title: DNA sequencing from AML patient UD10 after Relapse


title: Kidney_day7_scATAC

status: Public on Jul 11 2025

type: SRA

city: Aachen

first: Mingbo

last: Cheng

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: Uniklinik RWTH Aachen

description:
Library name: Sample 2
10X multiome

library_source: genomic single cell

data_processing:
The Cell Ranger ARC Software Suite (version 1.0.1) was used for processing sequencing information and single cell barcodes.
scATAC-seq fragments for each timepoint was merged, then macs2(version 2.2.7.1) was used to do peakcalling.
Seurat (version 3.2.3) was used to process snRNA-seq data and ArchR(version 1.0.2) was used to process snATAC-seq data
hg38
barcodes: barcodes present in input data
Assembly: fragments: a BED-like tabular file, where each line represents a unique ATAC-seq fragment captured by the assay and positions are 0-based. The columns are defined as following: chrom, chromStart, chromEnd, barcode and duplicateCount.
Supplementary files format and content: matrix: a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line.  The rest of the lines represent  nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to  the number of cut sites.
Supplementary files format and content: features: a bed file contains the gene expression.

molecule: genomic DNA

organism: Homo sapiens

source_name: Kidney organoid

extract_protocol: All protocols to generate 10X Single Cell Multiome ATAC + Gene Expression, including sample prep, library prep, instrument and sequencing settings, are available here: https://www.10xgenomics.com/products/single-cell-multiome-atac-plus-gene-expre

tag: tissue

value: Kidney organoid

tag: treatment

value: Day 7


title: NT_3

city: London

first: Simon

middle: J

last: Boulton

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

library_source: genomic

data_processing:
Raw data were trimmed, aligned to sgRNA sequences from the Brunello library (https://www.nature.com/articles/s41467-018-07901-8), and counted using the built-in count function of MaGeCK (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0554-4). The MaGeCK test command was used to compare sgRNA counts between indicated experimental conditions and to generate sgRNA ranking analyses.
Assembly: sgRNA sequences from the Brunello library (https://www.nature.com/articles/s41467-018-07901-8)
Supplementary files format and content: Tab separated counts per sgRNA per sample.
Library strategy: sgRNA amplicon-seq

source_name: blood cells

growth_protocol: eHAP iCas9 cells were grown in IMDM media + 10% Tet-free FBS + 1% penicillin/streptomycin. Knockout induction was achieved through Cas9 expression by addition of doxycycline.

extract_protocol:
At day 10 cells were collected (60 million cells per sample) for genomic DNA preps with PureLink Genomic DNA Mini Kit (Invitrogen; 16 columns per sample).
200ug gDNA (to maintain representation) was used for PCRs with Ex Taq polymerase (TaKaRa) to prepare sgRNA libraries following Broad Institute’s protocol with P5 mix of oligos and barcoded P7 oligos. Libraries (354 nt product) were gel purified with QIAquick Gel Extraction Kit (QIAGEN), followed by MinElute PCR Purification kit (QIAGEN) for buffer exchange.

treatment_protocol: Doxycycline added to the transduced cells was at final concentration of 1µg/ml, and was kept on cells for 10 days (cells were passaged every 2-3 days).

value: blood cells

tag: cell line

value: eHAP iCas9

tag: cell type

value: myeloid cells (CML)

tag: genotype

value: near diploid, derived from male CML patient

value: Cas9 expression with doxycycline to induce KO (4 days)


title: 4-week HP Akap11 +/- Bulk RNA-seq Sample 3

city: Cambridge

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

country: USA

institute: Broad Institute

library_source: transcriptomic

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Akap11 mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.

value: Hippocampus

tag: age


title: 4-week HP Akap11 +/- Bulk RNA-seq Sample 2


title: DNA sequencing from AML patient AML2 at initial diagnosis

city: Florence

first: Marta

last: Baragli

address: Via di S. Marta 3

department: Department of Information Engineering

country: Italy

institute: University of Florence

data_processing:
Sequencing reads were basecalled with Guppy and aligned to the GRCh37 reference genome version with minimap2. Methylation calling has been performed with Nanopolish.
Assembly: GRCh37
Supplementary files format and content: We provide tables reporting methylation frequency and entropy for each sample. Each file contains 6 columns indicating respectively: chromosome, position, methylation entropy, number of reads supporting methylation entropy value, methylaiton frequency,  number of reads supporting methylation frequency value

source_name: Bone Marrow

extract_protocol:
AML: DNA was extracted from cryopreserved bone marrow (BM) mononuclear cells using QIAGEN’s AllPrep DNA/RNA kit.
AML: DNA library preparation was performed with Sequencing Kit SQK-LSK109.

value: Bone Marrow


title: NT_2


title: Kidney_day7_scRNA

description:
Library name: Sample 1
10X multiome

library_source: transcriptomic single cell

molecule: nuclear RNA


title: DNA sequencing from AML patient AML2 after Relapse


title: NT_1


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day18

city: New York

first: Marko

last: Jovanovic

state: NY

address: 1212 Amsterdam Avenue

department: Biological Sciences

institute: Columbia University

data_processing:
Reads were pre-processed using cutadapt (v1.17) to remove the first three nucleotides and the poly-A tail (--cut 3 -a "A{15}" -j 8 --nextseq-trim=20 --minimum-length 17). Bowtie (v1.2.2) was used to align reads to the human 45S pre-rRNA (NR_146144.1, downloaded from GenBank) using the -v 0 and --un flags to remove rRNA reads from the analysis. Reads were aligned to the genome using STAR (--runMode alignReads --outSAMtype BAM SortedByCoordinate –alignSJoverhangMin 400 –outFilterMismatchNmax 0 --outFilterMatchNmin 15 --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM). Post-processing was performed using tools from the plastid package. The plastid P-site program was used to estimate the location of ribosomal P-sites for each read length in each library (--min_counts 50 --require_upstream --min_length 17 --max_length 35). P offsets were generally in the range of 6-13, and some manual corrections were necessary in cases where the P-site program identified an incorrect peak. All manual corrections were done blinded to library identity. A default of 13 was used in cases where the P-site could not be clearly determined. For all subsequent analyses, reads were reduced to single counts offset from the 5’ end of the read by the value computed by the P-site program.
Read counting was performed using genomic alignments and a custom Python script built using tools from the plastid package. Briefly, for each gene, all associated transcripts were combined to create a single “meta-transcript”. Any genomic position mapping to the CDS of any annotated transcript was assigned to the CDS of the meta-transcript. Conversely, the 5’- and 3’UTRs of the meta-transcript were comprised of genomic positions assigned to the 5’/3’UTR of at least one transcript but never to a CDS. Ribo-seq reads (reduced to a single count with a 5’ offset as defined above) in each defined meta region (5’UTR, CDS, 3’UTR) were counted. Count matrices were read into R and CDS counts were propagated forward into DESeq2 using the DESeqDataSetFromMatrix function
CDS counts from genome-aligned libraries were normalized using DESeq2’s median of ratios method.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample
Library strategy: Ribo-seq

growth_protocol: RUES2 human embryonic stem cells  were maintained and expanded in Matrigel-coated plates with mTeSR Plus medium (StemCell Technologies).

extract_protocol:
Homogenates were clarified by centrifugation at 13,000 x g for 10 min at 4°C. Clarified cell lysates were treated with E. coli RNase I (Ambion) and incubated for 30 min at room temperature. Ribosome-protected fragments were pelleted in 50% sucrose solution using an Ultracentrifuge (Beckman, with TLA-100.3 rotor) at 70,000 rpm for 3.5 hours at 4°C and isolated by Trizol extraction.
Ribosome-protected fragments in ~28-34 nucleotide length were size-selected by gel electrophoresis and later dephosphorylated by T4 Polynucleotide kinase (NEB). Ligation-free ribosome profiling libraries were generated from dephosphorylated footprints using the SMARTer small RNA-Seq Library Preparation Kit (Clontech) according to the manufacturer’s instructions. rRNA depletion was performed by using the oligo pool annealing to rRNAs. The rRNA-depleted libraries were amplified by PCR. The libraries were quantified using a Qubit dsDNA HS kit (Thermo Fisher Scientific), and the library quality was assessed by a Bioanalyzer (Agilent).

treatment_protocol: Cells were grown confluent (90%) before starting the differentiation. On Day 0 (start of differentiation), hESCs were treated with 1ml/well (6-well plates) Collagenase B (1 mg/ml) and DNase (10 ul/ml) for 30 min to form embryoid bodies (EBs). Collected cells were centrifuged at 300 relative centrifugal force (rcf) for 3 min and resuspended by gentle pipetting in the CM differentiation medium consisting of RPMI 1640 with ascorbic acid (50 ug/ml), L-glutamine (2 mM/L), and monothioglycerol (MTG) (4x10-4 M). Differentiation medium was also supplemented with BMP4 (2 ng/ml) and Rock Inhibitor (10 uM), and the EBs were cultured in low attachment 6-well plates (Corning) at 37°C in a humidified incubator with 5% CO2, 5% O2, and 90% N2. On Day 1, the medium was changed to the differentiation medium supplemented with BMP4 (20 ng/ml), Activin A (20 ng/ml), bFGF (5 ng/ml), and Rock Inhibitor (10 uM) for primitive streak/germ layer induction. On Day 3, the EBs were harvested and washed with DMEM to remove all residual cytokines, and the medium was changed to the differentiation medium supplemented with XAV (5 uM) and VEGF (5 ng/ml) to induce cardiac mesoderm. Retinoic acid (RA) (0.5 uM) was also added to the differentiation medium to generate atrial CMs. On Day 5, the medium was changed to the differentiation medium supplemented with VEGF (5ng/ml). On Day 7, the EBs were fed with the medium same as on Day 5. After Day 10, the medium was changed to the differentiation medium without any supplements every 3 to 4 days

value: human embryonic stem cells

value: WT

value: cardiomyocyte differentiation

tag: time


title: 6 month (6mo) Down syndrome, biological rep 3

type: RNA

city: Boston

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

description: Trisomic

hyb_protocol: A total of 500 genes were selected and assigned a 20-bit binary barcode which was used for generating MERFISH probes. Slides were prepared as per Vizgen protocol, briefly, slides were washed with 1x PBS followed by Sample Prep Wash Buffer (Vizgen, PN 20300001). Slides were incubated in Formamide Wash Buffer (Vizgen, PN 20300002) for 30 min at 37°C, then gene panel mix was spread on the section and incubated for 42-46 hr at 37°C in a humidified incubator. Slides were then incubated two times in Formamide Wash Buffer for 30 min each at 47°C, and washed with sample prep wash buffer for at least 2 min. Sections were coated in gel embedding solution (0.05% w/v ammonium persulfate, 0.05% v/v N,N,N’,N'-tetramethylethylenediamine in Gel Embedding Premix (Vizgen, PN 20300004)) and incubated at RT for 1.5 hr, tissue was cleared in 1:100 proteinase K in Clearing Premix (Vizgen, PN 20300003) at 37°C overnight or for a maximum of 7 days to clear lipids and proteins that may contribute to auto-fluorescence background noise. Prior to imaging, sections were washed two times with Sample Prep Wash Buffer, incubated in DAPI and PolyT Staining Reagent (Vizgen, PN 20300021) for 15 min on a rocking platform, incubated in Formamide Wash Buffer for 10 min, and washed again with Sample Prep Wash Buffer.

scan_protocol: Imaging was performed on the MERSCOPE platform (Vizgen, Cat: 10000001) according to manufacturer instructions.

