last: Rajandram

address: University of Malaya

country: Malaysia

institute: University of Malaya

hyb_protocol: According to the manufacturer's website

scan_protocol: According to the manufacturer's website

data_processing: The data analysis was performed using nSolver™ Analysis Software and Advanced Analysis Module (NanoString Technologies, USA).

source_name: Clear cell renal cell carcinoma

extract_protocol: Total RNA was extracted from 5µm formalin-fixed paraffin-embedded (FFPE) tissue using the Maxwell® 16 LEV RNA FFPE Purification Kit (Promega, USA) according to the manufacturer’s protocol.

tag: gender

value: Male

value: Adjacent normal kidney tissue


title: S4

value: Sarcomatoid component of renal cell carcinoma


title: C4

value: Clear cell component of renal cell carcinoma


title: S3


title: C3


title: day 16 conceptus-derived extracellular vesicles, female in vivo conceptus, rep 3

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

institute: University of Leeds

description:
A6568
readCounts-EVs_miRNAs.tsv

library_source: other

data_processing:
Endometrial poyA-enriched RNA-seq data: The adapter sequences of the samples >200nt were trimmed using Cutadapt and quality filtering and trimming were performed by PRINSEQ. We use STAR to align the reads, featureCounts to quantify the reads and DESeq2 to identify the differentially-expressed-genes.
Analysis of the miRNA cargo of EVs: For the <200nt samples, adapter trimming and quality trimming and filtering were performed using Cutadapt. We used Bowtie to align the reads, featureCounts to quantify the reads and DESeq2 to identify the differentially-expressed-genes.  The differentially expressed miRNAs were filtered for a fold change >1 or <-1 and a p-adjusted value <0.05.
Assembly: Ensembl Bos_taurus.ARS-UCD1.2 release 104
Supplementary files format and content: tab-delimited files contain raw read counts for each sample

molecule: other

organism: Bos indicus

extract_protocol:
Endometrium tissue total RNA was isolated using the Qiagen miRNeasy Mini Kit and Extracellular vesicle RNA isolated using the Qiagen miRNeasy Micro Kit, both with on-column Qiagen DNAse treatment, and separated into >200nt and <200nt as per the manufacturers protocol.
Endometrial RNA libraries were constructed using the Novogene NGS RNA library Prep Set. mRNA was purified ysing poly-T oligo-attached beads, fragmented, first strand cDNA synthesised with random hexamers, and second strand cDNA using dUTP. Extracellular vesicle RNA libraries were constructed using NUGEN Ovation SoLo RNA-Seq Systems. Adapters were ligated, then first strad cDNA synthesised after hybridisation with RT primers. Double-stranded cDNA was generated via PCR. Libraries were purified and size selected for 18-40bp.
Endometrial RNA- RNA-seq, Extracellular vesicle RNA- miRNA-seq

treatment_protocol: Endometrium was lysed using a TissueRupter from frozen in Qiazol prior to RNA extraction. Extracellular vesicles were pelleted and re-suspended in Qiazol prior to RNA extraction.

value: primary

value: day 16 conceptus-derived


title: C2


title: N3


title: S2


title: S1


title: N2


title: C1


title: day 16 conceptus-derived extracellular vesicles, female nuclear transfer conceptus, rep 5

description:
A6327
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male nuclear transfer conceptus, rep 7

description:
A6305
readCounts-EVs_miRNAs.tsv


title: N1


title: day 16 conceptus-derived extracellular vesicles, female IVF conceptus, rep 7

description:
A6256
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male in vivo conceptus, rep 2

description:
A6316
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, female IVF conceptus, rep 6

description:
A6242
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, female IVF conceptus, rep 5

description:
A6238
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, female nuclear transfer conceptus, rep 4

description:
A6234
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male nuclear transfer conceptus, rep 6

description:
A6182
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male IVF conceptus, rep 3