data_processing: Transcript barcodes were read and matched assigned to the correct gene. MERFISH images were segmented using Vizgen's post-processing tool and Cellpose v2. DAPI and PolyT signals were used to delinate the cell boundaries. Individual RNA molecules were assigned to a cell based on whether they were positioned within the marked boundary. Anatomical segmentation was performed using the MERSCOPE Visualizer software. Cells for MERFISH were processed using the Seurat V5 package in R v4.2.1.

label: Gene targeting probes

label_protocol: Single-cell spatial RNA imaging  was performed using a gene panel targeting 500 transcripts.

extract_protocol: Fresh frozen brain were cryo-sectioned at 10 μm thickness at -21°C, and mounted onto MERSCOPE beaded slides. Sections were allowed to refreeze, and then fixed for 15 minutes in 4% paraformaldehyde prepared in 1x PBS, followed by 3 washings with 1x PBS for 5 minutes each and stored in 70% ethanol overnight.

value: Brain section


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day12


title: dC-T, rep2

first: Xiaonan

last: Guan

address: 1150 St Nicholas Ave, 403

institute: Russ Berrie Medical Science Pavillion

data_processing:
library strategy: ChIP-BS-Seq
Adaptor sequences and low-quality reads were removed by Trim Galore.
Using Bismark, the high-quality reads were mapped to human GRCh38 version genome.
The methylation level in overlapped peak regions were called by methylpy.
CpG sites with at least 5 reads coverage were used to calculate the DNA methylation level in dCas9-Tet1/sgRNA-3 and dCas9-dTet1/sgRNA-3 samples.
Assembly: human GRCh38 version genome
Supplementary files format and content: tab-delimited text file including the mean DNA methylation level of each peak

source_name: human embryonic stem cells (hESC)

extract_protocol:
Anti-Cas9 ChIP experiment was performed and followed by BS conversion according to the Pico Methyl-Seq Library Prep Kit
Pico Methyl-Seq™ Library Prep Kit was used

value: human embryonic stem cells (hESC)

value: dC-T

tag: chip antibody

value: Anti-Cas9 ChIP


title: 6 month (6mo) Down syndrome, biological rep 2

description: Trisomic


title: FG_2


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day10


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day8


title: dC-dT, rep2

value: dC-dT


title: 6 month (6mo) Down syndrome, biological rep 1

description: Trisomic


title: Kidney_siRNA

description: 10X Xenium

data_processing:
Xenium data was processed by xenium (version 2.0.0.10)
Seurat (version 5.0.2) was used to process the spatial xenium data

source_name: kidney

extract_protocol: All protocols to generate 10X Xenium In Situ platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://www.10xgenomics.com/products/single-cell-multiome-atac-plus-gene-expre and https://www.10xgenomics.com/platforms/xenium

tag: condition

value: siRNA


title: Kidney_day19

description: 10X Xenium

value: day 19


title: dC-T, rep1


title: Kidney_scrambled

description: 10X Xenium

value: scrambled


title: 6 month (6mo) control, biological rep 3

description: Euploid

source_name: (C57BL/6JEiJ x C3Sn.BLiA-Pde6b+/DnJ)F1


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day6


title: dC-dT, rep1


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day4


title: dCpf1-CTCF

data_processing:
Trim Galore was used to remove adaptor and low-quality reads.
The high-quality reads were mapped to human GRCh38 version genome using Bowtie2 with default parameters.
To match sequencing depth, 7 million reads were randomly sampled from each library. Peaks were called by MACS2.
For dCas9-Tet1 with sgRNA-3 sample, input and dCas9-Tet1 with scrambled sgRNA were used as control separately to call peaks. Then the overlapped peaks were defined as binding sites for dCas9-Tet1 with sgRNA-3.  (dC-T_11+3_chip is the dCas9-Tet1 with sgRNA-3 sample; dC-T_11+3_input is the input sample; dC-T_11+sc_chip is the dCas9-Tet1 with scrambled sgRNA sample.)
Assembly: human GRCh38 version genome
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Briefly, cells were cross-linked by 1% formaldehyde in the medium for 10 min in room temperature, and then quenched by adding 0.125 M Glycine for 5 min. Collected cells were washed with PBS twice, and then re-suspended in 3.5 ml of sonication buffer. Sonication was performed for 10 cycles with 0.5 min pulse on and 1 min rest, and 24 watts in ice-water mixture. Then cell lysate was spun down with 14,000 x rpm for 10 min at 4 °C. 50 ul of supernatant was saved as input for gDNA. 10 ul of anti-Cas9 antibody (Active Motif) was added and incubate overnight at 4 °C. 50 ul protein G dynabeads was added into antibody-cell lysate mixture and incubate overnight at 4 °C. Then beads were washed with sonication buffer, sonication buffer with high salt (500 mM NaCl), LiCl wash buffer, and TE buffer. Bound protein-DNA complex was eluted from beads by incubation in a 65 °C oven for 15 min, and then reverse cross-linked under 65 °C over-night. The bound DNA was purified with Qiagen QIAquick PCR Purification Kit, and then subject to sequencing.
NEBNext® Ultra™ II DNA Library Prep Kit was used

value: derivative human cell line

value: dCpf1-CTCF edited HEK293T

value: anti-Cpf1-HA antibody


title: 6 month (6mo) control, biological rep 1

description: Euploid


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day3


title: Postnatal day 0 (P0) Down Syndrome, biological rep 3

description: Trisomic


title: dCpf1-CTCF-mock

value: HEK293T without dCpf1-CTCF editing


title: HypOA parental treatment / HypOA offspring treatment 4

city: Woods Hole

first: Christopher

last: Murray

state: Massachusetts

address: 266 Woods Hole Rd

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
Raw data files were trimmed of adaptor sequence/low-quality sequence using Trimmomatic (default parameters).
Trimmed reads were mapped to the M. menidia genome use the STAR alignment tool (v.2.6.1d)
Read count extraction was preformed using Htseq (v.0.11.1) and normalization were performed EdgeR (v.3.40.2).
Assembly: GRC.z10.90
Supplementary files format and content: Htseq

organism: Menidia menidia

source_name: Larval

growth_protocol: Silverside embryos were obtained from wild adults and reared at 20°C under ambient or hypoxic/acidified treatment. Upon hatching larvae were fed ad libitum ratios on newly hatched brine shrimp nauplii.

extract_protocol:
RNA was isolated from whole homogenized larvae using Qiagen RNeasy Mini extraction kit
cDNA libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®. cDNA libraries were sequenced on an NovaSeq 6000 platform (150 bp PE).

treatment_protocol: Silverside embryos and larvae were exposed to one of two conditions: ambient: (100% dissolved oxygen, 600 µatm pCO2) or hypoxic/acidified (35% dissolved oxygen, 2500 µatm pCO2) and sampled at 19 days post-fertilization (or 9 – 10 days post-hatch).

value: Larval

value: 19 days post-fertilization

value: whole animal

value: wild type


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day2

value: human embryonic stem cells

value: WT

value: cardiomyocyte differentiation


title: Kidney_day25

description: 10X Xenium

value: day 25


title: HypOA parental treatment / HypOA offspring treatment 3


title: dCpf1-CTCF-input


title: dC-dT_2+sc, chip

source_name: hESC

value: hESC

value: dCas9-dTet1 editing with scrambled sgRNA

value: anti-Cas9 antibody (Active Motif)


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day1


title: HypOA parental treatment / HypOA offspring treatment 2


title: Postnatal day 0 (P0) Down Syndrome, biological rep 2

description: Trisomic

value: Brain section


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day0


title: HypOA parental treatment / HypOA offspring treatment 6


title: Postnatal day 0 (P0) control, biological rep 3

description: Euploid


title: HypOA parental treatment / HypOA offspring treatment 1


title: HypOA parental treatment / control offspring treatment 6


title: dC-T_11+sc, chip

value: dCas9-Tet1 editing with scrambled sgRNA


title: dC-dT_2+3, chip

value: dCas9-dTet1 editing with sgRNA3


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day12


title: Postnatal day 0 (P0) control, biological rep 1

description: Euploid


title: Postnatal day 0 (P0) Down Syndrome, biological rep 1

description: Trisomic


title: dC-T_11+3, chip

value: dCas9-Tet1 editing with sgRNA3


title: HypOA parental treatment / HypOA offspring treatment 5


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day10


title: 6 month (6mo) control, biological rep 2

description: Euploid


title: HypOA parental treatment / control offspring treatment 4


title: PS15p_RNAP

city: Murcia

first: Carlos

last: Pérez-Arques

state: Murcia

address: Campus Universitario Espinardo, Facultad de Biología

department: Genética y Microbiología

country: Spain

institute: Universidad de Murcia

data_processing:
For alignment: bwa mem -t 36 -M $assembly $R1_reads $R2_reads
For broad peak calling: macs2 callpeak -t $antibody_bamfile -c $input_bamfile -g 37441900 -n $prefix --keep-dup all --extsize 200 --nomodel --broad
Assembly: PS15-- genome
Supplementary files format and content: XLS spreadsheet containing broad peaks

organism: Mucor circinelloides

source_name: mycelium

growth_protocol: Overnight, YPD broth cultures were processed for ChIP

extract_protocol:
Briefly, cultures were crosslinked, lysed, and chromatin sonicated throughout 35 cycles 30 s ON/OFF in a Bioruptor (Diogenode) to obtain 100-300 bp chromatin fragments. Sheared chromatin aliquots were stored as input DNA controls. ChIP-grade antibodies α-H3K9me2 (ab1220, Abcam) and α-RNA pol II (39497, Active Motif), as well as protein A or G magnetic beads accordingly, were utilized to immunoprecipitate chromatin-bound DNA. After washing and decrosslinking, DNA was purified by a phenol/chloroform-based extraction method
Libraries were prepared using Roche KAPA HyperPrep Kits and subjected to size selection ~200-500bp

treatment_protocol: Epimutants were treated with FK506 to maintain the epimutation

value: mycelium

value: wildtype

tag: antibody

value: α-RNA pol II (39497, Active Motif)