description:
A6186
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, female nuclear transfer conceptus, rep 3

description:
A6165
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, female IVF conceptus, rep 4

description:
A6132
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, female IVF conceptus, rep 3

description:
A6093
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male nuclear transfer conceptus, rep 5

description:
A6079
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male in vivo conceptus, rep 1

description:
A6100
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male IVF conceptus, rep 2

description:
A6086
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male in vivo conceptus, rep 3

description:
A6507
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, female IVF conceptus, rep 2

description:
A6059
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male nuclear transfer conceptus, rep 4

description:
A5998
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male nuclear transfer conceptus, rep 3

description:
A5781
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male IVF conceptus, rep 1

description:
A6046
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male nuclear transfer conceptus, rep 2

description:
A5776
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, male nuclear transfer conceptus, rep 1

description:
A5692
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, female nuclear transfer conceptus, rep 1

description:
A5328
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, female in vivo conceptus, rep 2

description:
A4705
readCounts-EVs_miRNAs.tsv


title: day 16 conceptus-derived extracellular vesicles, female IVF conceptus, rep 1

description:
A5154
readCounts-EVs_miRNAs.tsv


title: day 16 pregnant endometrium, male in vivo conceptus, rep 3

description:
H3_6507
readCounts-endometrial-RNAseq.tsv

source_name: endometrium

value: endometrium

value: ipsilateral intercaruncular endometrium

value: pregnant day 16


title: day 16 pregnant endometrium, male nuclear transfer conceptus, rep 5

description:
H1_6305
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, male nuclear transfer conceptus, rep 4

description:
G2_5776
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female IVF conceptus, rep 7

description:
G1_6242
readCounts-endometrial-RNAseq.tsv


title: day 16 conceptus-derived extracellular vesicles, female in vivo conceptus, rep 1

description:
A3397
readCounts-EVs_miRNAs.tsv


title: day 16 pregnant endometrium, male nuclear transfer conceptus, rep 6

description:
H2_5781
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, male in vivo conceptus, rep 2

description:
G3_6316
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female nuclear transfer conceptus, rep 5

description:
F1_6234
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, male nuclear transfer conceptus, rep 3

description:
F2_5692
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female nuclear transfer conceptus, rep 4

description:
E3_6165
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female nuclear transfer conceptus, rep 3

description:
E2_5328
readCounts-endometrial-RNAseq.tsv


title: qKO 2, biol rep 1, adult aorta, 3 aortas pooled

description: Library name: quantseq_sample_7


title: day 16 pregnant endometrium, male nuclear transfer conceptus, rep 1

description:
D1_6079
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female IVF conceptus, rep 6

description:
D3_6256
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, male nuclear transfer conceptus, rep 2

description:
E1_6182
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female IVF conceptus, rep 4

description:
C3_6238
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, male IVF conceptus, rep 3

description:
C4_6186
readCounts-endometrial-RNAseq.tsv


title: day 16 conceptus-derived extracellular vesicles, female nuclear transfer conceptus, rep 2

description:
A5957
readCounts-EVs_miRNAs.tsv


title: day 16 pregnant endometrium, female in vivo conceptus, rep 3

description:
C2_4705
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female IVF conceptus, rep 2

description:
B4_6132
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female IVF conceptus, rep 1

description:
B3_6093
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female IVF conceptus, rep 5

description:
D2_5154
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female in vivo conceptus, rep 2

description:
B2_3397
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female IVF conceptus, rep 3

description:
C1_6059
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, male in vivo conceptus, rep 1

description:
F3_6100
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female in vivo conceptus, rep 1

description:
A4_6568
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, male IVF conceptus, rep 1

description:
A3_6086
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, male IVF conceptus, rep 2

description:
B1_6046
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female nuclear transfer conceptus, rep 2