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day8


title: dC-T_11+sc, input

value: input


title: HypOA parental treatment / control offspring treatment 3

value: Larval

value: 19 days post-fertilization

value: whole animal


title: PS15p_K9me2

value: α-H3K9me2 (ab1220, Abcam)


title: dC-dT_2+3, input

value: human embryonic stem cells


title: PS15p_Input


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day18

value: WT

value: cardiomyocyte differentiation


title: Postnatal day 0 (P0) control, biological rep 2

description: Euploid


title: HypOA parental treatment / control offspring treatment 1

value: wild type


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day6


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day3


title: HypOA parental treatment / control offspring treatment 5


title: dC-T_11+3, input

value: hESC


title: hESC, dC-T, rep3

data_processing:
Adaptor sequences and low-quality reads were trimmed by Trim Galore.
Using hisat2, the high-quality reads were mapped to human GRCh38 version genome, tdTomato and GFP sequence.
The read counts were obtained using featureCounts.
Reads were normalized with DESeq2.
To avoid log20 as undefined value, the average number of reads for each gene was increased by one.
Assembly: human GRCh38 version genome
Supplementary files format and content: tab-delimited text file including normalized reads counts

molecule: polyA RNA

source_name: dCas9-Tet1 DNA methylation editing hESCs

extract_protocol:
Cells were harvested using Trizol followed by Direct-zol (Zymo Research), according to manufacturer’s instructions.
Illumina TruSeq stranded mRNA kit was used

value: dC-T


title: control parental treatment / HypOA offspring treatment 6


title: HypOA parental treatment / control offspring treatment 2


title: PS14WT_Input_RNAP


title: PS14WT_ChIP_RNAP


title: PS14WT_Input_K9me2


title: dC-dT_2+sc, input

value: dCas9-dTet1 editing with scrambled sgRNA


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day2


title: hESC, dC-T, rep1

value: dCas9-Tet1 DNA methylation editing hESCs


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day0


title: PS14E3_Input_RNAP

value: fkbA epimutant


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day18

data_processing:
RNA-seq reads were aligned to the genome using STAR. Unprocessed reads were fed to STAR using the --runMode alignReads --outSAMtype BAM SortedByCoordinate --outFilterType BySJout –outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField intronMotif and --outFilterMultimapNmax 10 flags.
Read counting was performed using genomic alignments and a custom Python script built using tools from the plastid package. Briefly, for each gene, all associated transcripts were combined to create a single “meta-transcript”. Any genomic position mapping to the CDS of any annotated transcript was assigned to the CDS of the meta-transcript. Conversely, the 5’- and 3’UTRs of the meta-transcript were comprised of genomic positions assigned to the 5’/3’UTR of at least one transcript but never to a CDS. RNA-seq reads (reduced to a single count at the 5’ end) were counted in the meta-CDS and for the full meta-transcript. Count matrices were read into R and CDS counts were propagated forward into DESeq2 using the DESeqDataSetFromMatrix function.
CDS counts from genome-aligned libraries were normalized using DESeq2’s median of ratios method.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

extract_protocol:
Homogenates were cleared by centrifugation at 13,000 x g for 10 min at 4°C. Total RNA was isolated from the collected supernatant by a QIAGEN RNeasy kit, and the quality of total RNA was checked by a Bioanalyzer (Agilent).
Ribosomal RNA was depleted by the NEBNext rRNA depletion kit (Human/Mouse/Rat) according to the manufacturer’s instructions. Strand-specific sequencing libraries were generated from rRNA-depleted total RNA samples by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions. The libraries were quantified using a Qubit dsDNA HS kit (Thermo Fisher Scientific), and the library quality was assessed by a Bioanalyzer (Agilent)


title: hESC, dC-dT, rep2

source_name: dCas9-dTet1 editing hESCs

value: dC-dT

value: dCas9-dTet1 editing hESCs


title: hESC, dC-T, rep2


title: control parental treatment / HypOA offspring treatment 5


title: control parental treatment / HypOA offspring treatment 4


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day1


title: PS14WT_ChIP_K9me2

value: mycelium

value: wildtype


title: hESC, dC-dT, rep3


title: control parental treatment / HypOA offspring treatment 3

value: Larval


title: PS14E3_Input_K9me2


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day12


title: AK_Riboseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day4


title: control parental treatment / HypOA offspring treatment 1

value: 19 days post-fertilization


title: PS14E3_ChIP_RNAP

value: α-RNA pol II (39497, Active Motif)


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day10


title: PS14E3_ChIP_K9me2

value: α-H3K9me2 (ab1220, Abcam)


title: control parental treatment / control offspring treatment 6

value: whole animal


title: hESC, dC-dT, rep1


title: WGBS_CC125, Chlamydomonas reinhardtii, DEA treatment

city: Shanghai

first: Fanchen

last: Wang

state: Shanghai

address: 1239 Siping Road

country: China

institute: Tongji University

description: Library name: CC125 DEA

data_processing:
The sequencing data derived from WGBS were trimmed and filtered using Trimmomatic[1] (v0.39), followed by using FastQC (v0.12.1). Clean reads were aligned to the reference sequence (C.reinhardtii CC_4532_707_v6.0) by used of Bismark (v0.24.2). Deduplication and methylation extraction were performed by used of deduplicate_bismark and bismark_methylation_extractor (both sub-tools in Bismark).
Assembly: C.reinhardtii CC_4532_707_v6.0 (JGI)
Supplementary files format and content: bedGraph files: tab-delimited text files include 5mC or 5gmC sites information and modification level for each Sample.

organism: Chlamydomonas reinhardtii

growth_protocol: The C. reinhardtii strains (CC125 and CC5325) were cultured mixotrophically in TAP medium on a rotary shaker at 25 °C, with a light intensity of 20 μmol photons m-2∙s-1.

extract_protocol:
Total DNA was isolated using the CTAB method.
The treated DNA was then for sequencing library preparation, following the manufacturer’s protocol (Vazyme). Briefly, DNA libraries were generated by 3' adapter ligation, extension, 5' adapter ligation and library amplification.

value: WT


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day8

value: human embryonic stem cells

value: cardiomyocyte differentiation


title: PS10E1_Input_RNAP


title: control parental treatment / control offspring treatment 5

value: wild type


title: WGBS_CC5325, Chlamydomonas reinhardtii, DEA treatment

description: Library name: CC5325 DEA


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day6


title: PS10E1_Input_K9me2


title: WGBS_CC125, Chlamydomonas reinhardtii, TET and bisulfite treatment

description: Library name: CC125 TET-BS


title: control parental treatment / control offspring treatment 3


title: PS10E1_ChIP_RNAP


title: WGBS_CC125, Chlamydomonas reinhardtii, bisulfite treatment

description: Library name: CC125 BS


title: control parental treatment / HypOA offspring treatment 2


title: PS10E1_ChIP_K9me2


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day2


title: WGBS_CC5325, Chlamydomonas reinhardtii, bisulfite treatment

description: Library name: CC5325 BS


title: E10p_RNAP


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day1


title: CC125, Chlamydomonas reinhardtii

description: Library name: CC125

data_processing:
The sequencing data derived RNA-seq were trimmed and filtered using Trimmomatic[1] (v0.39), followed by using FastQC (v0.12.1). Clean reads were aligned to the reference sequence (C.reinhardtii CC_4532_707_v6.0) by used of Hisat2 (v2.2.1). Transcript assembling and expression quantification were performed by used of StringTie (v2.2.3).
Assembly: C.reinhardtii CC_4532_707_v6.0 (JGI)
Supplementary files format and content: gtf files: tab-delimited text files include gene imformation and FPKM values for each Sample.

extract_protocol:
Total RNA was extracted using Trizol (Sangon) according to the manufacturer's instructions. rRNA was depleted from total RNA using the Ribo-off rRNA Depletion Kit (Vazyme).
RNA library construction was then performed using the VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme), following the manufacturer's instructions. The libraries were assessed using the Agilent 2100 Bioanalyzer and sequenced on the Illumina platform using 150 bp paired-end sequencing.


title: E10p_K9me2


title: 0022841__F

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description: Mice were vaccinated with ova-psDNA +VV, tissue sections were analyzed using the 10x Xenium platform

hyb_protocol: 10x Xenium in situ platform

scan_protocol: 10x Xenium in situ platform

data_processing: Downstream analysis including ova-psDNA quantification, gene expression normalization, cell clustering, and cell type annotation was performed using the Seurat R package.

source_name: lymph node

label_protocol: 10x Xenium in situ platform

extract_protocol: The popliteal lymph nodes were harvested either 21 or 42 days after immunization with 20mg of one or both ova-psDNA GeoMx tags and 1E4 pfu per foot of vaccinia virus. Lymph nodes were fixed for 24-hours in 10% phosphate buffered formalin, and then placed in 70% Ethanol until embedding. The lymph nodes were embedded in paraffin wax, 5 uM sections were cut using a microtome. 2 LNs were analyzed for each immunization group (21 day tag, 42 day tag, 21 and 42 day tag). Sections were placed on 10x Genomics Xenium slides, baked for 2 hours at 60C, followed by deparaffinization and decrosslinking. Oligonucleotide probe panels were used that included the 379 gene Xenium Mouse Tissue Atlassing Panel (1000627, 10x Genomics) and a custom panel (1000561, 10x Genomics) that included our antigen DNA barcode sequences and additional genes identified from our scRNA-seq data. Probes were hybridized to mRNA and spatial barcode targets in-situ and rolling circle amplification (RCA) was used to boost fluorescent signal according to the manufacturer’s instructions. Tissue was imaged using the Xenium Analyzer (PN-1000569). Regions were manually defined, one region per lymph node, before capture. Each lymph node was captured in technical duplicate (two 5 uM sections per lymph node on separate Xenium slides). DAPI nuclear staining was used to identify individual cells in the automated Xenium Analyzer cell segmentation pipeline. Additional cell segmentation reagents (e.g. membrane dyes) were not applied.

treatment_protocol: 6–8-week-old C57BL/6 (CD45.2) mice were immunized with 1E4 plaque-forming units (PFU) of Vaccinia Western Reserve and 20 µg of ova-psDNA in footpad.

tag: slide

value: section 2

tag: strain

value: lymph node

value: Immunized 21 days prior to harvest


title: E10p_Input

value: fkbA epimutant


title: CC5325, Chlamydomonas reinhardtii

description: Library name: CC5325


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day18


title: 0022841__E


title: Venus positive, mCherry negative cells Wildtype replicate 2

city: Marburg

first: Lukas

last: Herdt

address: Karl-von-Frisch-Straße 8

institute: Philipps-University Marburg

description: Library name: Exp_2

data_processing:
Sequencing data filtering was performed by using the SOAPnuke (v1.5.6) method and includes the removal of reads with adaptors, reads with N content >5% and low-quality reads.   Afterwards, fusion genes and differential splicing genes were detected by using Ericscript (0.5.5-5) and rMATS (v4.1.1), respectively.  Mapping was done with HISAT2 (v2.0.4) to the zebrafish reference genome GRCz11 and Bowtie2 (2.4.4) was used to align the processed reads to the gene set.  Gene expression levels were calculated by using RSEM (v1.2.28).  Transcriptomes were analyzed and compared using the DESeq2 method.
Assembly: GRCz11 zebrafish reference genome
Supplementary files format and content: Each processed data files are provided in .gz format. Processed data contain cleaned data of the raw data of each sample.

organism: Danio rerio

source_name: Head

extract_protocol:
At 48 hpf, heads of TgBAC(apln:Venus-PEST); Tg(kdrl:Hsa.HRAS-mCherry) larvae were disscected.
After dissection, the heads were washed in Ca2+/Mg2+-free Hank’s Balanced Salt Solution (HBSS,
Gibco, 14175-053) and cell dissociation was performed at 28,5°C for 30 min with TrypLE Express
(Gibco, 12604-013).  Cell dissociation was stopped by FBS addition and (Gibco, 12604-013)
and cells were centrifuged for 3 min at 3000 rpm. HBSS was removed and the cell pellet was
resuspended in ice-cold HBSS supplemented with 5% FBS and filtered through 40 µm filter caps.
Afterwards, the cells were centrifuged again for 3 min at 3000 rpm and resuspended in HBSS + 5% FBS.
Library construction was performed by BGI Genomics.

value: Head

tag: cell population

value: apln:Venus-PEST+, kdrl:mCherry-

value: mixed

value: Wildtype


title: control parental treatment / control offspring treatment 4

value: Larval


title: 0022841__D

value: Immunized 21 and 42 days prior to harvest


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day4


title: #34_RNAP

value: mycelium

value: α-RNA pol II (39497, Active Motif)