description:
A2_6327
readCounts-endometrial-RNAseq.tsv


title: day 16 pregnant endometrium, female nuclear transfer conceptus, rep 1

description:
A1_5957
readCounts-endometrial-RNAseq.tsv


title: MUT1, 23

city: Tampa

first: Zhiming

last: Ouyang

state: FL

address: 12901 Bruce B Downs Blvd

department: Molecular Medicine

institute: University of South Florida

data_processing:
Adapter sequences and poor-quality nucleotides were removed using Trimmomatic v.0.36.
Trimmed reads were mapped to the B. burgdoferi B31 genome using Bowtie2 v.2.2.6.,
FeatureCounts Subread package v.1.5.2 was used to identify unique gene hit counts.
Differential gene expression analysis was performed using DESeq2
Assembly: (NCBI) Genome Assembly ASM868v2
Supplementary files format and content: Two-column text file (WT, MUT) including raw count.

organism: Borreliella burgdorferi

extract_protocol:
RNA was isolated from Cell Culture of B. burgdorferi using Trizol and purified with RNeasy Mini Kit (Qiagen). Samples were treated with TURBO DNase (Thermo Fisher Scientific) to remove DNA contaminants and rRNA depletion was performed using QIAGEN FastSelect–5S/16S/23S Kit
RNA sequencing libraries were prepared by using NEB Next Ultra II RNA Library Preparation Kit for Illumina

value: Bacterial cell

value: badR Mutant


title: WT3, 23

value: WT


title: MUT2, 23


title: WT2, 23


title: MUT3, 37, Stationary

value: 37, Stationary


title: MUT2, 37, Stationary


title: MUT1, 37, Stationary


title: WT1, 23


title: WT1, 37, Stationary


title: WT2, 37, Stationary


title: MUT1, 37, Mid-log

value: 37, Mid-log


title: MUT3, 37, Mid-log


title: MUT2, 37, Mid-log


title: MUT3, 23


title: ID28, SOMA-Cells, Female, Young

city: Geelong

first: Séverine

last: Lamon

state: VIC

address: 1 Gheringhap St

department: School of Exercise and Nutrition Sciences

country: Australia

institute: Deakin University

description:
Library name: SOMA-Cells
Column name in raw_counts.csv: SOMA-Cells

data_processing:
Adapter trimming via Skewer (phred > 10)
Read alignment via Kallisto
Quality control monitoring via FastQC and MultiQC
Assembly: human transcriptome from Ensembl: GRCh38, release-111
Supplementary files format and content: csv text file includes raw counts for each sample

source_name: vastus lateralis muscle

extract_protocol:
TruSeq Stranded Total RNA Library Prep Gold Kit
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol and sequenced with 150-bp paired-end reads

value: vastus lateralis muscle

tag: Sex

value: Female

value: Young


title: WT1, 37, Mid-log


title: MCF7 cell, treated by DMSO, 8h

city: Singapore

first: Fuying

last: Dao

address: 50 Nanyang Avenue

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
Library name: Sample1
MCF7 cells treated with DMSO (control group) for Hi-C analysis

data_processing:
Fastq files from Illumina sequencing were first trimmed with trimmomatic (PMID: 24695404) [settings: ILLUMINACLIP:Adapters:2:30:10:8:true \ HEADCROP:5 \ SLIDINGWINDOW:4:10 \ LEADING:3 \ TRAILING:3 \ MINLEN:30 ]. Reads were aligned on hg19 genome using bwa (PMID: 20080505) default settings. Pairtools (PMID: 38809952) was used to prepare the paired interaction using the parse [settings: --min-mapq 10 --walks-policy 5unique –max-inter-align-gap 30], sort [settings: default], dedup [settings: --mark-dups] and split [settings: default] followed by samtools (PMID: 19505943) indexing and sorting of resulting .bam files and pairix (PMID: 34978573) indexing of resulting .pairs files. Finally, contact matrices were generated using cooler (PMID: 31290943) using the cload [settings: pairix] and zoomify [settings: --balance] commands.
Assembly: hg19 (GRCh37.p13)
Supplementary files format and content: Processed data are cool format interaction matrices, ICE normalized