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day12


title: Venus positive, mCherry negative cells Wildtype replicate 1

description: Library name: Exp_1


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day3


title: #34_K9me2

value: α-H3K9me2 (ab1220, Abcam)


title: 0022841__C


title: control parental treatment / control offspring treatment 2

value: 19 days post-fertilization

value: whole animal


title: 0022841__B

value: Immunized 42 days prior to harvest


title: double negative cells Wildtype replicate 2

description: Library name: Ctrl_2

value: transgene negative cells


title: control parental treatment / control offspring treatment 1

value: wild type


title: WGBS_CC5325, Chlamydomonas reinhardtii, TET and bisulfite treatment

description: Library name: CC5325 TET-BS

value: WT


title: #34_Input


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day8

value: human embryonic stem cells

value: cardiomyocyte differentiation


title: double negative cells Wildtype replicate 1

description: Library name: Ctrl_1

value: Head


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day10


title: 0022841__A

value: section 2

value: lymph node


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day6


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep2_Day0


title: KPC-IMPACT-OVEREXPRESSION - GEX

city: Bethesda

first: Jonathan

last: Hernandez

state: Maryland

address: 10 Center Drive

department: Surgical Oncology Program

institute: National Cancer Institute

description: Library name: Impact - GEX

data_processing:
The demultiplexing, barcoded processing, gene counting and contig generation were made using the CellRanger software v9.0.0
Gene expression count matrices were processed in R(4.1.3) using the Seurat workflow
Assembly: Mouse GRCm39
Supplementary files format and content: Matrix files produced by CellRanger

source_name: liver

growth_protocol: KPC control and IMPACT-overexpressing cells were grown in DMEM/F12 with 10% FBS and 1X PS

extract_protocol:
Liver extirpated from a euthanized mouse was disrupted through a 0.75um cell strainer using the rubber side of a 3cc syringe into a 50ml tube with 5-10ml of RPMI media for each liver/lung. The media containing cells from the liver/lung was centrifuged at 30g for 3 minutes to remove the hepatocytes and tumor cells, and the supernatant was transferred to a new tube. Following centrifugation at 1500 rpm for 5 mins, the cell pellet was resuspended in 32% Percoll solution and again centrifuged at 140C, 2000 rpm with no brake for 15 mins. RBCs were removed by washing the cell pellet with 5 ml of ACK lysis buffer and centrifuging the samples at 1500 rpm for 5 mins. The cell pellet containing only immune cells was further washed 2X in complete RPMI media and used for surface and intracellular staining with specific antibodies.
Single-cell suspensions were prepared and cell counts and viability measurements were taken for each suspension sample using a fluorescent cell counter with dual viability dyes composed of propidium iodide and acridine orange (Luna-FL, Logos Biosystems). Sample concentrations were adjusted and loaded onto the 10x Genomics Chromium platform using the 10x Genomics 3’ v4 Gene Expression Assay, targeting roughly 20,000 cells per sample. Preparation of single-cell gene expression libraries was performed according to the vendor’s recommendations.

value: liver

value: mouse KPC

value: pancreatic tumor cells


title: 0022624__F

value: section 1

value: Immunized 21 days prior to harvest


title: KPC-IMPACT-OVEREXPRESSION - FBC

description: Library name: Impact - FBC


title: HA-treated wt rep3

city: Seoul

first: Sungmin

last: Hwang

address: Hwarang-ro 14-gil, Seongbuk-gu

department: Clean Energy Research Center

country: South Korea

institute: Korea Institute of Science and Technology

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
Raw reads which range from 20 to 31 million (mean of 24 million) from the paired-end (100-bp) sequencing were assessed by FastQC v.0.11.7 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) and miscellaneous information, such as adapter, poor-quality and short reads (< 10 bp), was removed.
The preprocessed reads were aligned to the reference genome of Y. lipolytica CLIB122 (GCF 000002525.2 ASM252v1) by STAR v.2.7.9a, followed by sorting and indexing by Samtools v.1.9.
Assembly: GCF_000002525.2 ASM252v1
Supplementary files format and content: The number of reads that mapped to each gene was counted by HTSeq v.0.11.0. DESeq2 v.1.32.0 was used to normalize the counts and identify differentially expressed genes (DEGs).

organism: Yarrowia lipolytica

source_name: HA-treated wt

growth_protocol: Three independent colonies of Y. lipolytica strains were grown in YPC medium with or without 1 g/L of hexanoic acid and harvested when cells reached at exponential phase (OD600nm, 1.2-1.5).

extract_protocol:
The RNA was extracted using TRI Reagent(Thermo Fisher Scientific, Waltham, MA, USA). RNA concentration and integrity were measured by a NanoDropTM 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), respectively.
The qualified total RNA was used for cDNA library construction with a NEBNext Ultra II Directional RNA-Seq kit (NEB, Ipswich, MA, USA) and sequenced under an Illumina NovaSeq 6000 platform by ebiogen Inc. (Seoul, Korea).

value: wt

value: 1 g/L hexanoic acid


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day4


title: 0022624__D

value: Immunized 21 and 42 days prior to harvest


title: 0022624__E


title: KPC-CONTROL - GEX

description: Library name: Control - GEX


title: HA-treated wt rep2


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day3


title: 0022624__C


title: HA-treated wt rep1


title: KPC-CONTROL - FBC

description: Library name: Control - FBC


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day2


title: untreated wt rep3

source_name: untreated wt

value: untreated


title: untreated wt rep2


title: 0022624__B

value: Immunized 42 days prior to harvest


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day1


title: untreated wt rep1


title: 0022624__A


title: AK_RNAseq_hESCtoCardiomyocyteDifferentiation_Rep1_Day0


title: heart, tricaine-treated,96hpf, rep2

city: Hangzhou

first: Shuo

last: Chen

address: Yuhang tang Road 866

department: school of medicine

institute: Zhejiang university

description: Library name: tricaine_4_2

data_processing:
Raw sequencing reads were preprocessed to remove adapters and filter low-quality reads. Clean sequencing reads were then mapped to  Danio rerio genome Ensembl Release 92 (GRCz11) using STAR with default parameters.
Gene quantification was carried out with RSEM
The gene expected count was applied to identify differential expression genes (DEGs), retaining only genes with counts per million (CPM) of 10 in at least two samples
DESeq2 was employed for differential expression analysis, and P-values were adjusted using BH correction
Assembly: GRCz11
Supplementary files format and content: csv files include gene expected counts for each sample

source_name: heart

extract_protocol:
Total RNA was extracted from 96 hpf Tg(myl7:mCherry) or tricaine-treated Tg(myl7:mCherry)  zebrafish hearts using TRIzol (Invitrogen) following the manufacturer’s instruction.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription,followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA(ssCir DNA) was formatted as the final library.

value: heart

tag: developmental stage

value: 96 hpf

value: tricaine


title: HA-treated mutant rep3

source_name: HA-treated mutant

value: {delta}pex10 harboring DGA1 overexpression plasmid


title: heart, tricaine-treated,96hpf, rep1

description: Library name: tricaine_4_1


title: U251MG exosomal RNA EF

city: Taoyuan

first: Hsieh-Fu

last: Tsai

state: Taiwan

address: E0408, no.259 Wenhua 1st road

country: Taiwan

institute: Chang Gung University

description: gene expression from exosomal RNA after dcEF stimulation in conditional medium after differential centrifugation

hyb_protocol: 130ng of total cellular RNA or exosomal RNA were hybridized in miRNA4.0 microarray. For 18hours at 48deg celsius with 60 rpm rotation in GeneChip hybridization oven 645 and washed by GeneChip Fluidics Station 450

scan_protocol: The scanning was done on all chips with a GeneChip scanner 3000 7G by standard setting .

data_processing: The CEL files were imported, and the miRNA QC tool was used to assess the quality of the array data using all the hybridization and spike-in controls. The data was normalized by the robust microarray analysis (RMA) and detection above background (DABG) with human-only probe sets using the TAC software.     A comparative analysis between dcEF-stimulated samples and control (sham) samples was carried out using log2 fold change (FC) > 1. A probeset is considered expressed if more than 50% samples have DABG values below the threshold of 0.05. Differential expression were statistically calculated using ebayes algorithm. A P value smaller than 0.05 indicate the probe set has fold changes rejecting the null hypothesis at 95% confidence level. Hierarchical clustering was conducted using complete linkage and Euclidean distance as the similarity measure for the differentially expressed miRNAs. Comparisons among samples from dcEF and sham (Ctrl) were conducted.

label: biotin

source_name: U251MG exosomal RNA EF

label_protocol: The duplicatd total RNAS were pooled and tagged with biotin using FlashTag HSR RNA labelling kit following the following the manufacturer's instruction. The RNA quality were evaluted using the TapeStation 4200 and nanodrop spectrophotometry

growth_protocol: The T98G and U251MG cells were cultured in MEMalpha medium with 10%FBS under 5% CO2 5%O2 environment. Primary astrocyte was cultured in DMEM medium with 10% FBS  under the same environment routinely. Before dcEF stimulation experiment, the cells were dissociated by trypLE and 5x10^5 cells were seeded and cultued in 5%CO2 5%O2 physioxia environment for 3 hours

extract_protocol: Cells were collected using a scraper. Exosomes were purified from the conditioned medium by differential centrifugation of 300xg 10min, 1000xg10min, 10000xg 45min, 235000xg 2hour.  The total cellular RNA and exosomal RNA were extracted using mirVana isolation kit following the total RNA extraction protocol. DPBS-washed cells and exosome pellets were lysed in 600uL of lysis buffer and mixed with 60ul homogenate additive and 660uL acid phenol chloroform. total RNAweere isolated by adding 0.1mg glycogen and 1.25(v/v) ethanol and binding through glass ifber filter in the mirVana kit. The total RNAs were eluted in nuclease-free water.

treatment_protocol: After sealing of the cells cultured at the bottom of the bioreactor, the top PMMA assembly was sealed on top of the chamber underneath 1X DPBS. The buffer was replaced by their medium with 5% exosome-depleted FBS and 100V/m dcEF was applied for 48 hours using a sourcemeter. The medium was perfused at 250ul/hr.

value: U251MG Glioblastoma (IFO50288, JCRB, Japan)

tag: fraction

value: Exosomal RNA

value: EF


title: HA-treated mutant rep2


title: U251MG exosomal RNA Sham

description: gene expression from exosomal RNA in conditional medium after differential centrifugation

source_name: U251MG exosomal RNA Sham

value: Ctrl


title: HA-treated mutant rep1


title: heart, 96hpf, rep2

description: Library name: ctrl_4_2


title: U251MG cellular RNA EF

description: gene expression from total cells RNA after dcEF stimulation

source_name: U251MG cellular RNA EF

value: Total RNA


title: Yy1KO_Rep1

city: Madison

first: Xuan

last: Pan

state: WI

address: 4470 Veterinary Medicine Building

institute: University of Wisconsin

description: Library name: Yy1KO_Rep1

data_processing:
ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline, version 2.2.3) was used to align sequencing reads to mouse genome (mm10), call peaks, and calculate signals.
Assembly: mm10
Supplementary files format and content: bigWig files of ATAC-seq signals
Supplementary files format and content: bigBed files of ATAC-seq peaks

source_name: E14.5 fetal liver Lin- cells

extract_protocol:
ATAC-seq libraries were prepared from 1×10⁵ cells using the Active Motif ATAC-seq Kit (cat#53150), following the manufacturer’s instructions. Briefly, cells were washed with 1 mL of ice-cold PBS and lysed with 100 μL of ice-cold ATAC Lysis Buffer. Cells were spun down at 500 x g for 10 minutes at 4°C, and cell pellets were incubated in 50 μL of Tagmentation Master Mix at 37°C for 30 min in a thermomixer set at 800 RPM. Cells were incubated with Tagmentation Master Mix, and tagmented DNA was purified via DNA columns.
Indexing was performed by 12-cycle PCR enrichment using Illumina UDP Indexes, followed by double-sided size selection (L=1.1; R=0.6) with Ampure beads (KAPA, Roche). Library size and quality were assessed on an Agilent 2100 Bioanalyzer with a High Sensitivity DNA Kit and quantified by qPCR. Equimolar libraries were sequenced as 100 bp paired-end reads (PE100) on a NovaSeq X (Illumina), generating ~70M fragments per sample.

value: E14.5 fetal liver Lin- cells

value: Yy1f/f Vav-Cre


title: Yy1KO_Rep2

description: Library name: Yy1KO_Rep2


title: Yy1WT_Rep2

description: Library name: Yy1WT_Rep2


title: untreated mutant rep2

source_name: untreated mutant


title: Yy1WT_Rep1

description: Library name: Yy1WT_Rep1


title: heart, 96hpf, rep1

description: Library name: ctrl_4_1


title: heart, depletion,120hpf, rep2

description: Library name: id2b_2

extract_protocol:
Total RNA was extracted from 120 hpf id2b+/+; Tg(myl7:mCherry) or id2b-/-; Tg(myl7:mCherry)  zebrafish hearts using TRIzol (Invitrogen) following the manufacturer’s instruction.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription,followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA(ssCir DNA) was formatted as the final library.

value: 120 hpf

value: id2b-/-; Tg(myl7:mCherry)


title: untreated mutant rep1


title: Control (PBS treated) Embryonic day 12.5 female biological rep 4

description: snATAC-seq

data_processing:
Raw reads were demultiplexed and mapped to the mm10 mouse reference genome using CellRanger pipeline for ATAC-seq v2.1 (10X Genomics). The resulting data from each sample was combined and analyzed using Signac pipeline (v1.13.0;) with default parameters.
Assembly: mm10
Supplementary files format and content: tab separated Index file, fragment file and peak matrix

source_name: Brain

extract_protocol:
Frozen tissue was thawed in 1 ml buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 0.15 mM spermine tetrahydrochloride, 0.5 mM spermidine trihydrochloride, 1 mM DTT). The samples were dounced in HB and 5% IGEPAL CA-630 (Sigma-Aldrich) and equal volume of 50% iodixanol was added. 1 ml 30% iodixanol was layered on top of 1 ml 40% iodixanol in a Corex tube (ThermoFisher). The sample was layered on top of the 30% iodixanol and ultra-centrifuged at 7600 × g for 18 min at 4C. Nuclei were collected from the interface of 30–40% iodixanol.
Nuclei were processed for scATAC-seq using 10X Genomics standard protocols.

value: Brain

value: Embryonic day 12.5

value: Brain cells

tag: Sex

value: Female


title: Control (PBS treated) Embryonic day 12.5 female biological rep 3

description: snATAC-seq


title: T98G exosomal RNA Sham

source_name: T98G exosomal RNA Sham

value: T98G Glioblastoma (CRL-1690, ATCC, USA)


title: Slide_seq_DS_3

description: Slide-seq

data_processing:
To reconstruct the spatial mapping of gene expression, the Curio Seeker bioinformatics pipeline was performed according to the manufacturer’s protocol using the GRCh37 genome reference from UCSC. Pixels with ≥ 100 logUMI, ≥ 5% mitochondrial genes, ≤ 200 unique features were excluded from the dataset. RCTD was used to decompose RNA sequencing mixtures into individual cell types using our human snRNA-seq dataset as a reference.
As the entirety of the tile was not covered by tissue, we adapted the CellSelector tool in Seurat v5 to select one sample per tile, remove additional off-target beads and demarcate the ventricular zone and cortex for each individual sample. Replicates were then normalized using SCTransform, integrated using Seurat v5, and scaled.
Assembly: hg38
Supplementary files format and content: Curio Seeker output files: MatchedBeadLocation.csv, barcodes.tsv, and genes.tsv
Library strategy: Slide-seq

source_name: Brain section

extract_protocol:
Six optimal cutting temperature compound-embedded (OCT) brain tissue (n = 3 DS, n = 3 euploid) were obtained for Slide-Seq. Cryosectioning was performed with consideration of anatomical landmarks, specifically targeting regions where the ventricular zone or cortical layers were discernible. OCT-embedded brain tissue was sectioned at a thickness of 10 μm at -21°C using the CM1950 Leica cryostat and immediately mounted onto a 10x10 mm Slide-seq chip. In cases where the tissue covered less than 50% of the tile, an additional serial section was placed adjacently on the same tile to increase coverage.
Libraries were sequenced on a Novaseq X flowcell 10B (100 cycles). Genome alignment, filtration, and normalization were performed using the Curio Seeker bioinformatic pipeline as per the manufacturer’s recommendations.

value: Brain section

value: 14 pcw

value: Down Syndrome


title: Control (PBS treated) Embryonic day 12.5 female biological rep 2

description: snATAC-seq


title: heart, 120hpf, rep2

description: Library name: wt_2

value: heart

value: id2b+/+; Tg(myl7:mCherry)


title: T98G cellular RNA EF

source_name: T98G cellular RNA EF

value: EF


title: heart, 120hpf, rep1

description: Library name: wt_1


title: Slide_seq_DS_2

description: Slide-seq

value: 16 pcw

value: Male


title: U251MG cellular RNA Sham

description: gene expression from total cells RNA

source_name: U251MG cellular RNA Sham

value: U251MG Glioblastoma (IFO50288, JCRB, Japan)

value: Total RNA

value: Ctrl


title: T98G cellular RNA Sham

description: gene expression from total cells RNA

source_name: T98G cellular RNA Sham


title: Slide_seq_DS_1

description: Slide-seq

value: 15 pcw


title: Astrocyte exosomal RNA EF

source_name: Astrocyte exosomal RNA EF

value: cryopreserve human Astrocyte (N7805, Thermo Fisher Scientific, USA)

value: primary cell

value: Exosomal RNA


title: Control (PBS treated) Embryonic day 12.5 female biological rep 1

description: snATAC-seq

value: Brain

value: Embryonic day 12.5

value: Brain cells

value: Female


title: y[1]w[1118]_male_control

city: Moscow

first: Maxim

last: Tikhonov

address: Vavilova

department: Regulation of Genetic Processes

country: Russia

institute: Institute of Gene Biology RAS

description: Library name: y1w1118

data_processing:
Alignment of sequencing reads to the D. melanogaster dm6 genome was performed using STAR v2.7, which simultaneously assessed splice junction coverage.
Assembly: dm6
Supplementary files format and content: The file is a tab-delimited text (.txt) file. Each row corresponds to a splice junction from different isoforms, and columns represent different samples. The values in the table indicate the splice junction counts for each sample.

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Drosophila standard culture condition.

extract_protocol:
Total RNA was extracted from imago males of the control y[1]w[1118] line and the y[1]w[1118]; mod(mdg4)[c13] line. An aliquot of 50 µL of hydrophilic streptavidin magnetic beads (NEB) were washed with 500 µL of wash/binding buffer (0.5 M NaCl, 20 mM Tris-HCl pH 7.5, 1 mM EDTA), magnetically pelleted, and subsequently blocked with 100 µL of wash/binding buffer containing 250 ng/µL of sonicated salmon sperm DNA. After an additional wash with 500 µL of wash/binding buffer, the beads were incubated for 15 min at room temperature, with rotation, in 25 µL of wash/binding buffer containing 200 pmol of a biotinylated oligonucleotide complementary to exon 4 (8 pmol/µL, bio-ACATTTGCGGAGGTGCTTGTCTTGGA) RNA. This incubation was followed by two subsequent washes with 100 µL of wash/binding buffer. Total RNA (100 µg) was denatured at 65°C, chilled on ice, and then added to the beads. This mixture was incubated at 55°C for 30 min with agitation. Five sequential washes followed. The first two washes used wash buffer (1 M NaCl, 20 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.05% Tween-20) at 55°C. The third wash employed the same buffer but without Tween-20. The fourth wash used low salt buffer (150 mM NaCl, 20 mM Tris-HCl (pH 7.5), and 1 mM EDTA), and the fifth was with ice-cold low salt buffer. RNA was eluted by adding 200 µL of TRI Reagent® (MRC) and then extracted following the manufacturer’s protocol with glycogen added prior to isopropanol precipitation.
Preparation of RNA-seq libraries followed the manufacturer’s instructions for the NEBNext® Ultra RNA Library Prep kit (NEB, USA).

value: male

value: imago

value: whole fly

value: No treatment


title: Astrocyte exosomal RNA sham

source_name: Astrocyte exosomal RNA sham


title: Control (PBS treated) Embryonic day 12.5 male biological rep 3

description: snATAC-seq


title: Control (PBS treated) Embryonic day 12.5 male biological rep 2

description: snATAC-seq


title: Astrocyte cellular RNA EF

source_name: Astrocyte cellular RNA EF

value: EF


title: T98G exosomal RNA EF

source_name: T98G exosomal RNA EF

value: T98G Glioblastoma (CRL-1690, ATCC, USA)


title: D39 LSP

city: Dublin

first: Karsten

last: Hokamp

state: Dublin

address: Stephen's Green

department: Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
reference genomes and annotation files were downloaded from GenBank
read mapping against the reference genomes was carried out through bowtie2 version 2.4.2 with the flag ‘--very-sensitive-local'; hits with an XS:i tag (indicating detection of additional alignments for a read) were excluded to focus only on uniquely mapped reads
reads were aggregated into read-count matrices for each strain through featureCounts version 2.0.3 in stranded mode
read counts from all four strains were combined into a single file based on homology prediction by Panaroo version 1.5.0 with the settings ‘--clean-mode sensitive --refind-mode off --remove-invalid-genes’
Assembly: NC_008533 (D39), CP071871 (ST217), FQ312039 (ST306), NZ_LN831051 (ST615)
Supplementary files format and content: tab-delimited text file contains raw read counts for each sample and homology mappings between the four strains

organism: Streptococcus pneumoniae

source_name: Serotype 1 strain D39

growth_protocol: Each pneumococcal strain was inoculated at a density of 2.5x10^6 in 250ml of Brain Heart Infusion (BHI) broth and incubated at 37ºC in a water bath for a pre-determined duration, depending on the targeted growth phase.

extract_protocol:
Ribonucleic acid (RNA) from each phase was stabilised by incubating the bacteria in a 5% phenol (Invitrogen) and 95% ethanol solution for 30 minutes on ice. Following stabilisation, RNA was extracted using a phase separation method using TRIzol® (Invitrogen). Briefly, the cells were centrifuged and re-suspended in TRIzol® to allow bacterial lysis. The lysed bacteria were mixed with chloroform to separate the RNA from DNA, lipids and proteins. Once the aqueous phase was collected (RNA), the sample was washed and the RNA was precipitated using ethanol. Finally, the RNA was re-suspended in DNase/RNase free distilled water (Invitrogen). The RNA extraction was done in an RNase-free area and using RNase-free materials to avoid RNA degradation. The quantity of RNA was determined using the Qubit® Fluorometer (Thermo Scientific). A 2100 Bioanalyzer (Agilent Technologies, Stanta Clara, USA) was used to assess the quality of the RNA.
RNA libraries for samples 1-5 were assumably prepared for sequencing using standard Illumina protocols. RNA samples 6-20  were fragmented with ultrasound (4 pulses of 30 sec at 4°C) followed by a treatment with antarctic phosphatase and re-phosphorylated with polynucleotide kinase (PNK). Afterwards, the RNA fragments were poly(A)-tailed using poly(A) polymerase and a RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit. The cDNA samples were pooled in equimolar amounts in three different pools. The cDNA in the size range of 150 – 500 bp was eluted from preparative agarose gels. Aliquots of the size fractionated cDNAs were analyzed by capillary electrophoresis.