source_name: Breast

growth_protocol: MCF7 cells were grown in DMEM+10%FBS medium before and during treatment

extract_protocol:
Hi-C was performed following Dovetails TopoLink V2 kit and protocol.
Library preparation was performed following Dovetails TopoLink V2 kit and protocol

treatment_protocol: Treatment lasted for 8h, at doses indicated above, based on the cell viability effect of each compounds

value: Breast

value: Epithelial

value: Wild type for BRCA1/BRCA2

value: DMSO

tag: batch

value: Batch 1, Batch 2


title: ID29, TOHO-Tissue, Male, Young

description:
Library name: TOHO-Tissue
Column name in raw_counts.csv: TOHO-Tissue

value: Male


title: ID29, TOHO-Cells, Male, Young

description:
Library name: TOHO-Cells
Column name in raw_counts.csv: TOHO-Cells


title: ID30, VKYT-Tissue, Male, Young

description:
Library name: VKYT-TIssue
Column name in raw_counts.csv: VKYT-Tissue


title: MCF7 cell, treated by 25 uM JQ1, 8h

description:
Library name: Sample4
MCF7 cells treated with JQ1 (25 µM, 8 hours) for Hi-C analysis


title: MCF7 cell, treated by 25uM Radezolid, 8h

description:
Library name: Sample3
MCF7 cells treated with Radezolid (25 µM, 8 hours) for Hi-C analysis

value: Radezolid


title: ID27, RUCH-Cells, Female, Young

description:
Library name: RUCH-Cells
Column name in raw_counts.csv: RUCH-Cells


title: ID26, ROWI-Tissue, Male, Young

description:
Library name: ROWI-TIssue
Column name in raw_counts.csv: ROWI-Tissue


title: MCF7 cell, treated by 25uM Eperezolid, 8h

description:
Library name: Sample2
MCF7 cells treated with Eperezolid (25 µM, 8 hours) for Hi-C analysis

value: Eperezolid


title: WT2, 37, Mid-log


title: ID28, SOMA-Tissue, Female, Young

description:
Library name: SOMA-Tissue
Column name in raw_counts.csv: SOMA-Tissue


title: ID27, RUCH-Tissue, Female, Young

description:
Library name: RUCH-Tissue
Column name in raw_counts.csv: RUCH-Tissue


title: ID25, RAIM-Tissue, Male, Old

description:
Library name: RAIM-Tissue
Column name in raw_counts.csv: RAIM-Tissue

value: Old


title: ID25, RAIM-Cells, Male, Old

description:
Library name: RAIM-Cells
Column name in raw_counts.csv: RAIM-Cells


title: ID23, PHDE-Tissue, Male, Old

description:
Library name: PHDE-Tissue
Column name in raw_counts.csv: PHDE-Tissue


title: ID24, QUVU-Tissue, Male, Young

description:
Library name: QUVU-TIssue
Column name in raw_counts.csv: QUVU-Tissue


title: ID22, PEST-Tissue, Male, Old

description:
Library name: PEST-TIssue
Column name in raw_counts.csv: PEST-Tissue


title: ID23, PHDE-Cells, Male, Old

description:
Library name: PHDE-Cells
Column name in raw_counts.csv: PHDE-Cells


title: WT3, 37, Stationary

value: Bacterial cell


title: ID22, PEST-Cells, Male, Old

description:
Library name: PEST-Cells
Column name in raw_counts.csv: PEST-Cells


title: ID21, PEBU-Cells, Male, Old

description:
Library name: PEBU-Cells
Column name in raw_counts.csv: PEBU-Cells


title: ID21, PEBU-Tissue, Male, Old

description:
Library name: PEBU-TIssue
Column name in raw_counts.csv: PEBU-Tissue


title: ID24, QUVU-Cells, Male, Young

description:
Library name: QUVU-Cells
Column name in raw_counts.csv: QUVU-Cells


title: WT3, 37, Mid-log


title: ID30, VKYT-Cells, Male, Young

description:
Library name: VKYT-Cells
Column name in raw_counts.csv: VKYT-Cells


title: ID26, ROWI-Cells, Male, Young

description:
Library name: ROWI-Cells
Column name in raw_counts.csv: ROWI-Cells


title: ID20, PEBE-Tissue, Male, Old

description:
Library name: PEBE-TIssue
Column name in raw_counts.csv: PEBE-Tissue


title: ID20, PEBE-Cells, Male, Old

description:
Library name: PEBE-Cells
Column name in raw_counts.csv: PEBE-Cells


title: ID19, NIVI-Tissue, Male, Young

description:
Library name: NIVI-Tissue
Column name in raw_counts.csv: NIVI-Tissue


title: ID15, MEEM-Tissue, Female, Young

description:
Library name: MEEM-TIssue
Column name in raw_counts.csv: MEEM-Tissue


title: ID19, NIVI-Cells, Male, Young

description:
Library name: NIVI-Cells
Column name in raw_counts.csv: NIVI-Cells


title: ID17, NAWO-Cells, Female, Young

description:
Library name: NAWO-Cells
Column name in raw_counts.csv: NAWO-Cells


title: ID18, NICR-Cells, Male, Old

description:
Library name: NICR-Cells
Column name in raw_counts.csv: NICR-Cells


title: ID16, MINI-Cells, Male, Old

description:
Library name: MINI-Cells
Column name in raw_counts.csv: MINI-Cells


title: ID14, MECA-Tissue, Female, Young

description:
Library name: MECA-Tissue
Column name in raw_counts.csv: MECA-Tissue


title: ID17, NAWO-Tissue, Female, Young

description:
Library name: NAWO-TIssue
Column name in raw_counts.csv: NAWO-Tissue


title: ID15, MEEM-Cells, Female, Young

description:
Library name: MEEM-Cells
Column name in raw_counts.csv: MEEM-Cells


title: ID12, JUGR-Cells, Female, Young

description:
Library name: JUGR-Cells
Column name in raw_counts.csv: JUGR-Cells


title: ID11, HECH-Tissue, Female, Young

description:
Library name: HECH-TIssue
Column name in raw_counts.csv: HECH-Tissue


title: MCF7 cell, treated by 25uM Trihexyphenidyl, 8h

description:
Library name: Sample5
MCF7 cells treated with Trihexyphenidyl (25 µM, 8 hours) for Hi-C analysis

value: Trihexyphenidyl


title: ID11, HECH-Cells, Female, Young

description:
Library name: HECH-Cells
Column name in raw_counts.csv: HECH-Cells


title: ID12, JUGR-Tissue, Female, Young

description:
Library name: JUGR-Tissue
Column name in raw_counts.csv: JUGR-Tissue


title: ID9, GELI-Tissue, Male, Old

description:
Library name: GELI-Tissue
Column name in raw_counts.csv: GELI-Tissue


title: ID10, HEBA-Cells, Female, Young

description:
Library name: HEBA-Cells
Column name in raw_counts.csv: HEBA-Cells


title: ID9, GELI-Cells, Male, Old

description:
Library name: GELI-Cells
Column name in raw_counts.csv: GELI-Cells


title: ID8, FLCO-Tissue, Male, Young

description:
Library name: FLCO-TIssue
Column name in raw_counts.csv: FLCO-Tissue


title: ID10, HEBA-Tissue, Female, Young

description:
Library name: HEBA-Tissue
Column name in raw_counts.csv: HEBA-Tissue