treatment_protocol: Ribonucleic acid (RNA) from each sample was stabilised to avoid sacrificing the integrity of the RNA by incubating the bacterial pellet with a solution of 5% phenol (Invitrogen) and 95% ethanol for a minimum of 30min in ice. Following this stabilisation step, the RNA was extracted.

value: Serotype 1 strain D39

value: WT

tag: growth phase

value: Late stationary phase


title: Slide_seq_CTL_1

description: Slide-seq

tag: tissue

value: Brain section

value: 15 pcw

value: Male

value: Euploid


title: mod(mdg4)[c13]_male_rep2

description: Library name: c13_rep2

tag: treatment


title: heart, depletion,120hpf, rep1

description: Library name: id2b_1

source_name: heart

value: heart

value: 120 hpf

value: id2b-/-; Tg(myl7:mCherry)


title: Slide_seq_CTL_3

description: Slide-seq

value: 13 pcw

value: Female


title: mod(mdg4)[c13]_male_rep3

description: Library name: c13_rep3

value: male

value: imago


title: Astrocyte cellular RNA sham

description: gene expression from total cells RNA

source_name: Astrocyte cellular RNA sham

value: cryopreserve human Astrocyte (N7805, Thermo Fisher Scientific, USA)

tag: cell line

value: primary cell

value: Total RNA

value: Ctrl


title: mod(mdg4)[c13]_male_rep1

description: Library name: c13_rep1

value: whole fly

value: No treatment


title: D39 ESP

value: Serotype 1 strain D39

value: WT

value: Early stationary phase


title: Umbilical cord blood, donor 1997

status: Public on Jul 10 2025

city: Stanford

first: Esmond

last: Lee

address: 450 Jane Stanford Way

institute: Stanford University

description:
Library name: Sample 4
10x Genomics

data_processing:
10x Genomics' Cell Ranger software was used to filter and align FASTQ files.
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: Tab-separated values (TSV) and matrix files

source_name: Umbilical cord blood

extract_protocol:
Umbilical cord blood (UCB) mononuclear cells (MNCs) were isolated from the UCB of term deliveries (≥34 weeks of gestation) at Lucile Packard Children’s Hospital-Stanford. UCB collections were performed through the Binns Program for Cord Blood Research with donor consent and institutional review board approval. Within 24 hours of collection, MNCs of UCB were obtained by density gradient separation of whole blood (Ficoll Paque Plus, GE Healthcare; 400g, room temperature, 30 minutes, deceleration off), followed by ammonium chloride red blood cell lysis (9:1 NH4Cl lysis buffer to cell suspension). Adult peripheral blood (PB) was collected from the Stanford Blood Center (SBC). Within 24 hours of collection, whole blood was diluted by 1:1 ratio with MACs buffer (1x PBS, EDTA, FBS). MNCs of PB were then obtained by density gradient separation (Ficoll Paque Plus, GE Healthcare; 400g, room temperature, 30 minutes, deceleration off), followed by ammonium chloride red blood cell lysis (9:1 NH4Cl lysis buffer to cell suspension). While our initial aims were to capture mononuclear cells, multinucleated cells such as neutrophils found in the MNC fraction were also included as part of the study.
Libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 according to the manufacturer’s protocol (10x Genomics), targeting 10,000 cells per sample. 12 cycles of cDNA amplification were done for all samples. Individual libraries were quality checked on an Agilent 4200 Tapestation 827 using D5000 screen tape. Next, the KAPA library quantification kit (#KK4923) was used for qPCR on a BioRad CFX96 RT PCR thermal cycler. Libraries were sequenced on the Novaseq S1 platform.

value: Umbilical cord blood

tag: cell type

value: Immune mononuclear cells

value: Donor 1997


title: Adult peripheral blood, donor 1974

description:
Library name: Sample 3
10x Genomics

source_name: Peripheral blood

value: Peripheral blood

tag: genotype

value: Donor 1974


title: Umbilical cord blood, donor 1998

description:
Library name: Sample 5
10x Genomics

value: Donor 1998


title: Adult peripheral blood, donor 1970

description:
Library name: Sample 2
10x Genomics

value: Donor 1970


title: Adult peripheral blood, donor 1966

description:
Library name: Sample 1
10x Genomics

value: Donor 1966


title: LNCaP_siMOCOS#1_TG_R2

city: Oslo

first: Omer

middle: Faruk

last: Kuzu

address: Blindernveien 31

country: Norway

institute: Oslo University

description: Library name: LNCaP_siMOCOS_1_TG_R2

data_processing:
The nf-core RNA-seq pipeline (v3.6) was used for transcriptomic data processing. Briefly, Trim Galore (v0.6.7) and Cutadapt (v3.4) were used for adapter trimming and quality filtering, while FastQC (v0.11.9) provided read quality assessments. Reads were aligned using STAR (v2.6.1d), and gene quantification was performed with Salmon (v1.5.2).
Assembly: hg38
Supplementary files format and content: tab delimitted file lngth scaled raw read counts for each sample

source_name: Prostate

growth_protocol: Cells grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 50 U/ml penicillin, 50 µg/ml streptomycin, and 4 mM L-glutamine (all reagents were from Cambrex).

extract_protocol:
RNA was isolated from LNCaP and C4-2B cells using Trizol and purified using RNeasy columns (Qiagen)
Strand-specific TruSeqTM mRNA-seq library prep was used.

value: Prostate

value: LNCaP

value: Prostate Cancer Cell Line

value: siMOCOS #1 + TG


title: LNCaP_siMOCOS#1_TG_R1

description: Library name: LNCaP_siMOCOS_1_TG_R1


title: LNCaP_siMOCOS#2_TG_R1

description: Library name: LNCaP_siMOCOS_2_TG_R1

value: siMOCOS #2 + TG


title: LNCaP_siCTRL_TG_R3

description: Library name: LNCaP_siCTRL_TG_R3

value: siCTRL + TG


title: LNCaP_siCTRL_TG_R4

description: Library name: LNCaP_siCTRL_TG_R4


title: LNCaP_siCTRL_TG_R2

description: Library name: LNCaP_siCTRL_TG_R2


title: Slide_seq_CTL_2

description: Slide-seq

value: Brain section

value: 18 pcw

value: Female

value: Euploid


title: LNCaP_siCTRL_TG_R1

description: Library name: LNCaP_siCTRL_TG_R1


title: LNCaP_siMOCOS#1_R1

description: Library name: LNCaP_siMOCOS_1_R1

value: siMOCOS #1


title: Control (PBS treated) Embryonic day 12.5 male biological rep 1

description: snATAC-seq

source_name: Brain

value: Brain

tag: age

value: Embryonic day 12.5

value: Brain cells

value: Male


title: LNCaP_siCTRL_R4

description: Library name: LNCaP_siCTRL_R4

value: siCTRL


title: LNCaP_siCTRL_R2

description: Library name: LNCaP_siCTRL_R2


title: LNCaP_siCTRL_R3

description: Library name: LNCaP_siCTRL_R3


title: C42B_siMOCOS#2_TG_R2

description: Library name: C42B_siMOCOS_2_TG_R2


title: LNCaP_siCTRL_R1

description: Library name: LNCaP_siCTRL_R1


title: C42B_siMOCOS#1_TG_R2

description: Library name: C42B_siMOCOS_1_TG_R2


title: C42B_siMOCOS#2_TG_R1

description: Library name: C42B_siMOCOS_2_TG_R1


title: C42B_siCTRL_TG_R4

description: Library name: C42B_siCTRL_TG_R4


title: LNCaP_siMOCOS#2_TG_R2

description: Library name: LNCaP_siMOCOS_2_TG_R2


title: C42B_siMOCOS#1_TG_R1

description: Library name: C42B_siMOCOS_1_TG_R1


title: C42B_siCTRL_TG_R2

description: Library name: C42B_siCTRL_TG_R2


title: C42B_siCTRL_TG_R3

description: Library name: C42B_siCTRL_TG_R3


title: C42B_siMOCOS#2_R1

description: Library name: C42B_siMOCOS_2_R1

value: siMOCOS #2


title: C42B_siCTRL_TG_R1

description: Library name: C42B_siCTRL_TG_R1

value: Prostate


title: C42B_siMOCOS#2_R2

description: Library name: C42B_siMOCOS_2_R2


title: C42B_siMOCOS#1_R1

description: Library name: C42B_siMOCOS_1_R1


title: C42B_siMOCOS#1_R2

description: Library name: C42B_siMOCOS_1_R2


title: C42B_siCTRL_R2

description: Library name: C42B_siCTRL_R2


title: C42B_siCTRL_R3

description: Library name: C42B_siCTRL_R3


title: C42B_siCTRL_R1

description: Library name: C42B_siCTRL_R1


title: C42B_siCTRL_R4

description: Library name: C42B_siCTRL_R4


title: LNCaP_siMOCOS#2_R1

description: Library name: LNCaP_siMOCOS_2_R1

value: LNCaP


title: LNCaP_siMOCOS#2_R2

description: Library name: LNCaP_siMOCOS_2_R2

value: Prostate Cancer Cell Line


title: LNCaP_siMOCOS#1_R2

description: Library name: LNCaP_siMOCOS_1_R2


title: TSC2-deficient 621-101 exposed to oleic acid (30 mM, 1% FBS) replicate 2

city: L'Hospitalet del llobregat

first: Miquel Angel

last: Pujana

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals

department: ProCURE

institute: Catalan Institute of Oncology IDIBELL

description:
Library name: 621-101 OA 2
0110_2025

data_processing:
Illumina Casava 2.20 software used for basecalling.
The RNA sequencing reads were trimmed for adaptors, masked for low-complexity or low-quality sequence, and subsequently mapped to the mouse genome using STAR (2.7.10a)
The SAM/BAM files were further processed using the SAMtools (v1.18) and read count quantitations were obtained using BEDTools multicov (v2.31.0).
Gene expression was quantified by as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: TPM data matrix of gene expression.

growth_protocol: DMEM + 1 % FBS, 70 % confluence

extract_protocol:
Total RNA from tumor tissue lines was extracted using the RNeasy kit (Qiagen) and RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

treatment_protocol: DMEM + 1 % FBS +/-  oleic acid (30 mM) for 72 hours

value: Oleic acid


title: TSC2-deficient 621-101 basal (1% FBS) replicate 2

description:
Library name: 621-101 CNTRL 2
0108_2025

value: Basal


title: TSC2-deficient 621-101 basal (1% FBS) replicate 1

description:
Library name: 621-101 CNTRL 1
0107_2025


title: TSC2-deficient 621-101 exposed to oleic acid (30 mM, 1% FBS) replicate 1

description:
Library name: 621-101 OA 1
0109_2025


title: HS5 si-TLR4-plus 20 uM TQ  bio replicate 1

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

description:
Library name: KBr_HS5_si_TLR4_plusTQ_1
KBr_HS5_si_TLR4_plusTQ_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

source_name: HS5 stromal cells

growth_protocol: AML cells UCSD-AML1, AML191, and AML242 PDX cells were cultured in 20% FBS containing RPMI media and supplemented with 10 ng/mL of GMCSF.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility. Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.

treatment_protocol: AML cells were treated with FHD-286 (100 nM) for 16 hours at 37°C and harvested into RNA lysis buffer. Lysed cells were frozen at -80°C until they were processed for total RNA.