title: ID8, FLCO-Cells, Male, Young

description:
Library name: FLCO-Cells
Column name in raw_counts.csv: FLCO-Cells


title: ID13, KAVA-Tissue, Male, Young

description:
Library name: KAVA-Tissue
Column name in raw_counts.csv: KAVA-Tissue


title: ID7, DOHU-Tissue, Male, Old

description:
Library name: DOHU-Tissue
Column name in raw_counts.csv: DOHU-Tissue


title: ID7, DOHU-Cells, Male, Old

description:
Library name: DOHU-Cells
Column name in raw_counts.csv: DOHU-Cells


title: ID18, NICR-Tissue, Male, Old

description:
Library name: NICR-Tissue
Column name in raw_counts.csv: NICR-Tissue


title: ID16, MINI-Tissue, Male, Old

description:
Library name: MINI-TIssue
Column name in raw_counts.csv: MINI-Tissue


title: ID6, CICA-Tissue, Female, Young

description:
Library name: CICA-Tissue
Column name in raw_counts.csv: CICA-Tissue


title: ID6, CICA-Cells, Female, Young

description:
Library name: CICA-Cells
Column name in raw_counts.csv: CICA-Cells


title: ID14, MECA-Cells, Female, Young

description:
Library name: MECA-Cells
Column name in raw_counts.csv: MECA-Cells


title: ID5, CHVE-Tissue, Male, Old

description:
Library name: CHVE-Tissue
Column name in raw_counts.csv: CHVE-Tissue


title: ID13, KAVA-Cells, Male, Young

description:
Library name: KAVA-Cells
Column name in raw_counts.csv: KAVA-Cells


title: ID5, CHVE-Cells, Male, Old

description:
Library name: CHVE-Cells
Column name in raw_counts.csv: CHVE-Cells


title: ID3, ANLE-Tissue, Female, Young

description:
Library name: ANLE-TIssue
Column name in raw_counts.csv: ANLE-Tissue


title: ID4, CHLI-Cells, Male, Young

description:
Library name: CHLI-Cells
Column name in raw_counts.csv: CHLI-Cells


title: ID2, ANKA-Tissue, Male, Young

description:
Library name: ANKA-Tissue
Column name in raw_counts.csv: ANKA-Tissue


title: ID2, ANKA-Cells, Male, Young

description:
Library name: ANKA-Cells
Column name in raw_counts.csv: ANKA-Cells


title: ID3, ANLE-Cells, Female, Young

description:
Library name: ANLE-Cells
Column name in raw_counts.csv: ANLE-Cells


title: ID1, ANER-Cells, Male, Young

description:
Library name: ANER-Cells
Column name in raw_counts.csv: ANER-Cells


title: Figure 3, Donor 26, CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 2

city: St. Louis

first: Nathan

last: Singh

address: 660 S Euclid Ave

institute: Washington University School of Medicine in St Louis

description:
Library name: sample 61
Column name in all.gene_counts.tsv: sample.bbs_2

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04
Assembly: figure 2, hg38 (GRCh38.76). figure 3, hg38 (GRCh38.101)
Supplementary files format and content: tab separated value file that contains the raw gene counts for each sample

source_name: Peripheral blood mononuclear cells

growth_protocol: Primary Human T cells  were grown in RPMI media with 10% FBS, 1% Pen/Strep, 1% HEPES, 1% L-glutamine and 10ng/mL IL7+IL15 in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested from 1 million CAR positive Primary T cells using Quick-RNA™ Microprep Kit” from zymo research. 10ng of total RNA was used for creation of sequencing libraries.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Cells were stimulated on CD3/CD28 dynabeads at a ratio of 3 beads : 1 T cell. The following day, two different lentiviral vectors encoding CAR or BACH2 were co-transduced into T cells. Beads were removed on day 6 after bead stimulation and cells were expanded for 8 more days prior to collection for RNA purification.

value: Peripheral blood mononuclear cells

value: primary human T cells

value: WT

value: CD22-targeted-4-1BBs-CD3z CAR