value: HS5 stromal cells

value: Acute myeloid leukemia

value: si_TLR4-plus 20 uM TQ


title: HS5 si-NT transfected + 20 µM tasquinimod bio replicate 2

description:
Library name: KBr_HS5_20uM_TQ_2
KBr_HS5_20uM_TQ_2

value: si-NT transfected + 20 µM tasquinimod


title: HS5 si-TLR4-plus 20 uM TQ bio replicate 2

description:
Library name: KBr_HS5_si_TLR4_plusTQ_2
KBr_HS5_si_TLR4_plusTQ_2


title: HS5 si-NT transfected bio replicate 2

description:
Library name: KBr_HS5_siNT_0_2
KBr_HS5_siNT_0_2

value: si-NT transfected


title: HS5 si-TLR4 transfected bio replicate 2

description:
Library name: KBr_HS5_si_TLR4_3
KBr_HS5_si_TLR4_3

value: si-TLR4 transfected


title: HS5 si-NT transfected + 20 µM tasquinimod bio replicate 1

description:
Library name: KBr_HS5_20uM_TQ_1
KBr_HS5_20uM_TQ_1


title: HS5 si-NT transfected bio replicate 1

description:
Library name: KBr_HS5_siNT_0_1
KBr_HS5_siNT_0_1


title: SET2 20 µM tasquinimod 16 hrs bio replicate 2

description:
Library name: KBr_SET2_20_nM_TQ_2
KBr_SET2_20_nM_TQ_2

value: 20 µM tasquinimod 16 hrs


title: SET2 20 µM tasquinimod 16 hrs bio replicate 1

description:
Library name: KBr_SET2_20_nM_TQ_1
KBr_SET2_20_nM_TQ_1


title: SET2 DMSO Control bio replicate 1

description:
Library name: KBr_SET2_0_nM_1
KBr_SET2_0_nM_1

value: DMSO Control


title: SET2 DMSO Control bio replicate 2

description:
Library name: KBr_SET2_0_nM_2
KBr_SET2_0_nM_2


title: LER113 20 µM tasquinimod 16 hrs bio replicate 2

description:
Library name: KBr_LER_20uM_Tasq_2
KBr_LER_20uM_Tasq_2

source_name: lymphocyte

value: lymphocyte

value: Patient derived sAML


title: LER113 DMSO Control bio replicate 1

description:
Library name: KBr_LER_0nM_1
KBr_LER_0nM_1


title: PD MF DMSO Control bio replicate 2

description:
Library name: KBr_PDMF_0-2
KBr_PDMF_0-2


title: LER113 20 µM tasquinimod 16 hrs bio replicate 1

description:
Library name: KBr_LER_20uM_Tasq_1
KBr_LER_20uM_Tasq_1


title: PD MF 20 µM tasquinimod 16 hrs bio replicate 2

description:
Library name: KBr_PDMF_20M_Tasq_2
KBr_PDMF_20M_Tasq_2


title: LER113 DMSO Control bio replicate 2

description:
Library name: KBr_LER_0nM_2
KBr_LER_0nM_2


title: ALE421 20 µM tasquinimod 16 hrs bio replicate 2

description:
Library name: KBr_ALE421_20_TQ_2
KBr_ALE421_20_TQ_2


title: PD MF 20 µM tasquinimod 16 hrs bio replicate 1

description:
Library name: KBr_PDMF_20M_Tasq_1
KBr_PDMF_20M_Tasq_1


title: PD MF DMSO Control bio replicate 1

description:
Library name: KBr_PDMF_0-1
KBr_PDMF_0-1


title: ALE421 20 µM tasquinimod 16 hrs bio replicate 1

description:
Library name: KBr_ALE421_20_TQ_1
KBr_ALE421_20_TQ_1


title: ALE421 DMSO Control bio replicate 1

description:
Library name: KBr_ALE421_0_1
KBr_ALE421_0_1


title: sAML197 5ug/mL S100A9 stimulated + 20 µM tasquinimod bio replicate 2

description:
Library name: KBr_sAML197_S100A9_plusTQ_3
KBr_sAML197_S100A9_plusTQ_3


title: sAML197 5ug/mL S100A9 stimulated + 20 µM tasquinimod bio replicate 1

description:
Library name: KBr_sAML197_S100A9_plusTQ_2
KBr_sAML197_S100A9_plusTQ_2


title: HS5 si-TLR4 transfected bio replicate 1

description:
Library name: KBr_HS5_si_TLR4_1
KBr_HS5_si_TLR4_1


title: ALE421 DMSO Control bio replicate 2

description:
Library name: KBr_ALE421_0_3
KBr_ALE421_0_3


title: sAML197 5ug/mL S100A9 stimulated bio replicate 2

description:
Library name: KBr_sAML197_S100A9_2
KBr_sAML197_S100A9_2

value: 5ug/mL S100A9 stimulated


title: miR52to53_1

city: Baltimore

first: Luisa

last: Cochella

address: 725 N. Wolfe Street, PCTB 803

institute: Johns Hopkins School of Medicine

description:
Library name: 141874
SR50

data_processing:
Small RNA reads were mapped and processed as in (Dexheimer et al., 2020).
Briefly, both mapped sequences and associated random nucleotides (functioning as UMIs) from the raw reads were quantified for miRNAs and piRNAs as well as spike-ins with the Nextflow pipeline in https://github.com/lengfei5/smallRNA_nf/tree/master/dev_sRBC.
To accurately quantify sRNAs, To alleviate PCR amplification bias, UMI counts were used and normalized with spike-in (amol/mug of total RNA) as described in (Lutzmayer et al., 2017).
Assembly: C. elegans (WBcel235)
Supplementary files format and content: text file format for UMI count table

organism: Caenorhabditis elegans

source_name: Whole embryos

growth_protocol: C. elegans strains were grown at 20C on OP50 bacteria. Adult hermaphrodites were bleached to release embryos. 2-cell embryos were collected by mouth pipetting and allowed to develop to the comma stage. 50 embryos were collected per replicate.

extract_protocol:
Total RNA was extracted using Trizol
Custom small RNA library preparation including size selection and adaptor ligation

treatment_protocol: No treatment

value: Whole embryos

tag: batch


title: miR52to53_2

description:
Library name: 141875
SR50


title: miR52to57seed_2

description:
Library name: 141873
SR50


title: sAML197 5ug/mL S100A9 stimulated bio replicate 1

description:
Library name: KBr_sAML197_S100A9_1
KBr_sAML197_S100A9_1


title: miR52to57seed_1

description:
Library name: 141872
SR50


title: sAML197 20 µM tasquinimod 16 hrs bio replicate 2

description:
Library name: KBr_sAML197_20uM_TQ_2
KBr_sAML197_20uM_TQ_2


title: miR-52to51_1

description:
Library name: 141870
SR50


title: miR-52to51_2

description:
Library name: 141871
SR50


title: sAML197 DMSO Control bio replicate 2

description:
Library name: KBr_sAML197_0_3
KBr_sAML197_0_3


title: miR-54_2

description:
Library name: 141869
SR50


title: miR-54_1

description:
Library name: 141868
SR50


title: miR-54+55_2

description:
Library name: 141867
SR50


title: Pool7_HTO

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description:
Library name: DR5PscRXP7
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger v6.0.0 multi pipeline and aligning to the cellranger-vdj-GRCh38-alts-ensembl-5.0.0 human reference genome.
Further processing was done with Seurat v4.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: 10x Genomics mRNA and HTO output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: PBMC

extract_protocol:
Mtb-specific CD4 T cells were sorted based on CD4 expression and combined expression of CD40L and CD69 over 7 runs; PBMCs from multiple donors were hastagged and pooled in each run.
10x 5’ scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics 1000263) according to the instructions provided.

treatment_protocol: Cryopreserved PBMCs were thawed and stimulated overnight with Mtb WCL at 37C in R10 media

value: PBMC

tag: antibodies/tags

tag: sorting markers

value: Live CD3+CD4+CD69+CD40L+


title: miR-54+55_1

description:
Library name: 141866
SR50


title: Pool6_HTO

description:
Library name: DR5PscRXP6
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: Anti-CD298 + anti-β2M TotalSeq anti-human Hashtag Antibodies 1 to 9 -C0251, C0252, C0253, C0254, C0255, C0256, C0257, C0258, and C0259


title: miR-54C_1

description:
Library name: 141864
SR50


title: Pool5_HTO

description:
Library name: DR5PscRXP5
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: Pool4_HTO

description:
Library name: DR5PscRXP4
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: miR-51null_2

description:
Library name: 141863
SR50


title: Pool3_HTO

description:
Library name: DR5PscRXP3
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: miR-54C_2

description:
Library name: 141865
SR50


title: Pool2_HTO

description:
Library name: DR5PscRXP2
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: Anti-CD298 + anti-β2M TotalSeq anti-human Hashtag Antibodies 1 to 8 -C0251, C0252, C0253, C0254, C0255, C0256, C0257, and C0258


title: miR-51null_1

description:
Library name: 141862
SR50


title: Pool7_GEX

description:
Library name: DR5PscRgXP7
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: N2_1

description:
Library name: 141860
SR50


title: sAML197 20 µM tasquinimod 16 hrs bio bio replicate 1

description:
Library name: KBr_sAML197_20uM_TQ_1
KBr_sAML197_20uM_TQ_1


title: N2_2

description:
Library name: 141861
SR50


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, MDD+LbGP Group, rep3

city: Nanjing

first: Yan

last: Liu

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

institute: Nanjing Medical University

description:
Library name: MDD_LbGp_S4_3
S4_3

data_processing:
For the bulk RNA-seq, RNA-seq reads were aligned to the human reference GRCh38 genome and transcriptome using HISAT2 (v.2.1.0) . RNA differential expression analysis was performed using the DESeq2 package (v.1.30.0) . The cutoff criterion was set as adjusted P value < 0.05, and absolute log2(fold change) ≥ 1
Assembly: hg38
Supplementary files format and content: normalized counts of bulk RNA-seq

source_name: brain organoids

extract_protocol:
For the bulk RNA-seq, total RNA was extracted using the Trizol reagent kit (Life Technology Inc) and mRNA was enriched by Oligo (dT) beads and then transcripted into cDNA
For the bulk RNA-seq, library construction and RNA sequencing was completed using the Illumina HiSeqTM 4000 platform.

value: brain organoids

value: neural cells


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, MDD+LbGP Group, rep2

description:
Library name: MDD_LbGp_S4_2
S4_2


title: Pool6_GEX

description:
Library name: DR5PscRgXP6
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger v6.0.0 multi pipeline and aligning to the cellranger-vdj-GRCh38-alts-ensembl-5.0.0 human reference genome.
Further processing was done with Seurat v4.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: 10x Genomics mRNA and HTO output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: Pool4_GEX

description:
Library name: DR5PscRgXP4
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Pool5_GEX

description:
Library name: DR5PscRgXP5
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, MDD+LbGP Group, rep1

description:
Library name: MDD_LbGp_S4_1
S4_1


title: Pool3_GEX

description:
Library name: DR5PscRgXP3
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, MDD Group, rep2

description:
Library name: MDD_S3_2
S3_2


title: Pool1_HTO

description:
Library name: DR5PscRXP1
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: Anti-CD298 + anti-β2M TotalSeq anti-human Hashtag Antibodies 1 to 10-C0251, C0252, C0253, C0254, C0255, C0256, C0257, C0258, C0259, and C0260


title: sAML197 DMSO Control bio replicate 1

description:
Library name: KBr_sAML197_0_1
KBr_sAML197_0_1

value: Acute myeloid leukemia


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, MDD Group, rep1

description:
Library name: MDD_S3_1
S3_1


title: Pool2_GEX

description:
Library name: DR5PscRgXP2
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Pool1_GEX

description:
Library name: DR5PscRgXP1
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, Ctrl+LbGP Group, rep3

description:
Library name: Ctrl_LbGp_S2_3
S2_3

value: RC-A


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, MDD Group, rep3

description:
Library name: MDD_S3_3
S3_3


title: hDPSCs, thy1+ co-cultured cell

first: Sol

last: Jeong

address: Gwanakgu, Gwanakro1

institute: SNU

description: Library name: cocultured-thy1

data_processing:
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human dental pulp stromal cells

growth_protocol: Human dentate stromal cells (hDPSCs) were maintained at 37°C in a humidified atmosphere with 5% CO₂ in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Human macrophages were induced with 100 ng/ml PMA for 2 days and then incubated under the same conditions as hDPSCs.

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: dental pulp

value: mesenchymal stromal cells

value: WT

value: co-cultured


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, Ctrl+LbGP Group, rep1

description:
Library name: Ctrl_LbGp_S2_1
S2_1


title: hDPSCs, thy1+ mono-cultured cell

description: Library name: mono-thy1


title: hMP, CD14+ mono-cultured cell

description: Library name: mono-CD14

source_name: U937 cell lline

value: bone marrow

value: macrophage

value: mono-cultured


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, Ctrl Group, rep2

description:
Library name: Ctrl_S1_2
S1_2


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, Ctrl Group, rep3

description:
Library name: Ctrl_S1_3
S1_3


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, Ctrl Group, rep1

description:
Library name: Ctrl_S1_1
S1_1


title: H1048 with sgNOTCH2_sgTRIM28_Rep2

city: Boston

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: NOTCH2_T28_2

data_processing:
Original data file from Illumina is transformed into sequenced reads (raw data, FASTQ formate files) by CASAVA base recognition.
Sequencing reads were mapped to the mm10 genome by STAR.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: NCI-H1048 cells were cultured with DMEM F12 with 5% FBS, P/S, and HITES (10 nM hydrocortisone (Sigma Aldrich # H0135), Insulin-Transferrin-Selenium (Gemini #400-145), and 10 nM beta-estradiol (Sigma Aldrich# E2257), 100 U/mL of penicillin (P), and 100 μg/mL of streptomycin (S)] and culture with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Quick-RNA™ Miniprep kit (Cat # R1055, Zymo Research, CA, USA) including a DNase digestion step according to the manufacturer’s instructions and RNA sequencing was performed.
For 1), the libraries for RNA-seq are prepared using NEBNext Ultra II non-stranded kit.  Paired end 150bp sequencing was performed on Novaseq6000 sequencer using S4 flow cell. For project 2), a strand-specific library was built, and paired-end 150bp sequencing was performed on a Novaseq6000 sequencer using an S4 flow cell.

value: SCLC cell line


title: H1048 with sgNOTCH2_sgTRIM28_Rep1

description: Library name: NOTCH2_T28_1


title: H1048 with sgNOTCH2_sgNT_Rep2

description: Library name: NOTCH2_NT_2


title: H1048 with sgNOTCH2_sgNT_Rep1

description: Library name: NOTCH2_NT_1


title: HEK293_NUT_RNA-seq_Rep2

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

data_processing:
RNA-seq read quantification: Kalisto
RNA-seq gene differentiatial expression analysis: Sleuth
Assembly: hg38
Supplementary files format and content: h5 is a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.

source_name: Embryonic Kidney

growth_protocol:
Dulbecco's Modified Eagle Medium (DMEM; Gibco 10566016), 10% FBS
Cells were grown according to ATCC recommendations (details in the Sample section above)

extract_protocol:
Total RNA extraction with TRIzol reagent followed by rRNA depletion (NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) with RNA Sample Purification Beads (cat. E6350L)
RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (cat. E7760S). Library concentration, quality and fragment size were assessed by Qubit fluorometric quantification (Qubit™ dsDNA HS Assay Kit, InvitrogenTM Q32851) qPCR and Fragment analyzer™. 10 multiplexed libraries were pooled and sequenced in one lane on the Illumina HiSeq4000 sequencing platform (100-bp, paired-end reads)

treatment_protocol: 20 uM Nutlin-3a (dissolved in EtOH) or the same volume of pure ethanol (mock-teated) for 4 hours.

value: Embryonic Kidney

value: Immortalized

tag: molecule subtype

value: rRNA-depleted RNA


title: HeLa_NUT_RNA-seq_Rep2

source_name: Cervical Adenocarcinoma

growth_protocol:
Eagle's Minimum Essential Medium (EMEM; ATCC 30-2003), 10% FBS
Cells were grown according to ATCC recommendations (details in the Sample section above)

value: Cervical Adenocarcinoma

value: HeLa

value: Cancer, Primary


title: HEK293_CTRL_RNA-seq_Rep2

value: mock-treated


title: H1048 with sgControl_sgTRIM28_Rep1

description: Library name: CO111_T28_1


title: MCF7_NUT_RNA-seq_Rep2

source_name: Breast Adenocarcinoma

value: Breast Adenocarcinoma

value: Cancer, Metastasis


title: HeLa_CTRL_RNA-seq_Rep2


title: H1048 with sgControl_sgNT_Rep2

description: Library name: CO111_NT_2

value: sgControl;sgNT


title: H1048 with sgControl_sgNT_Rep1

description: Library name: CO111_NT_1


title: H1048 with sgControl_sgTRIM28_Rep2

description: Library name: CO111_T28_2


title: MCF7_CTRL_RNA-seq_Rep2


title: H1048 with sgNOTCH2#2_Rep2

description: Library name: hsgNOTCH2#2_2


title: H1048 with sgNOTCH2#1_Rep1

description: Library name: hsgNOTCH2#1_1


title: RNA-seq of hiPSC-derived organoids: 40 days in vitro, Ctrl+LbGP Group, rep2

description:
Library name: Ctrl_LbGp_S2_2
S2_2

value: brain organoids

value: RC-A

value: neural cells


title: GM12878_NUT_RNA-seq_Rep2

source_name: B-Lymphocyte

growth_protocol:
RPMI-1640 (Gibco 11875085), 10% FBS
Cells were grown according to ATCC recommendations (details in the Sample section above)

value: B-Lymphocyte

value: Normal


title: hMP, CD14+ co-cultured cell

description: Library name: cocultured-CD14

value: bone marrow

value: macrophage

value: WT

value: mono-cultured


title: GM12878_CTRL_RNA-seq_Rep2

value: rRNA-depleted RNA


title: H1048 with sgNOTCH2#2_Rep1

description: Library name: hsgNOTCH2#2_1

value: SCLC cell line


title: H1048 with sgNOTCH2#1_Rep2

description: Library name: hsgNOTCH2#1_2


title: U2OS_NUT_RNA-seq_Rep2

source_name: Osteosarcoma

growth_protocol:
McCoy's 5A Medium (ATCC 30-2007), 10% FBS
Cells were grown according to ATCC recommendations (details in the Sample section above)

value: Osteosarcoma


title: A549_NUT_RNA-seq_Rep2

source_name: NSCKC Adenocarcinoma

growth_protocol:
F12-K Medium (Kaighn's Modification of Ham's F-12 medium; ATCC 30-2004), 10% FBS
Cells were grown according to ATCC recommendations (details in the Sample section above)

value: NSCKC Adenocarcinoma

value: Cancer, Primary


title: U2OS_CTRL_RNA-seq_Rep2

value: mock-treated


title: HPF cell, IL17A, 72 hrs, LIGHT, 24 hrs, rep3

city: La Jolla

first: Jeamin

last: Jung

address: 9420 Athena Cir

department: Bioinformatics Core

institute: La Jolla Institute for Immunology

description: Library name: 231107_NG_Sample_18

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2
Filtered reads were mapped against the human GRCh38 reference using STAR v2.6.1
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using FeatureCount v1.6.5 (“union” option) and features with 0 counts across all samples were removed
Assembly: GRCh38
Supplementary files format and content: tsv counts matrix with rows as genes and columns as samples

source_name: Lung

growth_protocol: Human pulmonary fibroblasts were cultured in fibroblast media, serum starved prior  cytokine treatment

extract_protocol:
Zymo Direct-zol
NEB mRNA Directional

treatment_protocol: Human pulmonary fibroblasts (HPF) stimulated with 50 ng/ml LIGHT, 25 ng/ml IL-13, and 100 ng/ml IL-17A and in combination of IL13 or Il17A with LIGHT. HPF were also pretreated with 50 ng/ml of IL13/ IL17A followed by 50 ng/ml LIGHT treatment.

value: Lung

value: HPF

value: Fibroblasts

value: IL17A 72hrs followed by LIGHT 24hrs


title: A549_CTRL_RNA-seq_Rep2


title: HCT116_NUT_RNA-seq_Rep2

source_name: Colorectal Adenocarcinoma

value: Colorectal Adenocarcinoma


title: SKNSH_NUT_RNA-seq_Rep2

source_name: Neuroblastoma

value: Neuroblastoma

value: SKSNH

value: Cancer, Metastasis


title: HPF cell, IL17A, 72 hrs, LIGHT, 24 hrs, rep1

description: Library name: 231107_NG_Sample_16


title: SKNSH_CTRL_RNA-seq_Rep2


title: HPF cell, IL17A, 72 hrs, rep2

description: Library name: 231107_NG_Sample_14

value: IL17A 72 hrs


title: HPF cell, IL17A, 72 hrs, rep3

description: Library name: 231107_NG_Sample_15


title: HCT116_CTRL_RNA-seq_Rep2


title: IMR90_NUT_RNA-seq_Rep2

source_name: Lung fibroblasts

value: Lung fibroblasts

value: Normal


title: HepG2_NUT_RNA-seq_Rep2

source_name: Hepatocellular Carcinoma

value: Hepatocellular Carcinoma

value: rRNA-depleted RNA


title: IMR90_CTRL_RNA-seq_Rep2


title: HEK293_NUT_RNA-seq_Rep1

value: Embryonic Kidney

value: Immortalized


title: HPF cell, IL13, 72 hrs, LIGHT, 24 hrs, rep2

description: Library name: 231107_NG_Sample_11

value: IL13 72hrs followed by LIGHT 24hrs


title: HPF cell, IL13, 72 hrs, LIGHT, 24 hrs, rep1

description: Library name: 231107_NG_Sample_10


title: HPF cell, IL13, 72 hrs, rep3

description: Library name: 231107_NG_Sample_9

value: IL13 72 hrs


title: HEK293_CTRL_RNA-seq_Rep1

value: mock-treated


title: HepG2_CTRL_RNA-seq_Rep2

value: Cancer, Primary


title: HPF cell, IL13, 72 hrs, rep2

description: Library name: 231107_NG_Sample_8

value: Lung

value: HPF

value: Fibroblasts


title: H1048 with sgControl_Rep1

description: Library name: hsgCO111_1

value: SCLC cell line

value: sgControl


title: H1048 with sgControl_Rep2

description: Library name: hsgCO111_2


title: HeLa_CTRL_RNA-seq_Rep1

value: Cervical Adenocarcinoma

value: HeLa


title: HeLa_NUT_RNA-seq_Rep1


title: HPF cell, IL17A, 72 hrs, LIGHT, 24 hrs, rep2

description: Library name: 231107_NG_Sample_17

value: IL17A 72hrs followed by LIGHT 24hrs


title: HPF cell, IL13, 72 hrs, rep1

description: Library name: 231107_NG_Sample_7